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1  structure 269  species 0  interactions 316  sequences 10  architectures

Family: COG2 (PF06148)

Summary: COG (conserved oligomeric Golgi) complex component, COG2

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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.

COG (conserved oligomeric Golgi) complex component, COG2 Provide feedback

The COG complex comprises eight proteins COG1-8. The COG complex plays critical roles in Golgi structure and function [1]. The proposed function of the complex is to mediate the initial physical contact between transport vesicles and their membrane targets. A comparable role in tethering vesicles has been suggested for at least six additional large multisubunit complexes, including the exocyst, a complex that mediates trafficking to the plasma membrane. COG2 structure reveals a six-helix bundle with few conserved surface features but a general resemblance to recently determined crystal structures of four different exocyst subunits. These bundles inCOG2 may act as platforms for interaction with other trafficing proteins including SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) and Rabs [2].

Literature references

  1. Ungar D, Oka T, Brittle EE, Vasile E, Lupashin VV, Chatterton JE, Heuser JE, Krieger M, Waters MG; , J Cell Biol 2002;157:405-415.: Characterization of a mammalian Golgi-localized protein complex, COG, that is required for normal Golgi morphology and function. PUBMED:11980916 EPMC:11980916

  2. Cavanaugh LF, Chen X, Richardson BC, Ungar D, Pelczer I, Rizo J, Hughson FM; , J Biol Chem. 2007;282:23418-23426.: Structural analysis of conserved oligomeric Golgi complex subunit 2. PUBMED:17565980 EPMC:17565980


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024602

This entry represents the uncharacterised N-terminal domain of subunit 2 of the COG complex. The COG complex comprises eight proteins COG1-8 and plays critical roles in Golgi structure and function [PUBMED:11980916].

Domain organisation

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

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Pfam Clan

This family is a member of clan Vps51 (CL0295), which contains the following 16 members:

COG2 COG5 COG6 Dor1 DUF2450 Exo70 Sec15 Sec3_C Sec3_C_2 Sec5 Sec6 Sec8_exocyst Vps51 Vps52 Vps53_N Zw10

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(19)
Full
(316)
Representative proteomes NCBI
(448)
Meta
(1)
RP15
(73)
RP35
(126)
RP55
(185)
RP75
(222)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(19)
Full
(316)
Representative proteomes NCBI
(448)
Meta
(1)
RP15
(73)
RP35
(126)
RP55
(185)
RP75
(222)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(19)
Full
(316)
Representative proteomes NCBI
(448)
Meta
(1)
RP15
(73)
RP35
(126)
RP55
(185)
RP75
(222)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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_9559 (release 9.0)
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 19
Number in full: 316
Average length of the domain: 134.30 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 23.60 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.9 24.9
Trusted cut-off 24.9 24.9
Noise cut-off 24.8 24.8
Model length: 133
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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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...

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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 COG2 domain has been found. There are 1 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 seqence.

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