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- PDB-4zqk: Structure of the complex of human programmed death-1 (PD-1) and i... -

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Basic information

Entry
Database: PDB / ID: 4zqk
TitleStructure of the complex of human programmed death-1 (PD-1) and its ligand PD-L1.
Components
  • Programmed cell death 1 ligand 1
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / complex / co-stimulation / receptor-ligand complex
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / 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 ...negative regulation of tolerance induction / regulatory T cell apoptotic process / 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 / humoral immune response / 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 / Potential therapeutics for SARS / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / external side of plasma membrane / apoptotic process / 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-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Programmed cell death protein 1 / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsZak, K.M. / Dubin, G. / Holak, T.A.
CitationJournal: Structure / Year: 2015
Title: Structure of the Complex of Human Programmed Death 1, PD-1, and Its Ligand PD-L1.
Authors: Zak, K.M. / Kitel, R. / Przetocka, S. / Golik, P. / Guzik, K. / Musielak, B. / Domling, A. / Dubin, G. / Holak, T.A.
History
DepositionMay 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,3863
Polymers26,3632
Non-polymers231
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-12 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.862, 70.862, 114.367
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 13134.085 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NZQ7
#2: Protein Programmed cell death protein 1 / / hPD-1


Mass: 13228.716 Da / Num. of mol.: 1 / Fragment: UNP Residues 33-150 / Mutation: C93S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15116
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M BIS-Tris pH 5.5, 1.84 M ammonium sulfate

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91843 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91843 Å / Relative weight: 1
ReflectionResolution: 2.45→61.37 Å / Num. obs: 12737 / % possible obs: 99.98 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 35.22
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.21 / % possible all: 99.92

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chain A -3BIK, chain B 3RRQ

3bik

3rrq


Resolution: 2.45→61.37 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2392 / WRfactor Rwork: 0.2009 / FOM work R set: 0.8095 / SU B: 16.316 / SU ML: 0.175 / SU R Cruickshank DPI: 0.2862 / SU Rfree: 0.2339 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 625 4.9 %RANDOM
Rwork0.2071 ---
obs0.2092 12082 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.62 Å2 / Biso mean: 57.568 Å2 / Biso min: 31.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.36 Å2-0 Å2
2---0.72 Å20 Å2
3---2.33 Å2
Refinement stepCycle: final / Resolution: 2.45→61.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 1 15 1666
Biso mean--50.06 59.49 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191684
X-RAY DIFFRACTIONr_bond_other_d0.0010.021535
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9512296
X-RAY DIFFRACTIONr_angle_other_deg0.8633514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.675218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54424.92567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36615254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.728155
X-RAY DIFFRACTIONr_chiral_restr0.10.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02373
X-RAY DIFFRACTIONr_mcbond_it3.2314.015881
X-RAY DIFFRACTIONr_mcbond_other3.2334.015880
X-RAY DIFFRACTIONr_mcangle_it4.8856.0111096
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 49 -
Rwork0.225 863 -
all-912 -
obs--99.89 %
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)
13.12471.15810.45261.9953-0.26081.5961-0.13160.00090.0248-0.1420.04720.0077-0.0151-0.05670.08440.2385-0.0829-0.01510.03940.01020.0139-9.754145.1745114.2792
22.353-0.1853-0.75613.211.67452.4375-0.01950.1309-0.11840.2490.0563-0.10490.35380.5131-0.03680.16110.0465-0.05630.2330.0150.043311.871250.2693104.1425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 132
2X-RAY DIFFRACTION2B33 - 146

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