Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
50  structures 5524  species 0  interactions 12131  sequences 182  architectures

Family: SMC_hinge (PF06470)

Summary: SMC proteins Flexible Hinge Domain

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

SMC proteins Flexible Hinge Domain Provide feedback

This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction ([1]).

Literature references

  1. Hirano M, Hirano T; , EMBO J 2002;21:5733-5744.: Hinge-mediated dimerization of SMC protein is essential for its dynamic interaction with DNA. PUBMED:12411491 EPMC:12411491


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010935

This entry represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that its precise structure is an essential determinant of the specificity of the DNA-protein interaction [ PUBMED:12411491 ].

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...

Loading domain graphics...

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...

View options

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
(97)
Full
(12131)
Representative proteomes UniProt
(35556)
RP15
(2155)
RP35
(5811)
RP55
(10665)
RP75
(15690)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(97)
Full
(12131)
Representative proteomes UniProt
(35556)
RP15
(2155)
RP35
(5811)
RP55
(10665)
RP75
(15690)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(97)
Full
(12131)
Representative proteomes UniProt
(35556)
RP15
(2155)
RP35
(5811)
RP55
(10665)
RP75
(15690)
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: ADDA_5420
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Yeats C
Number in seed: 97
Number in full: 12131
Average length of the domain: 116.60 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 9.72 %

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 22.5 22.5
Trusted cut-off 22.5 22.5
Noise cut-off 22.4 22.4
Model length: 117
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 SMC_hinge domain has been found. There are 50 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.

Loading structure mapping...

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
A0A0G2L6F5 View 3D Structure Click here
A0A0N7KUG0 View 3D Structure Click here
A0A0R0GQ23 View 3D Structure Click here
A0A0R0HP07 View 3D Structure Click here
A0A1D6KLM4 View 3D Structure Click here
A0A1D6M7C7 View 3D Structure Click here
A0A1D6MEC8 View 3D Structure Click here
A0A1D6N452 View 3D Structure Click here
A0A1D8PI59 View 3D Structure Click here
A0A1D8PJK7 View 3D Structure Click here
A0A1D8PSI8 View 3D Structure Click here
A0A2R8QCL7 View 3D Structure Click here
A4HSG2 View 3D Structure Click here
A4HTF1 View 3D Structure Click here
A4HZD1 View 3D Structure Click here
A4IBP1 View 3D Structure Click here
A6NHR9 View 3D Structure Click here
B2FDA8 View 3D Structure Click here
B8A5K9 View 3D Structure Click here
D3ZE73 View 3D Structure Click here
D4A5Q2 View 3D Structure Click here
D4AAG8 View 3D Structure Click here
E7F0X6 View 3D Structure Click here
E7FGC2 View 3D Structure Click here
F1MAD9 View 3D Structure Click here
I1JIN1 View 3D Structure Click here
I1LVC8 View 3D Structure Click here
I1LWK5 View 3D Structure Click here
I1LYK3 View 3D Structure Click here
I1M0W9 View 3D Structure Click here
I1M7D7 View 3D Structure Click here
I1N651 View 3D Structure Click here
K7KDL4 View 3D Structure Click here
O01789 View 3D Structure Click here
O42649 View 3D Structure Click here
O94383 View 3D Structure Click here
O95347 View 3D Structure Click here
P32908 View 3D Structure Click here
P38989 View 3D Structure Click here
P41003 View 3D Structure Click here
P41004 View 3D Structure Click here
P47037 View 3D Structure Click here
P48996 View 3D Structure Click here
P97690 View 3D Structure Click here
P9WGF3 View 3D Structure Click here
Q09591 View 3D Structure Click here
Q12267 View 3D Structure Click here
Q14683 View 3D Structure Click here
Q1LVV8 View 3D Structure Click here
Q20060 View 3D Structure Click here
Q2FZ49 View 3D Structure Click here
Q4D0W6 View 3D Structure Click here
Q4D2P9 View 3D Structure Click here
Q4D5A9 View 3D Structure Click here
Q4DL10 View 3D Structure Click here
Q4DUB1 View 3D Structure Click here
Q4E1T5 View 3D Structure Click here
Q54E85 View 3D Structure Click here
Q54LV0 View 3D Structure Click here
Q54PK4 View 3D Structure Click here
Q552D9 View 3D Structure Click here
Q56YN8 View 3D Structure Click here
Q59037 View 3D Structure Click here
Q5A4Y2 View 3D Structure Click here
Q5N6W1 View 3D Structure Click here
Q6P5D8 View 3D Structure Click here
Q6Q1P4 View 3D Structure Click here
Q7KK96 View 3D Structure Click here
Q8CG47 View 3D Structure Click here
Q8CG48 View 3D Structure Click here
Q8I1U7 View 3D Structure Click here
Q8I413 View 3D Structure Click here
Q8IED2 View 3D Structure Click here
Q8II57 View 3D Structure Click here
Q8NDV3 View 3D Structure Click here
Q920F6 View 3D Structure Click here
Q9C5Y4 View 3D Structure Click here
Q9CU62 View 3D Structure Click here
Q9CW03 View 3D Structure Click here
Q9FJL0 View 3D Structure Click here
Q9NTJ3 View 3D Structure Click here
Q9SN90 View 3D Structure Click here
Q9UQE7 View 3D Structure Click here
Q9V3A7 View 3D Structure Click here
Q9VCD8 View 3D Structure Click here
Q9VXE9 View 3D Structure Click here
Q9Z1M9 View 3D Structure Click here
X1WEJ1 View 3D Structure Click here