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- PDB-3bik: Crystal Structure of the PD-1/PD-L1 Complex -

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Basic information

Entry
Database: PDB / ID: 3bik
TitleCrystal Structure of the PD-1/PD-L1 Complex
Components
  • Programmed cell death 1 ligand 1
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / CO-STIMULATION / RECEPTOR-LIGAND COMPLEX / IMMUNOGLOBULIN-LIKE BETA-SANDWICH / T CELL / B CELL / PROGRAMMED DEATH / TRANSMEMBRANE / INHIBITORY RECEPTOR / Glycoprotein / Immunoglobulin domain / Apoptosis
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 / negative regulation of CD4-positive, alpha-beta T cell proliferation / B cell apoptotic process ...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 / negative regulation of CD4-positive, alpha-beta T cell proliferation / B cell apoptotic process / negative regulation of immune response / 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 / PD-1 signaling / regulation of immune response / 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 speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLin, D.Y. / Tanaka, Y. / Iwasaki, M. / Gittis, A.G. / Su, H.P. / Mikami, B. / Okazaki, T. / Honjo, T. / Minato, N. / Garboczi, D.N.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors.
Authors: Lin, D.Y. / Tanaka, Y. / Iwasaki, M. / Gittis, A.G. / Su, H.P. / Mikami, B. / Okazaki, T. / Honjo, T. / Minato, N. / Garboczi, D.N.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,6734
Polymers55,5803
Non-polymers921
Water1,36976
1
A: Programmed cell death 1 ligand 1
B: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)40,4892
Polymers40,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
MethodPISA
2
C: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1842
Polymers15,0921
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.46, 63.94, 159.92
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / PD-L1 / PDCD1 ligand 1 / B7 homolog 1 / B7-H1 / CD274 antigen


Mass: 25396.779 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 (DE3) / References: UniProt: Q9NZQ7
#2: Protein Programmed cell death protein 1 / / Protein PD-1 / mPD-1 / CD279 antigen


Mass: 15091.828 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdcd1, Pd1 / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 (DE3) / References: UniProt: Q02242
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG 3350, 200MM NH4H2PO4, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97943
DetectorType: SBC-3 / Detector: CCD / Date: Apr 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 17320 / % possible obs: 98.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.3
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.434

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NPU FOR CHAINS B,C, EARLY MODEL FOR CHAIN A

1npu


Resolution: 2.65→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.826 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 898 5.2 %RANDOM
Rwork0.211 ---
obs0.214 17225 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20 Å2
2---1.41 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3562 0 6 76 3644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223649
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9464960
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47324.494178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.42115622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5441524
X-RAY DIFFRACTIONr_chiral_restr0.0820.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21294
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22364
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3221.52230
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.04423622
X-RAY DIFFRACTIONr_scbond_it2.84231419
X-RAY DIFFRACTIONr_scangle_it4.8174.51338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 52 -
Rwork0.285 1050 -
obs--88.44 %

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