7AMP

Crystal structure of the complex of HuJovi-1 Fab with the human A6 T-cell receptor TRBC1

• PDB DOI: https://doi.org/10.2210/pdb7AMP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2020-10-09 Released: 2022-04-20 
• Deposition Author(s): Ferrari, M., Bulek, A., Bughda, R., Jha, R., Welin, M., Logan, D.T., Sewell, A., Onuoha, S., Pule, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.289 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 

Literature

Structure-Guided Engineering of Immunotherapies Targeting TRBC1 and TRBC2 in T Cell Malignancies

Ferrari, M., Baldan, V., Wawrzyniecka, P., Bulek, A., Kinna, A., Ma, B., Bugda, R., Akbar, Z., Srivastava, S., Ghongane, P., Gannon, I., Robson, M., Sillibourne, J., Jha, R., Lim, W., Hopkins, J., Welin, M., Surade, S., Dyson, M., McCafferty, J., Cordoba, S., Thomas, S., Logan, D., Sewell, A., Maciocia, P., Onuoha, S., Pule, M.

(2022) Res Sq 

• DOI: https://doi.org/10.21203/rs.3.rs-1475171/v1

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 99.07 kDa 
• Atom Count: 6,858 
• Modelled Residue Count: 880 
• Deposited Residue Count: 896 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha chain of A6 T-cell receptor	A	206	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta chain 1 of A6 T-cell receptor TRBC1	B	246	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HuJovi-1 Fab heavy chain	C [auth H]	225	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HuJovi-1 Fab light chain	D [auth L]	219	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	F [auth H], H [auth L], I [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.289 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.39	α = 90
b = 91.05	β = 93.82
c = 125.26	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-04-20 
Deposition Author(s): Ferrari, M., Bulek, A., Bughda, R., Jha, R., Welin, M., Logan, D.T., Sewell, A., Onuoha, S., Pule, M.

Revision History  

• Version 1.0: 2022-04-20
  Type: Initial release
  
• Version 1.1: 2022-04-27
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description