Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
77  structures 304  species 1  interaction 3438  sequences 3  architectures

Family: Late_protein_L1 (PF00500)

Summary: L1 (late) protein

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 "Late protein". More...

Late protein Edit Wikipedia article

L1 (late) protein
PDB 1dzl EBI.jpg
l1 protein of human papillomavirus 16
Identifiers
Symbol Late_protein_L1
Pfam PF00500
InterPro IPR002210
SCOP 1dzl
SUPERFAMILY 1dzl
Late Protein L2
Identifiers
Symbol Late_protein_L2
Pfam PF00513
InterPro IPR000784

A late protein is a viral protein that is formed after replication of the virus.[1] One example is VP4 from simian virus 40 (SV40).[2]

In Human papillomavirus, two late proteins are involved in capsid formation: a major (L1) and a minor (L2) protein, in the approximate proportion 95:5%. L1 forms a pentameric assembly unit of the viral shell in a manner that closely resembles VP1 from polyomaviruses. Intermolecular disulphide bonding holds the L1 capsid proteins together.[3] L1 capsid proteins can bind via its nuclear localisation signal (NLS) to karyopherins Kapbeta(2) and Kapbeta(3) and inhibit the Kapbeta(2) and Kapbeta(3) nuclear import pathways during the productive phase of the viral life cycle.[4] Surface loops on L1 pentamers contain sites of sequence variation between HPV types. L2 minor capsid proteins enter the nucleus twice during infection: in the initial phase after virion disassembly, and in the productive phase when it assembles into replicated virions along with L1 major capsid proteins. L2 proteins contain two nuclear localisation signals (NLSs), one at the N-terminal (nNLS) and the other at the C-terminal (cNLS). L2 uses its NLSs to interact with a network of karyopherins in order to enter the nucleus via several import pathways. L2 from HPV types 11 and 16 was shown to interact with karyopherins Kapbeta(2) and Kapbeta(3).[5][6] L2 capsid proteins can also interact with viral dsDNA, facilitating its release from the endocytic compartment after viral uncoating.

References

  1. ^ "DNA Virus Replication". 
  2. ^ Daniels R, Sadowicz D, Hebert DN (July 2007). "A very late viral protein triggers the lytic release of SV40". PLoS Pathog. 3 (7): e98. doi:10.1371/journal.ppat.0030098. PMC 1924868. PMID 17658947. 
  3. ^ Sapp M, Volpers C, Muller M, Streeck RE (September 1995). "Organization of the major and minor capsid proteins in human papillomavirus type 33 virus-like particles". J. Gen. Virol. 76 (9): 2407–12. doi:10.1099/0022-1317-76-9-2407. PMID 7561785. 
  4. ^ Nelson LM, Rose RC, Moroianu J (February 2003). "The L1 major capsid protein of human papillomavirus type 11 interacts with Kap beta2 and Kap beta3 nuclear import receptors". Virology 306 (1): 162–9. doi:10.1016/S0042-6822(02)00025-9. PMID 12620808. 
  5. ^ Bordeaux J, Forte S, Harding E, Darshan MS, Klucevsek K, Moroianu J (August 2006). "The l2 minor capsid protein of low-risk human papillomavirus type 11 interacts with host nuclear import receptors and viral DNA". J. Virol. 80 (16): 8259–62. doi:10.1128/JVI.00776-06. PMC 1563822. PMID 16873281. 
  6. ^ Darshan MS, Lucchi J, Harding E, Moroianu J (November 2004). "The l2 minor capsid protein of human papillomavirus type 16 interacts with a network of nuclear import receptors". J. Virol. 78 (22): 12179–88. doi:10.1128/JVI.78.22.12179-12188.2004. PMC 525100. PMID 15507604. 

This article incorporates text from the public domain Pfam and InterPro IPR002210

This article incorporates text from the public domain Pfam and InterPro IPR000784

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.

L1 (late) protein Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002210

This entry represents the major late capsid protein L1 from Papillomaviruses, such as Human papillomavirus (HPV) [PUBMED:10882140]. Papillomaviruses are members of the papovavirus superfamily. More than 70 different types of papillomavirus have been discovered in humans, some of which have been shown to cause genital carcinomas and cutaneous warts [PUBMED:17446671]. The viruses contain a circular dsDNA genome surrounded by an icosahedral capsid (non-enveloped). Two proteins are involved in capsid formation: a major (L1) and a minor (L2) protein, in the approximate proportion 95:5%. L1 forms a pentameric assembly unit of the viral shell in a manner that closely resembles VP1 from polyomaviruses. Intermolecular disulphide bonding holds the L1 capsid proteins together [PUBMED:7561785]. L1 capsid proteins can bind via its nuclear localisation signal (NLS) to karyopherins Kapbeta(2) and Kapbeta(3) and inhibit the Kapbeta(2) and Kapbeta(3) nuclear import pathways during the productive phase of the viral life cycle [PUBMED:12620808]. Surface loops on L1 pentamers contain sites of sequence variation between HPV types.

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...

Loading domain graphics...

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
(19)
Full
(3438)
Representative proteomes NCBI
(2486)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Jalview View  View          View   
HTML View  View             
PP/heatmap 1 View             
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(19)
Full
(3438)
Representative proteomes NCBI
(2486)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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
(19)
Full
(3438)
Representative proteomes NCBI
(2486)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Raw Stockholm Download   Download           Download    
Gzipped 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: Pfam-B_69 (release 1.0)
Previous IDs: late_protein_L1;
Type: Domain
Author: Finn RD
Number in seed: 19
Number in full: 3438
Average length of the domain: 179.90 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 98.21 %

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 18.9 18.9
Trusted cut-off 18.9 18.9
Noise cut-off 18.8 18.8
Model length: 500
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

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

Late_protein_L1

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 Late_protein_L1 domain has been found. There are 77 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.

Loading structure mapping...