9SQM | pdb_00009sqm

Structure of a disulfide-bridged complex between HLA-A*02:01-K127N/Y84C and ERp57/tapasin-K16C - State 4

• PDB DOI: https://doi.org/10.2210/pdb9SQM/pdb
• EM Map EMD-55111: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2025-09-23 Released: 2026-08-12 
• Deposition Author(s): Mitlehner, A., Loll, B., Hilal, T.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Dynamic states of an MHC class I molecule upon peptide release

Mitlehner, A., Pasos-Trejo, A.S., Becker, M., Hilal, T., Loll, B., Kuropka, B., Clementi, C., Freund, C.

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: 144.99 kDa 
• Atom Count: 9,383 
• Modeled Residue Count: 1,180 
• Deposited Residue Count: 1,286 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	A [auth B]	99	Homo sapiens	Mutation(s): 1  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
GTEx:  ENSG00000166710

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tapasin	B [auth D]	398	Homo sapiens	Mutation(s): 3  Gene Names: TAPBP, NGS17, TAPA
UniProt & NIH Common Fund Data Resources
Find proteins for O15533 (Homo sapiens) Explore O15533  Go to UniProtKB:  O15533
GTEx:  ENSG00000231925
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: O15533-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein disulfide-isomerase A3	C [auth E]	481	Homo sapiens	Mutation(s): 1  Gene Names: PDIA3, ERP57, ERP60, GRP58 EC: 5.3.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for P30101 (Homo sapiens) Explore P30101  Go to UniProtKB:  P30101
GTEx:  ENSG00000167004

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	D [auth A]	301	Homo sapiens	Mutation(s): 1  Gene Names: HLA-A
UniProt
Find proteins for Q9TQB6 (Homo sapiens) Explore Q9TQB6  Go to UniProtKB:  Q9TQB6

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
LYS-ILE-LEU-GLY-PHE-VAL-NFA, pKV9	E [auth C]	7	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	6		N-Glycosylation

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NFA	E [auth C]	L-PEPTIDE LINKING	C9 H12 N2 O		PHE

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4.6.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-12 
Deposition Author(s): Mitlehner, A., Loll, B., Hilal, T.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FR 1325/20-1

Revision History  

• Version 1.0: 2026-08-12
  Type: Initial release