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22  structures 372  species 0  interactions 1118  sequences 12  architectures

Family: Sld5 (PF05916)

Summary: GINS complex protein

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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.

GINS complex protein Provide feedback

The eukaryotic GINS complex is essential for the initiation and elongation phases of DNA replication [1-3]. It consists of four paralogous protein subunits (Sld5, Psf1, Psf2 and Psf3), all of which are included in this family. The GINS complex is conserved from yeast to humans, and has been shown in human to bind directly to DNA primase [4].

Literature references

  1. Kubota Y, Takase Y, Komori Y, Hashimoto Y, Arata T, Kamimura Y, Araki H, Takisawa H; , Genes Dev 2003;17:1141-1152.: A novel ring-like complex of Xenopus proteins essential for the initiation of DNA replication. PUBMED:12730133 EPMC:12730133

  2. Takayama Y, Kamimura Y, Okawa M, Muramatsu S, Sugino A, Araki H;, Genes Dev. 2003;17:1153-1165.: GINS, a novel multiprotein complex required for chromosomal DNA replication in budding yeast. PUBMED:12730134 EPMC:12730134

  3. Kanemaki M, Sanchez-Diaz A, Gambus A, Labib K;, Nature. 2003;423:720-724.: Functional proteomic identification of DNA replication proteins by induced proteolysis in vivo. PUBMED:12768207 EPMC:12768207

  4. De Falco M, Ferrari E, De Felice M, Rossi M, Hubscher U, Pisani FM;, EMBO Rep. 2007;8:99-103.: The human GINS complex binds to and specifically stimulates human DNA polymerase alpha-primase. PUBMED:17170760 EPMC:17170760


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR021151

DNA replication in eukaryotes results from a highly coordinated interaction between proteins, often as part of protein complexes, and the DNA template. One of the key early steps leading to DNA replication is formation of the pre- replication complex, or pre-RC. The pre-RC is formed by the sequential binding of the origin recognition complex (ORC), Cdc6 and Cdt1 proteins, and the MCM complex. Activation of the pre-RC into the initiation complex (IC) is achieved via the action of S-phase kinases, eventually leading to the loading of the replication machinery.

Recently, a novel replication complex, GINS (for Go, Ichi, Nii, and San; five, one, two, and three in Japanese), has been identified [PUBMED:12730133, PUBMED:12730134]. The precise function of GINS is not known. However, genetic and two-hybrid interactions indicate that it mediates the loading of the enzymatic replication machinery at a step after the action of the S-phase kinases [PUBMED:12730134]. Furthermore, GINS may be a part of the replication machinery itself, since it is found associated with replicating DNA [PUBMED:12730133, PUBMED:12730134]. Electron microscopy of GINS shows that it forms a ring-like structure [PUBMED:12730133], reminiscent of the structure of PCNA [PUBMED:8001157], the DNA polymerase delta replication clamp.This observation, coupled with the observed interactions for GINS, indicates that the complex may represent the replication clamp for DNA polymerase epsilon [PUBMED:12730133].

The GINS complex is essential for initiation of DNA replication in Xenopus egg extracts [PUBMED:12730133]. This 100 kDa stable complex includes Sld5, Psf1, Psf2, and Psf3. Homologues of these components are found also in other eukaryotes.

Domain organisation

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Alignments

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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
(176)
Full
(1118)
Representative proteomes NCBI
(1076)
Meta
(14)
RP15
(230)
RP35
(409)
RP55
(648)
RP75
(798)
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Format an alignment

  Seed
(176)
Full
(1118)
Representative proteomes NCBI
(1076)
Meta
(14)
RP15
(230)
RP35
(409)
RP55
(648)
RP75
(798)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(176)
Full
(1118)
Representative proteomes NCBI
(1076)
Meta
(14)
RP15
(230)
RP35
(409)
RP55
(648)
RP75
(798)
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.

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_8759 (release 8.0)
Previous IDs: DUF873;
Type: Family
Author: Moxon SJ, Studholme DJ
Number in seed: 176
Number in full: 1118
Average length of the domain: 113.40 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 50.89 %

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 21.0 21.0
Trusted cut-off 21.0 21.1
Noise cut-off 20.9 20.9
Model length: 108
Family (HMM) version: 6
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 Sld5 domain has been found. There are 22 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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