7PLN | pdb_00007pln

Structure of the APCbeta domain of Plasmodium vivax perforin-like protein 1

• PDB DOI: https://doi.org/10.2210/pdb7PLN/pdb

• Classification: CELL INVASION
• Organism(s): Plasmodium vivax
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-08-31 Released: 2022-06-29 
• Deposition Author(s): Williams, S.I., Ni, T., Yu, X., Gilbert, R.J.C.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC, United Kingdom), Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Structural, Functional and Computational Studies of Membrane Recognition by Plasmodium Perforin-Like Proteins 1 and 2

Williams, S.I., Yu, X., Ni, T., Gilbert, R.J., Stansfeld, P.J.

(2022) J Mol Biology 434: 167642

• DOI: https://doi.org/10.1016/j.jmb.2022.167642

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.57 kDa 
• Atom Count: 3,682 
• Modeled Residue Count: 483 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sporozoite micronemal protein essential for cell traversal, putative	A, B	271	Plasmodium vivax	Mutation(s): 0  Gene Names: PVC01_030012400, PVT01_030012800
UniProt
Find proteins for A0A1G4H7E1 (Plasmodium vivax) Explore A0A1G4H7E1  Go to UniProtKB:  A0A1G4H7E1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.74	α = 90
b = 42.02	β = 104.95
c = 87.22	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Williams, S.I., Ni, T., Yu, X., Gilbert, R.J.C.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M011224/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N000331/1
Wellcome Trust	United Kingdom	090532/Z/09/Z

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2023-05-10
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary