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72  structures 51  species 2  interactions 148  sequences 13  architectures

Family: AMA-1 (PF02430)

Summary: Apical membrane antigen 1

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This is the Wikipedia entry entitled "Apical membrane antigen 1". More...

Apical membrane antigen 1 Edit Wikipedia article

AMA-1
PDB 1hn6 EBI.jpg
solution structure of plasmodium falciparum apical membrane antigen 1 (residues 436-545)
Identifiers
Symbol AMA-1
Pfam PF02430
InterPro IPR003298
SCOP 1hn6
SUPERFAMILY 1hn6

In molecular biology, apical membrane antigen 1 is a novel antigen of Plasmodium falciparum which has been cloned. It contains a hydrophobic domain typical of an integral membrane protein. The antigen is designated apical membrane antigen 1 (AMA-1) by virtue of appearing to be located in the apical complex.[1] AMA-1 appears to be transported to the merozoite surface close to the time of schizont rupture.

The 66kDa merozoite surface antigen (PK66) of Plasmodium knowlesi, a simian malaria, possesses vaccine-related properties believed to originate from a receptor-like role in parasite invasion of erythrocytes.[2] The sequence of PK66 is conserved throughout plasmodium, and shows high similarity to P. falciparum AMA-1. Following schizont rupture, the distribution of PK66 changes in a coordinate manner associated with merozoite invasion. Prior to rupture, the protein is concentrated at the apical end, following which it distributes itself entirely across the surface of the free merozoite. Immunofluorescence studies suggest that, during invasion, PK66 is excluded from the erythrocyte at, and behind, the invasion interface.[2]

References

  1. ^ Peterson MG, Marshall VM, Smythe JA, Crewther PE, Lew A, Silva A, Anders RF, Kemp DJ (July 1989). "Integral membrane protein located in the apical complex of Plasmodium falciparum". Mol. Cell. Biol. 9 (7): 3151–4. PMC 362792Freely accessible. PMID 2701947. 
  2. ^ a b Waters AP, Thomas AW, Deans JA, Mitchell GH, Hudson DE, Miller LH, McCutchan TF, Cohen S (October 1990). "A merozoite receptor protein from Plasmodium knowlesi is highly conserved and distributed throughout Plasmodium". J. Biol. Chem. 265 (29): 17974–9. PMID 2211675. 

This article incorporates text from the public domain Pfam and InterPro IPR003298

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.

Apical membrane antigen 1 Provide feedback

Apical membrane antigen 1 (AMA-1) is a Plasmodium asexual blood-stage antigen. It has been suggested that positive selection operates on the AMA-1 gene in regions coding for antigenic sites [1].

Literature references

  1. Crewther PE, Matthew ML, Flegg RH, Anders RF; , Infect Immun 1996;64:3310-3317.: Protective immune responses to apical membrane antigen 1 of Plasmodium chabaudi involve recognition of strain-specific epitopes. PUBMED:8757869 EPMC:8757869


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003298

A novel antigen of Plasmodium falciparum has been cloned that contains a hydrophobic domain typical of an integral membrane protein. The antigen is designated apical membrane antigen 1 (AMA-1) by virtue of appearing to be located in the apical complex [PUBMED:2701947]. AMA-1 appears to be transported to the merozoite surface close to the time of schizont rupture.

The 66kDa merozoite surface antigen (PK66) of Plasmodium knowlesi, a simian malaria, possesses vaccine-related properties believed to originate from a receptor-like role in parasite invasion of erythrocytes [PUBMED:2211675]. The sequence of PK66 is conserved throughout plasmodium, and shows high similarity to P. falciparum AMA-1. Following schizont rupture, the distribution of PK66 changes in a coordinate manner associated with merozoite invasion. Prior to rupture, the protein is concentrated at the apical end, following which it distributes itself entirely across the surface of the free merozoite. Immunofluorescence studies suggest that, during invasion, PK66 is excluded from the erythrocyte at, and behind, the invasion interface [PUBMED:2211675].

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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Pfam Clan

This family is a member of clan PAN (CL0168), which has the following description:

PAN domains have significant functional versatility fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions [1]. These domains contain a hair-pin loop like structure, similar to knottins, but the pattern of disulphide bonds differs.

The clan contains the following 6 members:

AMA-1 MANEC PAN_1 PAN_2 PAN_3 PAN_4

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
(5)
Full
(148)
Representative proteomes UniProt
(3338)
NCBI
(3320)
Meta
(0)
RP15
(43)
RP35
(67)
RP55
(95)
RP75
(139)
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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
(5)
Full
(148)
Representative proteomes UniProt
(3338)
NCBI
(3320)
Meta
(0)
RP15
(43)
RP35
(67)
RP55
(95)
RP75
(139)
Alignment:
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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
(5)
Full
(148)
Representative proteomes UniProt
(3338)
NCBI
(3320)
Meta
(0)
RP15
(43)
RP35
(67)
RP55
(95)
RP75
(139)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped 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: Pfam-B_2016 (release 5.4)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mian N , Bateman A
Number in seed: 5
Number in full: 148
Average length of the domain: 271.50 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 38.31 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.1 21.5
Noise cut-off 20.9 20.9
Model length: 467
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Selections

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Interactions

There are 2 interactions for this family. More...

AMA-1 V-set

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 AMA-1 domain has been found. There are 72 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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