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14  structures 1104  species 2  interactions 1415  sequences 35  architectures

Family: FACT-Spt16_Nlob (PF14826)

Summary: FACT complex subunit SPT16 N-terminal lobe domain

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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.

FACT complex subunit SPT16 N-terminal lobe domain Provide feedback

The FACT or facilitator of chromatin transcription complex binds to and alters the properties of nucleosomes. This family represents the N-terminal lobe of the NTD, or N-terminal domain, and acts as a protein-protein interaction domain presumably with partners outside of the FACT complex [1]. Knockout of the whole NTD domain, 1-450 residues in UniProt:P32558 in yeast serves to tender the cells sensitive to DNA replication stress but is not lethal. The C-terminal half of NTD is structurally similar to aminopeptidases, and the most highly conserved surface residues line a cleft equivalent to the aminopeptidase substrate-binding site, family peptidase_M24, PF00557 [1].

Literature references

  1. VanDemark AP, Xin H, McCullough L, Rawlins R, Bentley S, Heroux A, Stillman DJ, Hill CP, Formosa T;, J Biol Chem. 2008;283:5058-5068.: Structural and functional analysis of the Spt16p N-terminal domain reveals overlapping roles of yFACT subunits. PUBMED:18089575 EPMC:18089575


This tab holds annotation information from the InterPro database.

InterPro entry IPR029148

Spt16 is a component of the FACT (facilitator of chromatin transcription) complex, a general chromatin factor that acts to reorganise nucleosomes [PUBMED:12815073, PUBMED:10413469]. In budding yeasts, the N-terminal domain (NTD) of Spt16 includes a smaller N-terminal lobe (residues 1-175) and a larger C-terminal lobe (residues 176-447). This entry represents the N-terminal lobe domain. Its structure is similar to the RuvC/RNase H family. It may act as a protein-protein interaction domain presumably with partners outside of the FACT complex [PUBMED:18089575]. The C-terminal lobe of NTD is structurally similar to aminopeptidases, and the most highly conserved surface residues line a cleft equivalent to the aminopeptidase substrate-binding site in peptidase family M24 (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 AMP_N-like (CL0356), which has the following description:

Bacterial amino-peptidases and creatinases, where the fold is a ribonuclease H-like motif, are grouped in this superfamily.

The clan contains the following 4 members:

AMP_N Creatinase_N Creatinase_N_2 FACT-Spt16_Nlob

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(142)
Full
(1415)
Representative proteomes UniProt
(2317)
NCBI
(2733)
Meta
(0)
RP15
(241)
RP35
(632)
RP55
(1028)
RP75
(1438)
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PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(142)
Full
(1415)
Representative proteomes UniProt
(2317)
NCBI
(2733)
Meta
(0)
RP15
(241)
RP35
(632)
RP55
(1028)
RP75
(1438)
Alignment:
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Order:
Sequence:
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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
(142)
Full
(1415)
Representative proteomes UniProt
(2317)
NCBI
(2733)
Meta
(0)
RP15
(241)
RP35
(632)
RP55
(1028)
RP75
(1438)
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.

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: CATH:3biq_A_01
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 142
Number in full: 1415
Average length of the domain: 157.20 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 15.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.7 27.3
Noise cut-off 25.7 26.9
Model length: 161
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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

Selections

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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 are 2 interactions for this family. More...

Peptidase_M24 Peptidase_M24

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 FACT-Spt16_Nlob domain has been found. There are 14 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.

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