9BN7 | pdb_00009bn7

X-ray crystal structure of TNFa-VNAR C4 complex

PDB DOI: https://doi.org/10.2210/pdb9BN7/pdb

Classification: Cytokine/Immune System
Organism(s): Homo sapiens, Squalus acanthias
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-02 Released: 2025-11-05
Deposition Author(s): Shi, K., Aihara, H.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.245 (Depositor), 0.244 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)
R-Value Observed:
0.200 (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

X-ray crystal structure of TNFa VNAR complex

Ubah, O.C., Shi, K., Moller, N., Aihara, H.

To be published.

Macromolecule Content

Total Structure Weight: 92.22 kDa
Atom Count: 6,397
Modeled Residue Count: 781
Deposited Residue Count: 816
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor	A, B, C	157	Homo sapiens	Mutation(s): 0 Gene Names: TNF, TNFA, TNFSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens) Explore P01375 Go to UniProtKB: P01375
PHAROS: P01375 GTEx: ENSG00000232810
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01375
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VNARC4	D, E, F	115	Squalus acanthias	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	H [auth B] I [auth B] J [auth B] K [auth B] M [auth C] H [auth B], I [auth B], J [auth B], K [auth B], M [auth C], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain Q [auth E] SDF format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain G [auth A]	G [auth A], L [auth C], N [auth D], Q [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Interactions & Density Focus chain G [auth A] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F] mmCIF format, chain T [auth F]	P [auth D], R [auth E], S [auth F], T [auth F]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Interactions & Density Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.245 (Depositor), 0.244 (DCC)
R-Value Work: 0.198 (Depositor), 0.198 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.588	α = 90
b = 89.452	β = 90
c = 342.772	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Shi, K.

Aihara, H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01-CA214279
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37-AI064064