8Z8M | pdb_00008z8m

Crystal structure of human TNF alpha in complex with TNF30(VHH) domain of ozoralizumab

PDB DOI: https://doi.org/10.2210/pdb8Z8M/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2024-04-22 Released: 2024-09-04
Deposition Author(s): Mima, M., Mishima-Tsumagari, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.269 (Depositor), 0.265 (DCC)
R-Value Work:
0.209 (Depositor), 0.212 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural design of the anti-TNF alpha therapeutic NANOBODY® compound, ozoralizumab, to support its potent and sustained clinical efficacy.

Mima, M., Mishima-Tsumagari, C., Nakano, K., Morimoto, M., Ogata, H., Sakata, M., Iwaoka, R., Iwata, K., Hachiuma, K., Iwamoto, K., Fujii, Y., Kurokawa, T.

(2024) Biochem Biophys Res Commun 734: 150454-150454

PubMed: 39083975 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2024.150454
Primary Citation of Related Structures:
8Z8M, 8Z8V

Organizational Affiliation

Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-cho, Kita-ku, Saitama, 331-9530, Japan.

Macromolecule Content

Total Structure Weight: 186.57 kDa
Atom Count: 12,130
Modeled Residue Count: 1,553
Deposited Residue Count: 1,680
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor	A, C, E, G, I A, C, E, G, I, K	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01375
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TNF30:VHH	B, D, F, H, J B, D, F, H, J, L	123	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: 2.59 Å
R-Value Free: 0.269 (Depositor), 0.265 (DCC)
R-Value Work: 0.209 (Depositor), 0.212 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.03	α = 90
b = 121.16	β = 94.58
c = 123.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Mishima-Tsumagari, C.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-09-04
Type: Initial release
Version 1.1: 2024-10-30
Changes: Structure summary

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.