9JEC | pdb_00009jec

Cryo-EM structure of canine TNF-alpha complexed with nanobody TNF30K

PDB DOI: https://doi.org/10.2210/pdb9JEC/pdb
EM Map EMD-61412: EMDB EMDataResource

Classification: CYTOKINE
Organism(s): Canis lupus familiaris, Lama glama
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-03 Released: 2025-09-24
Deposition Author(s): Weng, J., Li, Z., Xu, J., Wei, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of canine TNF-alpha complexed with nanobody TNF30K

Weng, J., Li, Z., Xu, J., Wei, Z.

To be published.

Macromolecule Content

Total Structure Weight: 100.76 kDa
Atom Count: 5,985
Modeled Residue Count: 771
Deposited Residue Count: 912
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor	A, B, C	173	Canis lupus familiaris	Mutation(s): 0 Gene Names: TNF, TNFA, TNFSF2
UniProt
Find proteins for P51742 (Canis lupus familiaris) Explore P51742 Go to UniProtKB: P51742
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51742
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody TNF30K	D, E, F	131	Lama glama	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: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32000032
Other government		SKLBEE2022007

Revision History (Full details and data files)

Version 1.0: 2025-09-24
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.