9DSS | pdb_00009dss

Crystal structure of Fab 7088 in complex with NPNA3 peptide from circumsporozoite protein

PDB DOI: https://doi.org/10.2210/pdb9DSS/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Plasmodium falciparum 3D7
Expression System: Cricetulus griseus, synthetic construct
Mutation(s): No

Deposited: 2024-09-28 Released: 2025-10-01
Deposition Author(s): Jain, M., Wilson, I.A.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.263 (Depositor), 0.263 (DCC)
R-Value Work:
0.229 (Depositor), 0.229 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Fab 7088 in complex with NPNA3 peptide from circumsporozoite protein

Jain, M., Wilson, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 49.05 kDa
Atom Count: 3,339
Modeled Residue Count: 436
Deposited Residue Count: 454
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab 7088	A [auth C]	227	Homo sapiens	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
Light Chain of Fab 7088	B	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Circumsporozoite protein	C [auth A]	12	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: CSP, PF3D7_0304600
UniProt
Find proteins for Q7K740 (Plasmodium falciparum (isolate 3D7)) Explore Q7K740 Go to UniProtKB: Q7K740
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7K740
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.263 (Depositor), 0.263 (DCC)
R-Value Work: 0.229 (Depositor), 0.229 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.114	α = 90
b = 72.114	β = 90
c = 195.786	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-004923
Bill & Melinda Gates Foundation	United States	INV-056202

Revision History (Full details and data files)

Version 1.0: 2025-10-01
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.