8QUS

Crystal structure of the Plasmodium vivax Apical membrane antigen (AMA1) in complex with single domain i-body WD34

PDB DOI: https://doi.org/10.2210/pdb8QUS/pdb

Classification: PROTEIN BINDING
Organism(s): Plasmodium vivax Sal-1, Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-10-17 Released: 2024-07-03
Deposition Author(s): Maddumage, J.C., Kvansakul, M.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.286
R-Value Work: 0.254
R-Value Observed: 0.256

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A broadly cross-reactive i-body to AMA1 potently inhibits blood and liver stages of Plasmodium parasites

Foley, M., Angage, D., Anders, R., Chmielewski, J., Maddumage, J.C., Hesping, E., Caiazzo, S., Lai, K.H., Yeoh, L., Opi, H., Cairns, C., Beeson, J., Kvansakul, M., Wilson, D., Boddey, J.

(2024) Res Sq

DOI: https://doi.org/10.21203/rs.3.rs-3671797/v1

Macromolecule Content

Total Structure Weight: 67.35 kDa
Atom Count: 3,698
Modelled Residue Count: 471
Deposited Residue Count: 591
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apical merozoite antigen 1	A [auth D]	465	Plasmodium vivax Sal-1	Mutation(s): 0 Gene Names: PVX_092275
UniProt
Find proteins for A5K4Z2 (Plasmodium vivax (strain Salvador I)) Explore A5K4Z2 Go to UniProtKB: A5K4Z2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5K4Z2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
single domain i-body WD34	B [auth H]	126	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.286
R-Value Work: 0.254
R-Value Observed: 0.256
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.386	α = 90
b = 55.265	β = 90
c = 229.549	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-03

Deposition Author(s):

Maddumage, J.C.

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1103871

Revision History (Full details and data files)

Version 1.0: 2024-07-03
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.