8Z8M

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.269 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Starting Model: experimental

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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 2 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TNF30:VHH	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 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• 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

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Mima, M., Mishima-Tsumagari, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release