8TQ6 | pdb_00008tq6

Crystal structure of Fab.B1.23.2 in complex with MHC-I (HLA-B*44:05)

• PDB DOI: https://doi.org/10.2210/pdb8TQ6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct, Mus musculus
• 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Fab.B1.23.2 in complex with MHC-I (HLA-B*44:05)

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: 182.3 kDa 
• Atom Count: 12,516 
• Modeled Residue Count: 1,607 
• Deposited Residue Count: 1,616 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen B alpha chain (HLA-B*44:05)	A, C	274	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
UniProt
Find proteins for Q860B7 (Homo sapiens) Explore Q860B7  Go to UniProtKB:  Q860B7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II antigen peptide	E, J [auth P]	9	synthetic construct	Mutation(s): 0
UniProt
Find proteins for Q9TQB0 (Homo sapiens) Explore Q9TQB0  Go to UniProtKB:  Q9TQB0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab B1.23.2 Heavy Chain	F, H	213	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab B1.23.2 Light Chain	G, I [auth L]	212	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.5	α = 90
b = 92.84	β = 90
c = 229.81	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.

---

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