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- PDB-5ius: Crystal structure of human PD-L1 in complex with high affinity PD... -

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Basic information

Entry
Database: PDB / ID: 5ius
TitleCrystal structure of human PD-L1 in complex with high affinity PD-1 mutant
Components
  • Programmed cell death 1 ligand 1
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / immune checkpoint / tumor surveillance / cancer / receptor
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 / Resolution: 2.889 Å
AuthorsPascolutti, R. / Sun, X. / Kao, J. / Maute, R. / Ring, A.M. / Bowman, G.R. / Kruse, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1DP5OD021345 United States
CitationJournal: Structure / Year: 2016
Title: Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor Mutant.
Authors: Pascolutti, R. / Sun, X. / Kao, J. / Maute, R.L. / Ring, A.M. / Bowman, G.R. / Kruse, A.C.
History
DepositionMar 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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
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 protein 1
B: Programmed cell death protein 1
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9275
Polymers79,8924
Non-polymers351
Water59433
1
A: Programmed cell death protein 1
C: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9813
Polymers39,9462
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-18 kcal/mol
Surface area18440 Å2
MethodPISA
2
B: Programmed cell death protein 1
D: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)39,9462
Polymers39,9462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-8 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.851, 86.851, 111.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 14175.635 Da / Num. of mol.: 2
Mutation: V64H, N66V, Y68H, M70E, N74G, K78T, C93A, L122V, A125V, A132I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Plasmid: pMAL / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
#2: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 25770.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Plasmid: pET28 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 0.1 M bis-TRIS pH 6.4, 17% PEG MME 5000, 2 mM LiCl

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.889→50 Å / Num. obs: 18559 / % possible obs: 99.8 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rsym value: 0.165 / Net I/σ(I): 8.37
Reflection shellResolution: 2.889→3.08 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 0.55 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRQ, 3SBW

3rrq

3sbw


Resolution: 2.889→47.02 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 1847 9.95 %
Rwork0.2075 --
obs0.2127 18559 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.889→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5080 0 1 33 5114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035204
X-RAY DIFFRACTIONf_angle_d0.5687094
X-RAY DIFFRACTIONf_dihedral_angle_d9.9611850
X-RAY DIFFRACTIONf_chiral_restr0.021825
X-RAY DIFFRACTIONf_plane_restr0.002919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8886-2.96670.4641370.39781222X-RAY DIFFRACTION96
2.9667-3.0540.39061440.35371271X-RAY DIFFRACTION99
3.054-3.15250.39541420.34951303X-RAY DIFFRACTION100
3.1525-3.26520.37991390.3191260X-RAY DIFFRACTION100
3.2652-3.39590.35381440.291300X-RAY DIFFRACTION100
3.3959-3.55040.34661410.27541287X-RAY DIFFRACTION100
3.5504-3.73750.34021440.26421292X-RAY DIFFRACTION100
3.7375-3.97160.29731390.23451295X-RAY DIFFRACTION100
3.9716-4.2780.24321400.20771281X-RAY DIFFRACTION100
4.278-4.70820.20141440.15821300X-RAY DIFFRACTION100
4.7082-5.38860.19771430.15281295X-RAY DIFFRACTION100
5.3886-6.78580.21991440.18181299X-RAY DIFFRACTION100
6.7858-47.02580.22941460.16951307X-RAY DIFFRACTION99
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)
18.16432.76533.57225.26042.60437.02250.11220.05820.3130.05330.2363-0.11560.13090.2011-0.21940.64040.10120.10270.90550.00780.7286-40.9259-12.1161-30.8789
22.6218-1.99083.076710.0512-1.14685.95752.06041.30271.26941.124-0.2205-1.66081.26911.1973-1.28191.43930.3206-0.25870.95230.05641.0908-35.2178-24.1369-25.6139
35.9798-1.8063.69765.4701-0.33338.4284-0.24060.3112-0.0401-0.17680.01490.01220.9216-0.22980.38650.853-0.18690.09040.7103-0.07820.5769-42.3023-17.5494-31.554
42.4911-0.1043.82296.26822.57457.34430.1011-0.00270.6370.0738-0.30940.5247-0.5576-0.38980.13410.44290.09030.03080.64710.08010.5777-43.3398-9.9098-29.112
53.1733.0531-3.25035.2525-1.58946.51870.34471.15590.46051.1475-0.6371-0.0392-1.7174-0.35670.13481.53130.2165-0.18030.75530.01770.8038-32.5549-4.861923.2841
60.8178-1.4065-1.90094.39443.99824.65180.8785-0.9073-1.50125.1682-0.4871.62194.6305-4.3781-0.73482.4578-0.3682-0.0661.92090.19881.2209-43.9853-19.229124.8224
75.33711.76814.42636.30690.22386.1702-0.42360.01190.109-0.34630.3602-0.0335-0.1782-0.0085-0.08450.93120.2173-0.06170.890.11420.7344-30.7693-12.808417.1195
82.450.0277-0.91653.05474.64487.4968-1.25050.29560.3638-2.72422.36081.2246-1.60563.4854-0.18411.3488-0.2932-0.13051.68540.59671.3564-19.2354-3.004414.3227
91.63560.072.39283.93632.20777.75010.07550.02340.36951.4590.16380.3959-0.1914-1.2843-0.25561.02930.3117-0.10261.02120.090.7797-41.6536-10.854816.5864
108.83370.80652.05758.86031.4567.8638-1.6675-2.47410.77390.6620.1475-0.3552-2.53281.37841.23262.01470.0135-0.45331.2350.20211.4944-22.32913.988518.5977
113.57161.99211.20438.07983.50636.01120.00250.0741-0.13740.0190.2838-1.2888-0.42021.4948-0.16360.4922-0.0691-0.07151.05650.00740.799-26.1362-1.9076-15.3944
121.7009-3.6337-0.12888.89972.66915.3176-0.4626-0.24980.8332-0.52181.2948-1.3613-2.54641.2354-0.41.3379-0.3482-0.06770.4426-0.04650.9196-40.08522.09610.0812
137.536-3.1682-1.6157.19975.79684.86720.19870.8950.5465-1.041-0.15520.2143-1.6995-0.9435-0.37091.29260.2751-0.04290.73610.20360.7829-46.87325.7613-1.2646
144.0727-3.39991.58976.72064.3369.04920.056-0.35810.4107-0.6066-0.4235-0.062-2.4984-0.58940.2711.8958-0.0667-0.01960.77040.13010.9021-47.115828.91566.9341
158.37830.87813.01946.35120.01369.85611.21170.1762-0.7232-0.15730.0765-0.17130.23940.5423-1.45760.69540.26240.10551.0544-0.00180.7101-63.028914.2051-21.2012
167.89-3.22252.63387.16880.15687.74110.59430.1631-0.1427-0.57050.10650.83471.0816-0.1592-0.38450.5251-0.110.03540.85740.19460.7549-44.2243-8.186-2.9492
178.3769-2.05945.38179.2819-4.15874.6460.116-0.3734-1.3127-0.37210.97111.27561.7636-0.3241-0.87271.19590.1052-0.1950.9954-0.00040.8754-44.3211-19.04462.9114
183.4757-2.8803-1.22885.7733-1.63853.53290.0252-0.466-3.0126-0.44060.47062.86211.6431-3.2633-0.67331.3415-0.2522-0.24281.57640.26611.9321-52.9377-21.57116.0713
193.75161.23231.77248.5754-4.27223.6793-0.94880.6853-0.8484-0.00751.66692.5160.4216-2.6105-0.59731.2687-0.1234-0.08741.46520.2911.5703-58.2691-16.66281.6123
209.5334-6.1989-0.0345.846-0.19367.05130.19782.0775-2.063-1.69650.20952.1512.570.3025-0.54161.46620.0346-0.27871.2421-0.18590.9651-45.8556-20.4264-4.4777
213.4889-0.06392.34783.84941.98547.35730.29110.78960.261-0.9075-0.07270.54320.0116-0.2453-0.07710.74660.08940.05690.66380.12830.9444-48.8449-11.57043.0587
223.568-6.08981.42554.3077-2.82134.81740.88841.888-0.0475-0.3705-0.98750.3481.2540.497-0.32460.87950.058-0.13651.02360.29640.952-49.7712-2.108-2.4673
233.7616-1.59110.50115.9901-4.33735.8303-0.2645-0.85580.28620.56780.57180.4105-1.2178-0.8348-0.30140.73770.25010.02390.7303-0.12920.5386-67.928419.057-17.8982
245.7702-2.26232.38688.2138-3.67667.6091-0.2837-0.3841-0.54850.5357-0.03790.5162-0.6147-0.32310.04710.65530.22970.00571.1688-0.06620.7504-66.532615.1822-13.7241
254.11472.50925.23711.15193.46217.5898-0.61330.88730.6518-0.43850.60660.9253-2.3025-0.1113-0.08211.3193-0.0238-0.0531.04120.13810.935-45.78521.47357.958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 127 )
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 147 )
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 55 )
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 62 )
7X-RAY DIFFRACTION7chain 'B' and (resid 63 through 110 )
8X-RAY DIFFRACTION8chain 'B' and (resid 111 through 118 )
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 139 )
10X-RAY DIFFRACTION10chain 'B' and (resid 140 through 147 )
11X-RAY DIFFRACTION11chain 'C' and (resid 18 through 120 )
12X-RAY DIFFRACTION12chain 'C' and (resid 121 through 159 )
13X-RAY DIFFRACTION13chain 'C' and (resid 160 through 190 )
14X-RAY DIFFRACTION14chain 'C' and (resid 191 through 213 )
15X-RAY DIFFRACTION15chain 'C' and (resid 214 through 231 )
16X-RAY DIFFRACTION16chain 'D' and (resid 18 through 35 )
17X-RAY DIFFRACTION17chain 'D' and (resid 36 through 61 )
18X-RAY DIFFRACTION18chain 'D' and (resid 62 through 73 )
19X-RAY DIFFRACTION19chain 'D' and (resid 74 through 88 )
20X-RAY DIFFRACTION20chain 'D' and (resid 89 through 101 )
21X-RAY DIFFRACTION21chain 'D' and (resid 102 through 120 )
22X-RAY DIFFRACTION22chain 'D' and (resid 121 through 137 )
23X-RAY DIFFRACTION23chain 'D' and (resid 138 through 177 )
24X-RAY DIFFRACTION24chain 'D' and (resid 178 through 213 )
25X-RAY DIFFRACTION25chain 'D' and (resid 214 through 229 )

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