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53  structures 902  species 0  interactions 30395  sequences 965  architectures

Family: zf-B_box (PF00643)

Summary: B-box zinc finger

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "B-box zinc finger". More...

B-box zinc finger Edit Wikipedia article

zf-B_box
PDB 1fre EBI.jpg
Structure of the xnf7 B-box, developmental protein
Identifiers
Symbolzf-B_box
PfamPF00643
InterProIPR000315
PROSITEPDOC50015
SCOPe1fre / SUPFAM
CDDcd00021

In molecular biology the B-box-type zinc finger domain is a short protein domain of around 40 amino acid residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains.

Occurrence

B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins.[1]

The microtubule-associated E3 ligase MID1 (EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers.[2][3]

Homologs

Prokaryotic homologs of the domain are present in several bacterial lineages and methanogenic archaea, and often show fusions to peptidase domains such as the rhomboid-like serine peptidase, and Zn-dependent metallopeptidase. Other versions typically contain transmembrane helices and might also show fusions to domains such as DNAJ, FHA, SH3, WD40 and tetratricopeptide repeats. Together these associations suggest a role for the prokaryotic homologs of the B-box zinc finger domain in proteolytic processing, folding or stability of membrane-associated proteins. The domain architectural syntax is remarkably similar to that seen in prokaryotic homologs of the AN1 zinc finger and LIM domains.[4]

References

  1. ^ Short KM, Cox TC (March 2006). "Subclassification of the RBCC/TRIM superfamily reveals a novel motif necessary for microtubule binding". J. Biol. Chem. 281 (13): 8970–80. doi:10.1074/jbc.M512755200. PMID 16434393.
  2. ^ Massiah MA, Matts JA, Short KM, Simmons BN, Singireddy S, Yi Z, Cox TC (May 2007). "Solution structure of the MID1 B-box2 CHC(D/C)C(2)H(2) zinc-binding domain: insights into an evolutionarily conserved RING fold". J. Mol. Biol. 369 (1): 1–10. doi:10.1016/j.jmb.2007.03.017. PMID 17428496.
  3. ^ Massiah MA, Simmons BN, Short KM, Cox TC (April 2006). "Solution structure of the RBCC/TRIM B-box1 domain of human MID1: B-box with a RING". J. Mol. Biol. 358 (2): 532–45. doi:10.1016/j.jmb.2006.02.009. PMID 16529770.
  4. ^ Burroughs AM, Iyer LM, Aravind L (July 2011). "Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system". Mol. Biosyst. 7 (1): 2261–77. doi:10.1039/C1MB05061C. PMC 5938088. PMID 21547297.

External links

See also

This article incorporates text from the public domain Pfam and InterPro: IPR000315

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

B-box zinc finger Provide feedback

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Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000315

This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitination. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins [ PUBMED:16434393 ].

The microtubule-associated E3 ligase MID1 ( EC ) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [ PUBMED:17428496 , PUBMED:16529770 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(91)
Full
(30395)
Representative proteomes UniProt
(52323)
RP15
(5160)
RP35
(12586)
RP55
(27475)
RP75
(35909)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(91)
Full
(30395)
Representative proteomes UniProt
(52323)
RP15
(5160)
RP35
(12586)
RP55
(27475)
RP75
(35909)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(91)
Full
(30395)
Representative proteomes UniProt
(52323)
RP15
(5160)
RP35
(12586)
RP55
(27475)
RP75
(35909)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 91
Number in full: 30395
Average length of the domain: 42.90 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 8.63 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.1 24.1
Trusted cut-off 24.1 24.1
Noise cut-off 24.0 24.0
Model length: 42
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the zf-B_box domain has been found. There are 53 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A060D895 View 3D Structure Click here
A0A060D895 View 3D Structure Click here
A0A0G2JWJ3 View 3D Structure Click here
A0A0G2JXN2 View 3D Structure Click here
A0A0G2JYE1 View 3D Structure Click here
A0A0G2K659 View 3D Structure Click here
A0A0G2K6C7 View 3D Structure Click here
A0A0G2KRG9 View 3D Structure Click here
A0A0G2L0E2 View 3D Structure Click here
A0A0G2LAJ1 View 3D Structure Click here
A0A0H2UJL0 View 3D Structure Click here
A0A0H2UKH6 View 3D Structure Click here
A0A0H2UKU5 View 3D Structure Click here
A0A0K2CTB7 View 3D Structure Click here
A0A0K2CTB7 View 3D Structure Click here
A0A0N4SU11 View 3D Structure Click here
A0A0P0UZC2 View 3D Structure Click here
A0A0P0VFH3 View 3D Structure Click here
A0A0R0FVE5 View 3D Structure Click here
A0A0R0FVE5 View 3D Structure Click here
A0A0R0GPY8 View 3D Structure Click here
A0A0R0H359 View 3D Structure Click here
A0A0R0HLR0 View 3D Structure Click here
A0A0R0HLR0 View 3D Structure Click here
A0A0R0JI42 View 3D Structure Click here
A0A0R0JI42 View 3D Structure Click here
A0A0R0LC00 View 3D Structure Click here
A0A0R4IB88 View 3D Structure Click here
A0A0R4IBN3 View 3D Structure Click here
A0A0R4IBP6 View 3D Structure Click here
A0A0R4IBT4 View 3D Structure Click here
A0A0R4ICD1 View 3D Structure Click here
A0A0R4ICE2 View 3D Structure Click here
A0A0R4ICU1 View 3D Structure Click here
A0A0R4IEH8 View 3D Structure Click here
A0A0R4IFW2 View 3D Structure Click here
A0A0R4IIJ3 View 3D Structure Click here
A0A0R4IIL0 View 3D Structure Click here
A0A0R4IJ94 View 3D Structure Click here
A0A0R4IJZ5 View 3D Structure Click here
A0A0R4IJZ5 View 3D Structure Click here
A0A0R4IKX5 View 3D Structure Click here
A0A0R4IL07 View 3D Structure Click here
A0A0R4IMV5 View 3D Structure Click here
A0A0R4INJ4 View 3D Structure Click here
A0A0R4IPB1 View 3D Structure Click here
A0A0R4IPI6 View 3D Structure Click here
A0A0R4IQ29 View 3D Structure Click here
A0A0R4ISE2 View 3D Structure Click here
A0A0R4IUF9 View 3D Structure Click here
A0A0R4IUM1 View 3D Structure Click here
A0A0R4IUT0 View 3D Structure Click here
A0A0R4IV10 View 3D Structure Click here
A0A0R4IZ97 View 3D Structure Click here
A0A0R4IZN1 View 3D Structure Click here
A0A0R4J3G1 View 3D Structure Click here
A0A0R4J3G1 View 3D Structure Click here
A0A0R4J3G9 View 3D Structure Click here
A0A0R4J3G9 View 3D Structure Click here
A0A0R4J428 View 3D Structure Click here
A0A140LGW2 View 3D Structure Click here
A0A140LH92 View 3D Structure Click here
A0A1B0GWP0 View 3D Structure Click here
A0A1D5NS95 View 3D Structure Click here
A0A1D5NSA3 View 3D Structure Click here
A0A1D6E4F7 View 3D Structure Click here
A0A1D6E4F7 View 3D Structure Click here
A0A1D6E763 View 3D Structure Click here
A0A1D6E7C3 View 3D Structure Click here
A0A1D6ETP7 View 3D Structure Click here
A0A1D6GW91 View 3D Structure Click here
A0A1D6H2A1 View 3D Structure Click here
A0A1D6HCU0 View 3D Structure Click here
A0A1D6HCU0 View 3D Structure Click here
A0A1D6HIW9 View 3D Structure Click here
A0A1D6HJB4 View 3D Structure Click here
A0A1D6L1R1 View 3D Structure Click here
A0A1D6LL88 View 3D Structure Click here
A0A1D6M067 View 3D Structure Click here
A0A1D6MHD6 View 3D Structure Click here
A0A1D6Q4M1 View 3D Structure Click here
A0A1D6Q662 View 3D Structure Click here
A0A1D6Q662 View 3D Structure Click here
A0A286Y8K8 View 3D Structure Click here
A0A286Y945 View 3D Structure Click here
A0A286YB14 View 3D Structure Click here
A0A286YBY1 View 3D Structure Click here
A0A2R8PYS6 View 3D Structure Click here
A0A2R8Q0H5 View 3D Structure Click here
A0A2R8Q2L3 View 3D Structure Click here
A0A2R8Q2R2 View 3D Structure Click here
A0A2R8Q525 View 3D Structure Click here
A0A2R8Q883 View 3D Structure Click here
A0A2R8Q9C0 View 3D Structure Click here
A0A2R8Q9S3 View 3D Structure Click here
A0A2R8Q9Y4 View 3D Structure Click here
A0A2R8QC46 View 3D Structure Click here
A0A2R8QEG7 View 3D Structure Click here
A0A2R8QJ74 View 3D Structure Click here
A0A2R8QR23 View 3D Structure Click here
A0A2R8QUE5 View 3D Structure Click here
A0A2R8RII6 View 3D Structure Click here
A0A2R8RZP6 View 3D Structure Click here
A0A2R8S055 View 3D Structure Click here
A0JPQ4 View 3D Structure Click here
A2BFT4 View 3D Structure Click here
A3KQE0 View 3D Structure Click here
A4FUN6 View 3D Structure Click here
A4I5R4 View 3D Structure Click here
A4I8G0 View 3D Structure Click here
A4IDC4 View 3D Structure Click here
A4IG09 View 3D Structure Click here
A6NDI0 View 3D Structure Click here
A6NK02 View 3D Structure Click here
A8E7R9 View 3D Structure Click here
A8WG17 View 3D Structure Click here
A8WG25 View 3D Structure Click here
A9JSZ8 View 3D Structure Click here
B0S6J1 View 3D Structure Click here
B0S6R8 View 3D Structure Click here
B0S6R9 View 3D Structure Click here
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B0S718 View 3D Structure Click here
B1H278 View 3D Structure Click here
B2RYH2 View 3D Structure Click here
B3DKE1 View 3D Structure Click here
B4FE60 View 3D Structure Click here
B4FMW2 View 3D Structure Click here
B4FUZ0 View 3D Structure Click here
B4FUZ0 View 3D Structure Click here
B4FXI0 View 3D Structure Click here
B4FXI0 View 3D Structure Click here
B5DF13 View 3D Structure Click here
B5DFI5 View 3D Structure Click here
B6TFB2 View 3D Structure Click here
B8A5M1 View 3D Structure Click here
B8JI86 View 3D Structure Click here
B8JLS7 View 3D Structure Click here
B9MSS5 View 3D Structure Click here
C0H4E5 View 3D Structure Click here
C0H4E5 View 3D Structure Click here
C0P687 View 3D Structure Click here
C0SVM5 View 3D Structure Click here
C0SVM5 View 3D Structure Click here
C6SXV9 View 3D Structure Click here
C6T445 View 3D Structure Click here
C6T445 View 3D Structure Click here
D0EP03 View 3D Structure Click here
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D0EP04 View 3D Structure Click here
D0EP05 View 3D Structure Click here
D3YVI9 View 3D Structure Click here
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D3ZA22 View 3D Structure Click here
D3ZA88 View 3D Structure Click here
D3ZL82 View 3D Structure Click here
D3ZN56 View 3D Structure Click here
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D3ZW47 View 3D Structure Click here
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D4A306 View 3D Structure Click here
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D4ACF2 View 3D Structure Click here
E7F136 View 3D Structure Click here
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E7FDZ1 View 3D Structure Click here
E9PV98 View 3D Structure Click here
E9PVL6 View 3D Structure Click here
E9PWL0 View 3D Structure Click here
E9QDQ1 View 3D Structure Click here
E9QHE3 View 3D Structure Click here
F1LMK2 View 3D Structure Click here
F1LMT9 View 3D Structure Click here
F1LY63 View 3D Structure Click here
F1M589 View 3D Structure Click here
F1M6Z0 View 3D Structure Click here
F1Q4Q5 View 3D Structure Click here
F1Q547 View 3D Structure Click here
F1Q5D7 View 3D Structure Click here
F1Q5R2 View 3D Structure Click here
F1QFW2 View 3D Structure Click here
F1QHA1 View 3D Structure Click here
F1QJ94 View 3D Structure Click here
F1QJH1 View 3D Structure Click here
F1QJY4 View 3D Structure Click here
F1QKR8 View 3D Structure Click here
F1QLY9 View 3D Structure Click here
F1QMZ7 View 3D Structure Click here
F1QN09 View 3D Structure Click here
F1QN31 View 3D Structure Click here
F1QQF9 View 3D Structure Click here
F1QQG3 View 3D Structure Click here
F1QQV8 View 3D Structure Click here
F1QS63 View 3D Structure Click here
F1QTC4 View 3D Structure Click here
F1QUB4 View 3D Structure Click here
F1QV80 View 3D Structure Click here
F1QWI8 View 3D Structure Click here
F1QXB4 View 3D Structure Click here
F1QXT0 View 3D Structure Click here
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F1QZB6 View 3D Structure Click here
F1QZK7 View 3D Structure Click here
F1QZQ5 View 3D Structure Click here
F1R0A0 View 3D Structure Click here
F1R3Q1 View 3D Structure Click here
F1R437 View 3D Structure Click here
F1R5V8 View 3D Structure Click here
F1R783 View 3D Structure Click here
F1R871 View 3D Structure Click here
F1R925 View 3D Structure Click here
F1R9D1 View 3D Structure Click here
F1R9P7 View 3D Structure Click here
F1R9Z3 View 3D Structure Click here
F2Z4W9 View 3D Structure Click here
F6P534 View 3D Structure Click here
F8W3P8 View 3D Structure Click here
G3UY57 View 3D Structure Click here
G3X8Y1 View 3D Structure Click here
I1JQH3 View 3D Structure Click here
I1JQH3 View 3D Structure Click here
I1JSK5 View 3D Structure Click here
I1JT58 View 3D Structure Click here
I1JU45 View 3D Structure Click here
I1JU45 View 3D Structure Click here
I1KE57 View 3D Structure Click here
I1KF89 View 3D Structure Click here
I1KQ52 View 3D Structure Click here
I1LEW9 View 3D Structure Click here
I1LHZ2 View 3D Structure Click here
I1LHZ2 View 3D Structure Click here
I1LQD6 View 3D Structure Click here
I1LQD6 View 3D Structure Click here
I1LRV3 View 3D Structure Click here
I1LUA3 View 3D Structure Click here
I1LWY2 View 3D Structure Click here
I1M3Z6 View 3D Structure Click here
I1M564 View 3D Structure Click here
I1M564 View 3D Structure Click here
I1ME84 View 3D Structure Click here
I1N4U7 View 3D Structure Click here
I1N6I8 View 3D Structure Click here
I1NFI8 View 3D Structure Click here
J3QNR8 View 3D Structure Click here
K7DY47 View 3D Structure Click here
K7KAI4 View 3D Structure Click here
K7KRL4 View 3D Structure Click here
K7L0J7 View 3D Structure Click here
K7LSW1 View 3D Structure Click here
K7LWJ8 View 3D Structure Click here
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K7MNZ7 View 3D Structure Click here
K7TR53 View 3D Structure Click here
K7TR53 View 3D Structure Click here
K7UJZ2 View 3D Structure Click here
K7UJZ2 View 3D Structure Click here
K7VBR1 View 3D Structure Click here
K7W7Y8 View 3D Structure Click here
M0R947 View 3D Structure Click here
M9MRI4 View 3D Structure Click here
O00635 View 3D Structure Click here
O08629 View 3D Structure Click here
O08629 View 3D Structure Click here
O15016 View 3D Structure Click here
O15164 View 3D Structure Click here
O15344 View 3D Structure Click here
O15553 View 3D Structure Click here
O23379 View 3D Structure Click here
O50055 View 3D Structure Click here
O60858 View 3D Structure Click here
O70277 View 3D Structure Click here
O70583 View 3D Structure Click here
O75382 View 3D Structure Click here
O80748 View 3D Structure Click here
O81834 View 3D Structure Click here
O82114 View 3D Structure Click here
O82115 View 3D Structure Click here
O82115 View 3D Structure Click here
O82116 View 3D Structure Click here
O82116 View 3D Structure Click here
O82117 View 3D Structure Click here
O82256 View 3D Structure Click here
O82617 View 3D Structure Click here
O94972 View 3D Structure Click here
O95361 View 3D Structure Click here
P0CI25 View 3D Structure Click here
P0CI26 View 3D Structure Click here
P14373 View 3D Structure Click here
P15533 View 3D Structure Click here
P19474 View 3D Structure Click here
P29590 View 3D Structure Click here
P34611 View 3D Structure Click here
P36406 View 3D Structure Click here
P36407 View 3D Structure Click here
P62603 View 3D Structure Click here
P82458 View 3D Structure Click here
Q08C26 View 3D Structure Click here
Q09623 View 3D Structure Click here
Q09654 View 3D Structure Click here
Q0DD26 View 3D Structure Click here
Q0IGM7 View 3D Structure Click here
Q12899 View 3D Structure Click here
Q13263 View 3D Structure Click here
Q13263 View 3D Structure Click here
Q14134 View 3D Structure Click here
Q14142 View 3D Structure Click here
Q19818 View 3D Structure Click here
Q19818 View 3D Structure Click here
Q1ECU9 View 3D Structure Click here
Q1G3I2 View 3D Structure Click here
Q1L8B2 View 3D Structure Click here
Q1L9F9 View 3D Structure Click here
Q1LXS0 View 3D Structure Click here
Q1MT09 View 3D Structure Click here
Q1MT11 View 3D Structure Click here
Q1PSW8 View 3D Structure Click here
Q1RLP5 View 3D Structure Click here
Q1XH17 View 3D Structure Click here
Q20548 View 3D Structure Click here
Q29RB6 View 3D Structure Click here
Q2Q1W2 View 3D Structure Click here
Q2QW41 View 3D Structure Click here
Q2QW41 View 3D Structure Click here
Q38HM4 View 3D Structure Click here
Q39057 View 3D Structure Click here
Q3UWZ0 View 3D Structure Click here
Q3V061 View 3D Structure Click here
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Q495X7 View 3D Structure Click here
Q4CWV2 View 3D Structure Click here
Q4DT67 View 3D Structure Click here
Q4DWM2 View 3D Structure Click here
Q503E5 View 3D Structure Click here
Q503I2 View 3D Structure Click here
Q505D9 View 3D Structure Click here
Q53RJ0 View 3D Structure Click here
Q54C10 View 3D Structure Click here
Q54DG7 View 3D Structure Click here
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