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- PDB-3sbw: Crystal structure of the complex between the extracellular domain... -

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Basic information

Entry
Database: PDB / ID: 3sbw
TitleCrystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1
Components
  • Programmed cell death 1 ligand 1
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / PD-1 / PD-L1 / B7-H1 / Programmed death-1 Ligand 1 / complex / costimulatory
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / PD-1 signaling / positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / B cell apoptotic process / negative regulation of immune response ...negative regulation of tolerance induction / regulatory T cell apoptotic process / PD-1 signaling / positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / B cell apoptotic process / negative regulation of immune response / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of T cell apoptotic process / STAT3 nuclear events downstream of ALK signaling / negative regulation of B cell apoptotic process / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / regulation of immune response / PD-1 signaling / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Programmed cell death protein 1 / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death protein 1 / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsLazar-Molnar, E. / Ramagopal, U.A. / Cao, E. / Nathenson, S.G. / Almo, S.C.
CitationJournal: To be published
Title: Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1
Authors: Lazar-Molnar, E. / Ramagopal, U.A. / Cao, E. / Nathenson, S.G. / Almo, S.C.
History
DepositionJun 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Derived calculations
Revision 1.2Aug 3, 2016Group: Derived calculations
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Programmed cell death protein 1
B: Programmed cell death protein 1
C: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)51,8943
Polymers51,8943
Non-polymers00
Water2,342130
1
B: Programmed cell death protein 1
C: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)38,6762
Polymers38,6762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-7 kcal/mol
Surface area16490 Å2
MethodPISA
2
A: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)13,2191
Polymers13,2191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.778, 62.843, 160.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe crystal corresponding to this particular PDB has the correct 1:1 PD-1:PD-L1 structure, as well as an additional artifactual PD-1 that is incorporated into the lattice.

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Components

#1: Protein Programmed cell death protein 1 / Protein PD-1


Mass: 13218.794 Da / Num. of mol.: 2 / Fragment: UNP residues 34-150 / Mutation: C83S, A132L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdcd1, Pd1 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q02242
#2: Protein Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 25456.898 Da / Num. of mol.: 1 / Fragment: UNP residues 19-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9NZQ7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Sodium citrate pH 5, 20% PEG 8000, Vapor diffusion, Sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.071 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. all: 26816 / Num. obs: 26816 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.093 / Χ2: 1.023 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.28-2.386.10.72926280.9831100
2.38-2.486.20.67726430.9941100
2.48-2.596.20.51126371.0261100
2.59-2.736.20.35926521.0061100
2.73-2.96.10.26126361.0331100
2.9-3.126.10.15726501.0131100
3.12-3.446.10.09926771.0571100
3.44-3.936.10.0726931.0561100
3.93-4.9560.04727400.981100
4.95-505.70.03728601.082199.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NPU

1npu


Resolution: 2.28→31.42 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2576 / WRfactor Rwork: 0.2081 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8195 / SU B: 15.222 / SU ML: 0.17 / SU R Cruickshank DPI: 0.2881 / SU Rfree: 0.2359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2704 1339 5 %RANDOM
Rwork0.2184 ---
obs0.221 26756 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 118.79 Å2 / Biso mean: 43.3543 Å2 / Biso min: 12.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---1.72 Å20 Å2
3---2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.28→31.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 0 130 3559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223521
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9454792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77424.821168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41815598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3291519
X-RAY DIFFRACTIONr_chiral_restr0.1010.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212665
X-RAY DIFFRACTIONr_mcbond_it0.691.52166
X-RAY DIFFRACTIONr_mcangle_it1.29523520
X-RAY DIFFRACTIONr_scbond_it1.8431355
X-RAY DIFFRACTIONr_scangle_it2.9694.51271
LS refinement shellResolution: 2.281→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 91 -
Rwork0.27 1630 -
all-1721 -
obs--88.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0615-1.1360.11722.0291-0.02731.3895-0.1619-0.13970.17840.15690.079-0.1439-0.13570.07970.08290.02680-0.01850.0624-0.020.0978-5.474-8.1184.044
23.05841.1432-0.02872.917-0.15522.8297-0.1110.31690.0544-0.33390.15320.2481-0.1429-0.2117-0.04220.0613-0.0089-0.02330.09780.00110.1411-14.9962.579-17.716
32.0882-0.0807-3.31470.0340.07576.1208-0.11960.12440.05950.0630.0344-0.06210.2824-0.55420.08520.30290.01480.02080.2798-0.03760.2441-8.986-11.546-49.921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 145
3X-RAY DIFFRACTION2B34 - 145
5X-RAY DIFFRACTION3C18 - 229

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