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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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 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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01375
Sequence Annotations Expand
Reference Sequence

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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

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

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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

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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.