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2  structures 106  species 0  interactions 155  sequences 12  architectures

Family: LBR_tudor (PF09465)

Summary: Lamin-B receptor of TUDOR 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.

Lamin-B receptor of TUDOR domain Provide feedback

The Lamin-B receptor, found on the TUDOR domain PF00567 is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner Nuclear Envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with Importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the NE [1].

Literature references

  1. Ma Y, Cai S, Lv Q, Jiang Q, Zhang Q, Sodmergen, Zhai Z, Zhang C; , J Cell Sci. 2007;120:520-530.: Lamin B receptor plays a role in stimulating nuclear envelope production and targeting membrane vesicles to chromatin during nuclear envelope assembly through direct interaction with importin beta. PUBMED:17251381 EPMC:17251381


This tab holds annotation information from the InterPro database.

InterPro entry IPR019023

The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope [PUBMED:17251381].

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 Tudor (CL0049), which has the following description:

This clan covers the Tudor domain 'royal family' [1]. This includes chromo, MBT, PWWP and tudor domains. The chromo domain is a comprised of approximately 50 amino acid residues. There are usually one to three Chromo domains found in a single protein. In some chromo domain containing proteins, a second related chromo domain has been found and is referred to as the Chromo-shadow domain. The structure of the Chromo and Chromo-shadow domains reveal an OB-fold, a fold found in a variety of prokaryotic and eukaryotic nucleic acid binding proteins. More specifically,the chromo-domain structure reveals a three beta strands that are packed against an alpha helix. Interestingly, a similar structure is found in the archaeal chromatin proteins (7kDa DNA-binding domain). These are sequence neutral DNA binding proteins. The DNA binding in these archaeal proteins is mediated through the triple stranded beta sheet. These archaeal domains are though to represent an ancestral chromo domain. Homologs of the chromo domain have been found in fission yeast, ciliated protozoa and all animal species, but appear to be absent in eubacteria, budding yeast and plants [2]. The precise function of the chromo domain is unclear, but the chromo domain is thought to act as a targeting module for chromosomal proteins, although the chromosomal contexts and functional contexts being targeted vary. In all cases studies, the chromo domains are found in proteins that are involved in transcription regulation, positive and negative [2].

The clan contains the following 17 members:

53-BP1_Tudor 7kD_DNA_binding Agenet Chromo Chromo_shadow Cul7 DUF1325 DUF4537 LBR_tudor MBT PWWP Rad9_Rad53_bind RBB1NT SMN TTD TUDOR Tudor-knot

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
(10)
Full
(155)
Representative proteomes UniProt
(243)
NCBI
(426)
Meta
(5)
RP15
(23)
RP35
(61)
RP55
(105)
RP75
(129)
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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
(10)
Full
(155)
Representative proteomes UniProt
(243)
NCBI
(426)
Meta
(5)
RP15
(23)
RP35
(61)
RP55
(105)
RP75
(129)
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
(10)
Full
(155)
Representative proteomes UniProt
(243)
NCBI
(426)
Meta
(5)
RP15
(23)
RP35
(61)
RP55
(105)
RP75
(129)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: pdb_2dig
Previous IDs: none
Type: Domain
Author: Coggill P
Number in seed: 10
Number in full: 155
Average length of the domain: 51.60 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 9.56 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 55
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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

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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 LBR_tudor domain has been found. There are 2 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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