9RUF | pdb_00009ruf

Cryo-EM structure of the LB_DQB0301_A Fab - HLA-DQB1*03:01/DQA1*05:02 human alloantibody-HLA complex

• PDB DOI: https://doi.org/10.2210/pdb9RUF/pdb
• EM Map EMD-54270: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-07-04 Released: 2026-07-15 
• Deposition Author(s): Zampieri, V., Priddey, A., Kosmoliaptsis, V., Marquez, J.A.
• Funding Organization(s): European Union (EU), National Institute for Health and Care Research, Terasaki Institute, NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the LB_DQB0301_A Fab - HLA-DQB1*03:01/DQA1*05:02 human alloantibody-HLA complex

Zampieri, V., Priddey, A., Kosmoliaptsis, V., Marquez, J.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 102.16 kDa 
• Atom Count: 6,045 
• Modeled Residue Count: 771 
• Deposited Residue Count: 921 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DQ alpha 1 chain	A	231	Homo sapiens	Mutation(s): 1  Gene Names: HLA-DQA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01909 (Homo sapiens) Explore P01909  Go to UniProtKB:  P01909
PHAROS:  P01909 GTEx:  ENSG00000196735

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DQ beta 1 chain	B	229	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DQB1, HLA-DQB
UniProt & NIH Common Fund Data Resources
Find proteins for P01920 (Homo sapiens) Explore P01920  Go to UniProtKB:  P01920
PHAROS:  P01920

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LB_DQB0301_A Heavy chain	C [auth H]	235	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
LB_DQB0301_A Light chain	D [auth L]	216	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide, unknown sequence.	E [auth P]	10	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-15 
Deposition Author(s): Zampieri, V., Priddey, A., 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	United Kingdom	PDF-2016-09-065
Terasaki Institute	United States	G106170
NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation	United Kingdom	NIHR203332

Revision History  

• Version 1.0: 2026-07-15
  Type: Initial release