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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free:
0.269 (Depositor), 0.246 (DCC)
R-Value Work:
0.212 (Depositor)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

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

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1G4H7E1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.269 (Depositor), 0.246 (DCC)
R-Value Work: 0.212 (Depositor)
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

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-29

Deposition Author(s):

Gilbert, R.J.C.

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 (Full details and data files)

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

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.