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- PDB-7oun: Structure of human PD-L1 in complex with macrocyclic inhibitor -

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Basic information

Entry
Database: PDB / ID: 7oun
TitleStructure of human PD-L1 in complex with macrocyclic inhibitor
Components
  • Programmed cell death 1 ligand 1
  • macrocyclic peptide
KeywordsCELL CYCLE / Programmed Death Ligand 1 / immune checkpoint inhibitor / cancer / IMMUNE SYSTEM
Function / homology
Function and homology information


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 / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...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 / STAT3 nuclear events downstream of ALK signaling / 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 / 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
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZyla, E. / Dubin, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2017/25/B/NZ1/00827 Poland
CitationJournal: Molecules / Year: 2021
Title: Structural Characterization of a Macrocyclic Peptide Modulator of the PD-1/PD-L1 Immune Checkpoint Axis.
Authors: Zyla, E. / Musielak, B. / Holak, T.A. / Dubin, G.
History
DepositionJun 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: macrocyclic peptide


Theoretical massNumber of molelcules
Total (without water)16,4952
Polymers16,4952
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-5 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.470, 86.470, 86.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23

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Components

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


Mass: 14792.861 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/peptide macrocyclic peptide


Mass: 1702.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.57 Å3/Da / Density % sol: 65.53 % / Mosaicity: 0.27 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.24 / Details: 0.1M sodium citrate 1.95M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.663→86.47 Å / Num. all: 17309 / Num. obs: 17309 / % possible obs: 100 % / Redundancy: 27.7 % / Rpim(I) all: 0.017 / Rrim(I) all: 0.092 / Rsym value: 0.091 / Net I/av σ(I): 5.5 / Net I/σ(I): 18.1 / Num. measured all: 480286
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-228.21.5760.57060725080.3011.6051.5762.6100
2-2.1226.81.0510.76331023630.2061.0711.0513.7100
2.12-2.2729.60.6451.26565622150.120.6560.6456.1100
2.27-2.4528.60.39625902320620.0750.4030.3969100
2.45-2.6925.90.2313.34953019130.0460.2360.23112.8100
2.69-327.30.1295.74758017460.0250.1310.12921.6100
3-3.4728.60.097.74394515380.0170.0910.0934.3100
3.47-4.2528.30.0729.33709513100.0140.0730.07248.5100
4.25-6.0125.70.05611.92682210420.0110.0570.05652.2100
6.01-61.14327.30.0415.4167186120.0080.0410.0453.499.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O45

5o45


Resolution: 1.9→61.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.955 / SU B: 11.141 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 873 5 %RANDOM
Rwork0.2324 ---
obs0.2331 16436 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.61 Å2 / Biso mean: 62.919 Å2 / Biso min: 30.93 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.9→61.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 0 37 1074
Biso mean---51.06 -
Num. residues----131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131089
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171010
X-RAY DIFFRACTIONr_angle_refined_deg2.2621.641481
X-RAY DIFFRACTIONr_angle_other_deg1.4661.5712336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9465139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.08222.556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41215183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.596156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021265
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02237
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 66 -
Rwork0.343 1215 -
all-1281 -
obs--100 %
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)
10.94271.33862.27243.37243.37145.9415-0.1904-0.15120.2892-0.4822-0.43160.5897-0.27090.07680.6220.590.127-0.29440.5913-0.21160.77335.6228.227-25.957
227.91856.2899-11.231713.3373-2.184112.75010.078-0.2791-2.4236-0.7972-1.0265-1.1879-2.4466-0.74810.94851.25880.4523-0.48210.2064-0.07230.78111.83438.042-37.855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 134
2X-RAY DIFFRACTION2B0 - 13

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