9D72 | pdb_00009d72

CryoEM structure of anti-MHC-I Fab M1/42 complex with H2-Dd

• PDB DOI: https://doi.org/10.2210/pdb9D72/pdb
• EM Map EMD-46600: EMDB EMDataResource

• Classification: ANTITUMOR PROTEIN/Immune System
• Organism(s): Mus musculus, Rattus norvegicus, synthetic construct
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): No 


• Deposited: 2024-08-16 Released: 2026-02-04 
• Deposition Author(s): Jiang, J., Natarajan, K., Margulies, D.H., Lei, H., Huang, R.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

CryoEM structure of anti-MHC-I Fab M1/42 complex with H2-Dd

Jiang, J., Natarajan, K., Margulies, D.H.

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: 91.73 kDa 
• Atom Count: 6,040 
• Modeled Residue Count: 790 
• Deposited Residue Count: 816 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	A [auth B]	98	Mus musculus	Mutation(s): 0  Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
IMPC:  MGI:88127

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab M1/42 Light Chain	B [auth L]	213	Rattus norvegicus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface protein gp120	C [auth P]	10	synthetic construct	Mutation(s): 0
UniProt
Find proteins for P04582 (Human immunodeficiency virus type 1 group M subtype B (isolate BH8)) Explore P04582  Go to UniProtKB:  P04582

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, D-D alpha chain	D [auth A]	273	Mus musculus	Mutation(s): 0  Gene Names: H2-D1
UniProt
Find proteins for P01900 (Mus musculus) Explore P01900  Go to UniProtKB:  P01900

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab M1/42 Heavy Chain	E [auth H]	222	Rattus norvegicus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2-4158
RECONSTRUCTION	cryoSPARC	4.4.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Jiang, J., Natarajan, K., Margulies, D.H., Lei, H., Huang, R.

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

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release