3RNK | pdb_00003rnk

Crystal structure of the complex between mouse PD-1 mutant and PD-L2 IgV domain

• PDB DOI: https://doi.org/10.2210/pdb3RNK/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-04-22 Released: 2011-06-01 
• Deposition Author(s): Lazar-Molnar, E., Ramagopal, U.A., Cao, E., Nathenson, S.G., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of the complex between mouse PD-1 mutant and PD-L2 IgV domain

Lazar-Molnar, E., Ramagopal, U.A., Cao, E., Nathenson, S.G., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 24.91 kDa 
• Atom Count: 1,818 
• Modeled Residue Count: 216 
• Deposited Residue Count: 221 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	A	117	Mus musculus	Mutation(s): 2  Gene Names: Pd1, Pdcd1
UniProt
Find proteins for Q02242 (Mus musculus) Explore Q02242  Go to UniProtKB:  Q02242

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 2	B	104	Mus musculus	Mutation(s): 0  Gene Names: B7dc, Btdc, Cd273, Murine, Pdcd1lg2, Pdl2
UniProt
Find proteins for Q9WUL5 (Mus musculus) Explore Q9WUL5  Go to UniProtKB:  Q9WUL5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.057	α = 90
b = 60.246	β = 90
c = 80.087	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Lazar-Molnar, E., Ramagopal, U.A., Cao, E., Nathenson, S.G., Almo, S.C.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-12-25
  Changes: Other
• Version 1.3: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary