9VNP | pdb_00009vnp

The complexes of IFN-gamma and A01BM-03 Fab

PDB DOI: https://doi.org/10.2210/pdb9VNP/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-06-30 Released: 2026-01-28
Deposition Author(s): Wang, X., Zhang, L., Wang, H., Yu, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.248 (Depositor), 0.248 (DCC)
R-Value Work:
0.229 (Depositor), 0.228 (DCC)

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

Identification and characterization of bone marrow plasma cells producing IFN-gamma-neutralizing autoantibodies in adult-onset immunodeficiency

Wang, X., Zhang, L., Wang, H., Yu, J.

To be published.

Macromolecule Content

Total Structure Weight: 69.57 kDa
Atom Count: 4,117
Modeled Residue Count: 528
Deposited Residue Count: 633
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon gamma	A [auth L]	192	Homo sapiens	Mutation(s): 1 Gene Names: IFNG
UniProt & NIH Common Fund Data Resources
Find proteins for P01579 (Homo sapiens) Explore P01579 Go to UniProtKB: P01579
PHAROS: P01579 GTEx: ENSG00000111537
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01579
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	B [auth A]	218	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain	C	223	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: 2.80 Å
R-Value Free: 0.248 (Depositor), 0.248 (DCC)
R-Value Work: 0.229 (Depositor), 0.228 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.328	α = 90
b = 59.103	β = 90
c = 77.788	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-01-28
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.