5E5M

Crystal structure of mouse CTLA-4 in complex with nanobody

• PDB DOI: https://doi.org/10.2210/pdb5E5M/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Camelidae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-08 Released: 2016-10-12 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Samanta, D., Bonanno, J.B., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.247 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Crystal structure of mouse CTLA-4 in complex with nanobody

Fedorov, A.A., Fedorov, E.V., Samanta, D., Bonanno, J.B., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106.54 kDa 
• Atom Count: 6,966 
• Modelled Residue Count: 906 
• Deposited Residue Count: 984 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxic T-lymphocyte protein 4	A, C, E, G	117	Mus musculus	Mutation(s): 0  Gene Names: Ctla4, Cd152
UniProt
Find proteins for P09793 (Mus musculus) Explore P09793  Go to UniProtKB:  P09793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CTLA-4 nanobody	B, D, F, H	129	Camelidae	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.247 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.22	α = 90
b = 111.572	β = 90
c = 112.881	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Samanta, D., Bonanno, J.B., Almo, S.C.

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary