8TQ4 | pdb_00008tq4

Crystal structure of Fab M142 in complex with MHC-I (H2-Dd)

• PDB DOI: https://doi.org/10.2210/pdb8TQ4/pdb

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


• Deposited: 2023-08-06 Released: 2025-02-05 
• Deposition Author(s): Jiang, J., Natarajan, K., Boyd, L.F., Margulies, D.H.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free: 
  0.270 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Fab M142 in complex with MHC-I (H2-Dd)

Jiang, J., Natarajan, K., Boyd, L.F., 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 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 183.47 kDa 
• Atom Count: 12,671 
• Modeled Residue Count: 1,632 
• Deposited Residue Count: 1,632 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H2 class I histocompatibility antigen D-d alpha chain (H2-Dd)	A, E	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, F	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab M142 Heavy Chain	C, H	222	Rattus norvegicus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab M142 Light Chain	D, I [auth L]	213	Rattus norvegicus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
HV1: HIV-1 P18-I10	G, J [auth P]	10	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free:  0.270 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.552	α = 90
b = 121.552	β = 90
c = 327.199	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-05 
Deposition Author(s): Jiang, J., Natarajan, K., Boyd, L.F., Margulies, D.H.

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

Revision History  

• Version 1.0: 2025-02-05
  Type: Initial release