8TNJ | pdb_00008tnj

Cryo-EM structure of HLA-B*73:01 bound to a 9mer peptide and two Fabs

PDB DOI: https://doi.org/10.2210/pdb8TNJ/pdb
EM Map EMD-41418: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): No

Deposited: 2023-08-02 Released: 2024-08-14
Deposition Author(s): Ross, P., Adams, E.J., Lodwick, J., Zhao, M., Slezak, T., Kossiakoff, A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

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

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of HLA-B*73:01 bound to a 9mer peptide and two Fabs

Ross, P., Adams, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 146.14 kDa
Atom Count: 8,073
Modeled Residue Count: 1,040
Deposited Residue Count: 1,340
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
9mer peptide,Beta-2-microglobulin,MHC class I antigen chimera	A	439	Homo sapiens	Mutation(s): 0 Gene Names: B2M, HLA-B
UniProt & NIH Common Fund Data Resources
Find proteins for A0A858LJX3 (Homo sapiens) Explore A0A858LJX3 Go to UniProtKB: A0A858LJX3
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	A0A858LJX3 P61769
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
B.8 Fab light chain	B [auth C]	216	Homo sapiens	Mutation(s): 0

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
B.8 Fab heavy chain	C [auth D]	232	Homo sapiens	Mutation(s): 0

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
B.1 Fab heavy chain	D [auth E]	238	Homo sapiens	Mutation(s): 0

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
B.1 Fab light chain	E [auth F]	215	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-08-14
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, 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.