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.
56  structures 1438  species 0  interactions 9433  sequences 185  architectures

Family: CID (PF04818)

Summary: CID 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.

CID domain Provide feedback

This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II [1,2]. This domain is known as the CTD-interacting domain (CID).

Literature references

  1. Becker R, Loll B, Meinhart A;, J Biol Chem. 2008;283:22659-22669.: Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the carboxyl-terminal domain of RNA polymerase II. PUBMED:18550522 EPMC:18550522

  2. Lunde BM, Reichow SL, Kim M, Suh H, Leeper TC, Yang F, Mutschler H, Buratowski S, Meinhart A, Varani G;, Nat Struct Mol Biol. 2010;17:1195-1201.: Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. PUBMED:20818393 EPMC:20818393


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006569

The C-terminal domain (CTD) of the large subunit of RNA polymerase II is a platform for mRNA processing factors and links gene transcription to mRNA capping, splicing and polyadenylation. CTD recognition is dependent on the phosphorylation state of the CTD itself, which varies during the course of transcription but has also been linked to the isomerization state of the CTD's proline residues. Several RNA-processing factors recognise the CTD by means of a conserved CTD-interacting domain (CID). Factors with CID domains include the serine/arginine-rich-like factors SCAF4 and SCAF8, Nrd1 (which is implicated in polyadenylation-independent RNA 3'-end formation) and Pcf11. Pcf11 is a conserved and essential subunit of the yeast cleavage factor 1A, which is required for 3'-RNA processing and transcription termination [ PUBMED:15241417 , PUBMED:15665873 ].

The CID domain is a right-handed superhelix of eight alpha-helices forming a compact domain. The CID fold closely resembles that of VHS domains INTERPRO and is related to armadillo-repeat proteins INTERPRO , except for the two amino-terminal helices. Amino acid residues in the hydrophobic core of the domain are highly conserved across CID domains [ PUBMED:15241417 , PUBMED:15665873 ].

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan TPR (CL0020), which has the following description:

Tetratricopeptide-like repeats are found in a numerous and diverse proteins involved in such functions as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.

The clan contains the following 176 members:

Adaptin_N Alkyl_sulf_dimr ANAPC3 ANAPC5 ANAPC8 APC_rep API5 Arm Arm_2 Arm_3 Arm_vescicular Atx10homo_assoc B56 BAF250_C BTAD CAS_CSE1 ChAPs CHIP_TPR_N CID CLASP_N Clathrin Clathrin-link Clathrin_H_link Clathrin_propel Cnd1 Cnd3 Coatomer_E Cohesin_HEAT Cohesin_load ComR_TPR COPI_C CPL CRM1_C CRM1_repeat CRM1_repeat_3 Cse1 CTK3 DHR-2 DIL DNA_alkylation Dopey_N Drf_FH3 Drf_GBD DUF1822 DUF2019 DUF2225 DUF3385 DUF3458_C DUF3808 DUF3856 DUF4042 DUF5588 DUF5691 DUF6340 DUF6377 DUF924 EAD11 EST1 EST1_DNA_bind FAT Fis1_TPR_C Fis1_TPR_N Foie-gras_1 GUN4_N HAT HEAT HEAT_2 HEAT_EZ HEAT_PBS HEAT_UF HemY_N HrpB1_HrpK HSM3_C HSM3_N IBB IBN_N IFRD Importin_rep Importin_rep_2 Importin_rep_3 Importin_rep_4 Importin_rep_5 Importin_rep_6 Insc_C KAP Leuk-A4-hydro_C LRV LRV_FeS MA3 MIF4G MIF4G_like MIF4G_like_2 MMS19_C Mo25 MRP-S27 Mtf2 NARP1 Neurochondrin Nipped-B_C Nro1 NSF Paf67 ParcG PC_rep PHAT PI3Ka PknG_TPR PPP5 PPR PPR_1 PPR_2 PPR_3 PPR_long PPTA Proteasom_PSMB PUF Rapsyn_N RIX1 RNPP_C RPM2 RPN7 Sel1 SHNi-TPR SNAP SPO22 SRP_TPR_like ST7 Suf SusD-like SusD-like_2 SusD-like_3 SusD_RagB SYCP2_ARLD TAF6_C TAL_effector TAtT Tcf25 TIP120 TOM20_plant TPR_1 TPR_10 TPR_11 TPR_12 TPR_14 TPR_15 TPR_16 TPR_17 TPR_18 TPR_19 TPR_2 TPR_20 TPR_21 TPR_22 TPR_3 TPR_4 TPR_5 TPR_6 TPR_7 TPR_8 TPR_9 TPR_MalT TTC7_N UNC45-central Upf2 V-ATPase_H_C V-ATPase_H_N Vac14_Fab1_bd Vitellogenin_N Vps39_1 W2 WSLR Wzy_C_2 Xpo1 YcaO_C YfiO Zmiz1_N

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
(213)
Full
(9433)
Representative proteomes UniProt
(16294)
RP15
(1530)
RP35
(4295)
RP55
(7749)
RP75
(10507)
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
(213)
Full
(9433)
Representative proteomes UniProt
(16294)
RP15
(1530)
RP35
(4295)
RP55
(7749)
RP75
(10507)
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
(213)
Full
(9433)
Representative proteomes UniProt
(16294)
RP15
(1530)
RP35
(4295)
RP55
(7749)
RP75
(10507)
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: Pfam-B_3687 (release 7.6)
Previous IDs: DUF618; CTD_bind;
Type: Repeat
Sequence Ontology: SO:0001068
Author: Mifsud W , Eberhardt R , Bateman A
Number in seed: 213
Number in full: 9433
Average length of the domain: 120.80 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 15.29 %

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 23.9 23.9
Trusted cut-off 23.9 23.9
Noise cut-off 23.8 23.8
Model length: 121
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 CID domain has been found. There are 56 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
A0A096R4D2 View 3D Structure Click here
A0A0G2JTD1 View 3D Structure Click here
A0A0P0WFI1 View 3D Structure Click here
A0A0P0X0F2 View 3D Structure Click here
A0A0R0EYS5 View 3D Structure Click here
A0A0R0F3F7 View 3D Structure Click here
A0A0R0G0B2 View 3D Structure Click here
A0A0R0HDU9 View 3D Structure Click here
A0A0R0JXH5 View 3D Structure Click here
A0A0R0JZP3 View 3D Structure Click here
A0A144A0W9 View 3D Structure Click here
A0A1D6DPQ4 View 3D Structure Click here
A0A1D6DWZ8 View 3D Structure Click here
A0A1D6ELY1 View 3D Structure Click here
A0A1D6G566 View 3D Structure Click here
A0A1D6I0L2 View 3D Structure Click here
A0A1D6IRC9 View 3D Structure Click here
A0A1D6K3N5 View 3D Structure Click here
A0A1D6NQJ4 View 3D Structure Click here
A0A1D6PUR4 View 3D Structure Click here
A0A1D6QGZ1 View 3D Structure Click here
A0A1D6QJJ2 View 3D Structure Click here
A0A1D8PHH9 View 3D Structure Click here
A0A1D8PN05 View 3D Structure Click here
A0A1D8PPQ9 View 3D Structure Click here
A0A1D8PUB3 View 3D Structure Click here
A0A2R8Q5V2 View 3D Structure Click here
A1Z9W4 View 3D Structure Click here
A4ICA0 View 3D Structure Click here
A5Z2V1 View 3D Structure Click here
A8DYK5 View 3D Structure Click here
B5DEK0 View 3D Structure Click here
B7ZVL5 View 3D Structure Click here
C0P9J3 View 3D Structure Click here
D3ZAI0 View 3D Structure Click here
D3ZAX5 View 3D Structure Click here
D3ZY40 View 3D Structure Click here
D4AAU4 View 3D Structure Click here
E7F4U8 View 3D Structure Click here
E7F882 View 3D Structure Click here
E9QCG7 View 3D Structure Click here
F1Q4R4 View 3D Structure Click here
F1QGD0 View 3D Structure Click here
F4IMY0 View 3D Structure Click here
F4IN78 View 3D Structure Click here
F4IZM8 View 3D Structure Click here
F4KIA8 View 3D Structure Click here
G3X9Z4 View 3D Structure Click here
G5ED97 View 3D Structure Click here
I1JFC3 View 3D Structure Click here
I1JNS1 View 3D Structure Click here
I1KWX3 View 3D Structure Click here
I1LT30 View 3D Structure Click here
I1MLE5 View 3D Structure Click here
I1MT78 View 3D Structure Click here
I1N7V7 View 3D Structure Click here
I1NAJ5 View 3D Structure Click here
K7KBY0 View 3D Structure Click here
K7KFY5 View 3D Structure Click here
K7L6K9 View 3D Structure Click here
K7LH02 View 3D Structure Click here
K7LHS7 View 3D Structure Click here
K7LLB6 View 3D Structure Click here
K7LNW8 View 3D Structure Click here
K7LRU4 View 3D Structure Click here
K7MXZ9 View 3D Structure Click here
K7MYJ3 View 3D Structure Click here
K7N3F0 View 3D Structure Click here
O01864 View 3D Structure Click here
O15042 View 3D Structure Click here
O49570 View 3D Structure Click here
O74814 View 3D Structure Click here
O94913 View 3D Structure Click here
O95104 View 3D Structure Click here
P34281 View 3D Structure Click here
P39081 View 3D Structure Click here
P53617 View 3D Structure Click here
Q05543 View 3D Structure Click here
Q09345 View 3D Structure Click here
Q0D412 View 3D Structure Click here
Q0IZJ8 View 3D Structure Click here
Q0WPF2 View 3D Structure Click here
Q10200 View 3D Structure Click here
Q10237 View 3D Structure Click here
Q1LXW2 View 3D Structure Click here
Q2QYA2 View 3D Structure Click here
Q4CX13 View 3D Structure Click here
Q4CX74 View 3D Structure Click here
Q54C48 View 3D Structure Click here
Q54PG0 View 3D Structure Click here
Q54TL3 View 3D Structure Click here
Q55CI7 View 3D Structure Click here
Q59E33 View 3D Structure Click here
Q5JKG7 View 3D Structure Click here
Q5VT52 View 3D Structure Click here
Q63623 View 3D Structure Click here
Q63627 View 3D Structure Click here
Q66GK1 View 3D Structure Click here
Q6DID3 View 3D Structure Click here
Q6NV83 View 3D Structure Click here
Q6NXI6 View 3D Structure Click here
Q6Z1Z8 View 3D Structure Click here
Q6ZAQ9 View 3D Structure Click here
Q7TSH6 View 3D Structure Click here
Q7ZUK9 View 3D Structure Click here
Q8CGZ0 View 3D Structure Click here
Q8GUK8 View 3D Structure Click here
Q8IHV7 View 3D Structure Click here
Q8IWX8 View 3D Structure Click here
Q8VDS4 View 3D Structure Click here
Q95YF1 View 3D Structure Click here
Q96P16 View 3D Structure Click here
Q9C5J3 View 3D Structure Click here
Q9CSU0 View 3D Structure Click here
Q9FJP7 View 3D Structure Click here
Q9LEY4 View 3D Structure Click here
Q9NQG5 View 3D Structure Click here
Q9UPN6 View 3D Structure Click here
Q9UTE3 View 3D Structure Click here
Q9W039 View 3D Structure Click here
Q9W2N6 View 3D Structure Click here
Q9XER9 View 3D Structure Click here
R4GE22 View 3D Structure Click here
X2JAA3 View 3D Structure Click here