9OSX | pdb_00009osx

PfCyRPA-EM epitope mimic bound to monoclonal antibody Cy.004

PDB DOI: https://doi.org/10.2210/pdb9OSX/pdb

Classification: IMMUNE SYSTEM
Organism(s): synthetic construct, Gallus gallus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-05-26 Released: 2025-12-24
Deposition Author(s): Alam, N., Higgins, M.K.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free:
0.292 (Depositor), 0.292 (DCC)
R-Value Work:
0.254 (Depositor), 0.254 (DCC)
R-Value Observed:
0.256 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure-guided design of a PfCyRPA-based vaccine against blood-stage malaria

Alam, N., Higgins, M.K.

To be published.

Macromolecule Content

Total Structure Weight: 71.87 kDa
Atom Count: 4,208
Modeled Residue Count: 538
Deposited Residue Count: 661
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PfCyRPA-EM	A	131	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cy.004 heavy chain	B	321	Gallus gallus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cy.004 light chain	C	209	Gallus gallus	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: 2.67 Å
R-Value Free: 0.292 (Depositor), 0.292 (DCC)
R-Value Work: 0.254 (Depositor), 0.254 (DCC)
R-Value Observed: 0.256 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.615	α = 90
b = 37.976	β = 92.47
c = 173.374	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	220797/Z/20/Z

Revision History (Full details and data files)

Version 1.0: 2025-12-24
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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.