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16  structures 253  species 0  interactions 368  sequences 8  architectures

Family: Nucleopor_Nup85 (PF07575)

Summary: Nup85 Nucleoporin

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Nup85 Nucleoporin Provide feedback

A family of nucleoporins conserved from yeast to human. THe nuclear pore complex is a large assembly composed of two essential complexes: the heptameric Nup84 complex and the heteromeric Nic96-containing complex. The Nup84 complex is composed of one copy each of Nup84, Nup85, Nup120, Nup133, Nup145C, Sec13, and Seh1. The structure of a complex of Nup85 and Seh1 was solved [3]. The N-terminus of Nup85 is inserted and forms a three-stranded blade that completes the Seh1 6-bladed beta-propeller in trans. Following its N-terminal insertion blade, Nup85 forms a compact cuboid structure composed of 20 helices, with two distinct modules, referred to as crown and trunk [3].

Literature references

  1. Fabre E, Hurt E; , Annu Rev Genet 1997;31:277-313.: Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. PUBMED:9442897 EPMC:9442897

  2. Siniossoglou S, Wimmer C, Rieger M, Doye V, Tekotte H, Weise C, Emig S, Segref A, Hurt EC; , Cell 1996;84:265-275.: A novel complex of nucleoporins, which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores. PUBMED:8565072 EPMC:8565072

  3. Brohawn SG, Leksa NC, Spear ED, Rajashankar KR, Schwartz TU;, Science. 2008;322:1369-1373.: Structural evidence for common ancestry of the nuclear pore complex and vesicle coats. PUBMED:18974315 EPMC:18974315


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011502

This is a family of nucleoporins conserved from yeast to human.

Nup85 Nucleoporin is an essential component of the nuclear pore complex (NPC) that seems to be required for NPC assembly and maintenance. As part of the NPC Nup107-160 subcomplex plays a role in RNA export and in tethering NUP98/Nup98 and NUP153 to the nucleus. The Nup107-160 complex seems to be required for spindle assembly during mitosis. NUP85 is required for membrane clustering of CCL2-activated CCR2. Seems to be involved in CCR2-mediated chemotaxis of monocytes and may link activated CCR2 to the phosphatidyl-inositol-3-kinase-Rac-lammellipodium protrusion cascade [PUBMED:15995708, PUBMED:12718872, PUBMED:16807356].

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(20)
Full
(368)
Representative proteomes NCBI
(381)
Meta
(1)
RP15
(86)
RP35
(137)
RP55
(210)
RP75
(255)
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  Seed
(20)
Full
(368)
Representative proteomes NCBI
(381)
Meta
(1)
RP15
(86)
RP35
(137)
RP55
(210)
RP75
(255)
Alignment:
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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
(20)
Full
(368)
Representative proteomes NCBI
(381)
Meta
(1)
RP15
(86)
RP35
(137)
RP55
(210)
RP75
(255)
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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_55990 (release 11.0)
Previous IDs: Nuceloporin_Nup85; Nucelopor_Nup85;
Type: Family
Author: Studholme DJ, Wood V
Number in seed: 20
Number in full: 368
Average length of the domain: 430.50 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 69.60 %

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 19.7 19.7
Trusted cut-off 19.8 19.8
Noise cut-off 19.2 19.5
Model length: 566
Family (HMM) version: 8
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 Nucleopor_Nup85 domain has been found. There are 16 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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