3SBW | pdb_00003sbw

Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1

PDB DOI: https://doi.org/10.2210/pdb3SBW/pdb

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

Deposited: 2011-06-06 Released: 2011-07-13
Deposition Author(s): Lazar-Molnar, E., Ramagopal, U.A., Cao, E., Nathenson, S.G., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.270 (Depositor), 0.262 (DCC)
R-Value Work:
0.218 (Depositor), 0.213 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1

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

To be published.

Macromolecule Content

Total Structure Weight: 51.89 kDa
Atom Count: 3,573
Modeled Residue Count: 432
Deposited Residue Count: 456
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	A, B	117	Mus musculus	Mutation(s): 2 Gene Names: Pdcd1, Pd1
UniProt
Find proteins for Q02242 (Mus musculus) Explore Q02242 Go to UniProtKB: Q02242
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02242
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	C	222	Homo sapiens	Mutation(s): 0 Gene Names: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ7 (Homo sapiens) Explore Q9NZQ7 Go to UniProtKB: Q9NZQ7
PHAROS: Q9NZQ7 GTEx: ENSG00000120217
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NZQ7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.270 (Depositor), 0.262 (DCC)
R-Value Work: 0.218 (Depositor), 0.213 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.778	α = 90
b = 62.843	β = 90
c = 160.863	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-07-13

Deposition Author(s):

Lazar-Molnar, E.

Ramagopal, U.A.

Nathenson, S.G.

Revision History (Full details and data files)

Version 1.0: 2011-07-13
Type: Initial release
Version 1.1: 2013-09-18
Changes: Derived calculations
Version 1.2: 2016-08-03
Changes: Derived calculations
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.