9QQE | pdb_00009qqe

Cryo-EM structure of the SN230G6 Fab - HLA-A*02:01 human alloantibody-HLA complex

• PDB DOI: https://doi.org/10.2210/pdb9QQE/pdb
• EM Map EMD-53299: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-03-31 Released: 2026-04-15 
• Deposition Author(s): Zampieri, V., Priddey, A., Schneider, S., Heidt, S., Kosmoliaptsis, V., Marquez, J.A.
• Funding Organization(s): European Union (EU), National Institute for Health and Care Research (NIHR), NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Terasaki Institute

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Cryo-EM structure of the SN230G6 Fab - HLA-A*02:01 human alloantibody-HLA complex

Zampieri, V., Priddey, A., Schneider, S., Heidt, S., Kosmoliaptsis, V., Marquez, J.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 93.3 kDa 
• Atom Count: 6,042 
• Modeled Residue Count: 769 
• Deposited Residue Count: 838 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for U5YJM1 (Homo sapiens) Explore U5YJM1  Go to UniProtKB:  U5YJM1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide VLHDDLLEA	B [auth P]	9	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	C [auth B]	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SN230G6 Fab Heavy Chain	D [auth H]	238	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
SN230G6 Fab Light Chain	E [auth L]	216	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-04-15 
Deposition Author(s): Zampieri, V., Priddey, A., Schneider, S., Heidt, S., Kosmoliaptsis, V., Marquez, J.A.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	101094131
European Union (EU)	European Union	847543
National Institute for Health and Care Research (NIHR)	United Kingdom	PDF-2016-09-065
NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation	United Kingdom	NIHR203332
Terasaki Institute	United States	G106170

Revision History  

• Version 1.0: 2026-04-15
  Type: Initial release