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110  structures 4898  species 1  interaction 10092  sequences 7  architectures

Family: SSB (PF00436)

Summary: Single-strand binding protein family

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 "Single-stranded DNA binding protein". More...

Single-stranded DNA binding protein Edit Wikipedia article

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.

Single-strand binding protein family Provide feedback

This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA.

Literature references

  1. Raghunathan S, Ricard CS, Lohman TM, Waksman G; , Proc Natl Acad Sci U S A 1997;94:6652-6657.: Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution. PUBMED:9192620 EPMC:9192620

  2. Yang C, Curth U, Urbanke C, Kang C; , Nat Struct Biol 1997;4:153-157.: Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution. PUBMED:9033597 EPMC:9033597

  3. Webster G, Genschel J, Curth U, Urbanke C, Kang C, Hilgenfeld R; , FEBS Lett 1997;411:313-316.: A common core for binding single-stranded DNA: structural comparison of the single-stranded DNA-binding proteins (SSB) from E. coli and human mitochondria. PUBMED:9271227 EPMC:9271227


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000424

The Escherichia coli single-strand binding protein [PUBMED:2087220] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.

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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Pfam Clan

This family is a member of clan OB (CL0021), which has the following description:

The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin [1]. The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands [1].

The clan contains the following 45 members:

BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF3127 DUF35 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_NTP_bind OB_RNB OmdA Phage_DNA_bind POT1 RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RuvA_N S1 S1-like S1_2 SSB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind

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
(70)
Full
(10092)
Representative proteomes NCBI
(6702)
Meta
(2778)
RP15
(640)
RP35
(1330)
RP55
(1739)
RP75
(2030)
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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
(70)
Full
(10092)
Representative proteomes NCBI
(6702)
Meta
(2778)
RP15
(640)
RP35
(1330)
RP55
(1739)
RP75
(2030)
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
(70)
Full
(10092)
Representative proteomes NCBI
(6702)
Meta
(2778)
RP15
(640)
RP35
(1330)
RP55
(1739)
RP75
(2030)
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: Prosite & COG2965
Previous IDs: none
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 70
Number in full: 10092
Average length of the domain: 102.00 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 65.61 %

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 21.9 21.9
Trusted cut-off 21.9 21.9
Noise cut-off 21.8 21.8
Model length: 104
Family (HMM) version: 20
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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Interactions

There is 1 interaction for this family. More...

SSB

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 SSB domain has been found. There are 110 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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