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81  structures 1526  species 0  interactions 7608  sequences 98  architectures

Family: NAP (PF00956)

Summary: Nucleosome assembly protein (NAP)

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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.

Nucleosome assembly protein (NAP) Provide feedback

NAP proteins are involved in moving histones into the nucleus, nucleosome assembly and chromatin fluidity. They affect the transcription of many genes.

Literature references

  1. Rodriguez P, Munroe D, Prawitt D, Chu LL, Bric E, Kim J, Reid LH, Davies C, Nakagama H, Loebbert R, Winterpacht A, Petruzzi MJ, Higgins MJ, Nowak N, Evans G, Shows T, Weissman BE, Zabel B, Housman DE, Pelletier J; , Genomics 1997;44:253-265.: Functional characterization of human nucleosome assembly protein-2 (NAP1L4) suggests a role as a histone chaperone. PUBMED:9325046 EPMC:9325046

  2. Schnieders F, Dork T, Arnemann J, Vogel T, Werner M, Schmidtke J; , Hum Mol Genet 1996;5:1801-1807.: Testis-specific protein, Y-encoded (TSPY) expression in testicular tissues. PUBMED:8923009 EPMC:8923009

  3. Park YJ, Luger K; , Proc Natl Acad Sci U S A. 2006;103:1248-1253.: The structure of nucleosome assembly protein 1. PUBMED:16432217 EPMC:16432217


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002164

It is thought that NAPs act as histone chaperones, shuttling both core and linker histones from their site of synthesis in the cytoplasm to the nucleus. The proteins may be involved in regulating gene expression and therefore cellular differentiation [ PUBMED:9325046 , PUBMED:8923009 ].

The centrosomal protein c-Nap1, also known as Cep250, has been implicated in the cell-cycle-regulated cohesion of microtubule-organizing centres. This 281kDa protein consists mainly of domains predicted to form coiled coil structures. The C-terminal region defines a novel histone-binding domain that is responsible for targeting CNAP1, and possibly condensin, to mitotic chromosomes [ PUBMED:12138188 ]. During interphase, C-Nap1 localizes to the proximal ends of both parental centrioles, but it dissociates from these structures at the onset of mitosis. Re-association with centrioles then occurs in late telophase or at the very beginning of G1 phase, when daughter cells are still connected by post-mitotic bridges. Electron microscopic studies performed on isolated centrosomes suggest that a proteinaceous linker connects parental centrioles and C-Nap1 may be part of a linker structure that assures the cohesion of duplicated centrosomes during interphase, but that is dismantled upon centrosome separation at the onset of mitosis [ PUBMED:12140259 ].

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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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
(192)
Full
(7608)
Representative proteomes UniProt
(12067)
RP15
(1181)
RP35
(2981)
RP55
(5424)
RP75
(7663)
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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
(192)
Full
(7608)
Representative proteomes UniProt
(12067)
RP15
(1181)
RP35
(2981)
RP55
(5424)
RP75
(7663)
Alignment:
Format:
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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
(192)
Full
(7608)
Representative proteomes UniProt
(12067)
RP15
(1181)
RP35
(2981)
RP55
(5424)
RP75
(7663)
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_1009 (release 3.0)
Previous IDs: NAP_family;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A
Number in seed: 192
Number in full: 7608
Average length of the domain: 211.60 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 61.98 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.6 28.6
Trusted cut-off 28.6 28.6
Noise cut-off 28.5 28.5
Model length: 272
Family (HMM) version: 21
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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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 NAP domain has been found. There are 81 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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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
A0A096MJ32 View 3D Structure Click here
A0A0G2K5L9 View 3D Structure Click here
A0A0N7KKD8 View 3D Structure Click here
A0A0R0FHA5 View 3D Structure Click here
A0A0R0FKU0 View 3D Structure Click here
A0A0R0JAQ5 View 3D Structure Click here
A0A0R0KF47 View 3D Structure Click here
A0A1D6FWR6 View 3D Structure Click here
A0A1D6LL45 View 3D Structure Click here
A0A1D8PT39 View 3D Structure Click here
A0A2R8Q4J7 View 3D Structure Click here
A0A2R8QJ70 View 3D Structure Click here
A0A494C1R9 View 3D Structure Click here
A2ZX50 View 3D Structure Click here
A4HY66 View 3D Structure Click here
A4HYX2 View 3D Structure Click here
A4I6V2 View 3D Structure Click here
A6NFF2 View 3D Structure Click here
A6NKD2 View 3D Structure Click here
B5DEL0 View 3D Structure Click here
B9FU45 View 3D Structure Click here
D3ZLU5 View 3D Structure Click here
D4A466 View 3D Structure Click here
D4AEJ0 View 3D Structure Click here
F1QRV6 View 3D Structure Click here
F4JEI8 View 3D Structure Click here
I1JWV7 View 3D Structure Click here
I1JZQ1 View 3D Structure Click here
I1KCS5 View 3D Structure Click here
I1L1J3 View 3D Structure Click here
I1LY05 View 3D Structure Click here
I1MD00 View 3D Structure Click here
I1MH86 View 3D Structure Click here
K7K338 View 3D Structure Click here
K7KCS2 View 3D Structure Click here
K7M3M8 View 3D Structure Click here
K7M7M8 View 3D Structure Click here
O59797 View 3D Structure Click here
O88852 View 3D Structure Click here
P0CV98 View 3D Structure Click here