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8  structures 289  species 0  interactions 2217  sequences 44  architectures

Family: ApoL (PF05461)

Summary: Apolipoprotein L

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 "Apolipoprotein L". More...

Apolipoprotein L Edit Wikipedia article

Apolipoprotein L
Identifiers
SymbolApoL
PfamPF05461
InterProIPR008405

Apolipoprotein L (Apo L) belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia[1].

Human proteins containing this domain

APOL1; APOL2; APOL3; APOL4; APOL5; APOL6; APOLD1;

References

  1. ^ Arai H, Mimmack ML, Ryan M, Baba H, Navarro-ruiz J, Iritani S, Faull RL, Mckenna PJ, Jones PB, Starkey M, Emson PC, Bahn S (2002). "Gene expression analysis in schizophrenia: reproducible up-regulation of several members of the apolipoprotein L family located in a high-susceptibility locus for schizophrenia on chromosome 22". Proc. Natl. Acad. Sci. U.S.A. 99 (7): 4680–4685. PMID 11930015.{{cite journal}}: CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR008405

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.

Apolipoprotein L Provide feedback

Apo L belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia [1].

Literature references

  1. Mimmack ML, Ryan M, Baba H, Navarro-Ruiz J, Iritani S, Faull RL, McKenna PJ, Jones PB, Arai H, Starkey M, Emson PC, Bahn S; , Proc Natl Acad Sci U S A 2002;99:4680-4685.: Gene expression analysis in schizophrenia: reproducible up-regulation of several members of the apolipoprotein L family located in a high-susceptibility locus for schizophrenia on chromosome 22. PUBMED:11930015 EPMC:11930015


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008405

Apo L belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia [ PUBMED:11930015 ]. The various functions of apoL are still not entirely clear. Apolipoprotein L-I has been identified as a trypanolytic agent [ PUBMED:12621437 ] and displays similar phylogenetic distribution to the programmed cell death protein Bcl-2 and BH-3 domain-containing proteins, suggesting a possible role in apoptosis [ PUBMED:16847577 ].

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
(31)
Full
(2217)
Representative proteomes UniProt
(3301)
RP15
(241)
RP35
(819)
RP55
(1702)
RP75
(2250)
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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
(31)
Full
(2217)
Representative proteomes UniProt
(3301)
RP15
(241)
RP35
(819)
RP55
(1702)
RP75
(2250)
Alignment:
Format:
Order:
Sequence:
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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
(31)
Full
(2217)
Representative proteomes UniProt
(3301)
RP15
(241)
RP35
(819)
RP55
(1702)
RP75
(2250)
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_16464 (release 8.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Moxon SJ
Number in seed: 31
Number in full: 2217
Average length of the domain: 229.2 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 50.74 %

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 25.9 25.9
Trusted cut-off 25.9 25.9
Noise cut-off 25.8 25.8
Model length: 298
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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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 ApoL domain has been found. There are 8 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
A0A0G2JXY3 View 3D Structure Click here
A0A0G2K7F8 View 3D Structure Click here
A0A0R4IF32 View 3D Structure Click here
A0A0R4IKX7 View 3D Structure Click here
A0A140LFV9 View 3D Structure Click here
A0A1D5NS86 View 3D Structure Click here
A0A2R9YJH8 View 3D Structure Click here
A2VDH7 View 3D Structure Click here
B1AQP7 View 3D Structure Click here
B2RT54 View 3D Structure Click here
B7ZC55 View 3D Structure Click here
E7F980 View 3D Structure Click here
E9PUZ0 View 3D Structure Click here
E9PZG0 View 3D Structure Click here
E9Q0X2 View 3D Structure Click here
F1M512 View 3D Structure Click here
F1QCQ0 View 3D Structure Click here
F1QKV1 View 3D Structure Click here
F1QVT2 View 3D Structure Click here
G3X9K7 View 3D Structure Click here
I3ISX5 View 3D Structure Click here
M0RCB7 View 3D Structure Click here
O14791 View 3D Structure Click here
O95236 View 3D Structure Click here
Q3UZ24 View 3D Structure Click here
Q5U1W1 View 3D Structure Click here
Q5XIB6 View 3D Structure Click here
Q6B959 View 3D Structure Click here
Q8C6E1 View 3D Structure Click here
Q8C7I4 View 3D Structure Click here
Q8CCA5 View 3D Structure Click here
Q8VDU3 View 3D Structure Click here
Q8WQF7 View 3D Structure Click here
Q8WQF8 View 3D Structure Click here
Q96LR9 View 3D Structure Click here
Q9BPW4 View 3D Structure Click here
Q9BQE5 View 3D Structure Click here
Q9BWW8 View 3D Structure Click here
Q9BWW9 View 3D Structure Click here
X1WBM3 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;