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- PDB-7xae: Crystal strucutre of PD-L1 and 3ONJA protein -

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Basic information

Entry
Database: PDB / ID: 7xae
TitleCrystal strucutre of PD-L1 and 3ONJA protein
Components
  • 2IC6
  • Programmed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1
Function / homology
Function and homology information


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 / negative regulation of T cell mediated immune response to tumor cell / 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 / negative regulation of type II interferon production ...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 / negative regulation of T cell mediated immune response to tumor cell / 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 / negative regulation of type II interferon production / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / negative regulation of T cell proliferation / T cell costimulation / response to cytokine / positive regulation of T cell proliferation / recycling endosome membrane / actin cytoskeleton / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / immune response / receptor ligand activity / 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)
chemical production metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 Å
AuthorsLiu, K.F. / Xu, Z.P. / Han, P. / Gao, G.F. / Chai, Y. / Tan, S.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92169208 China
CitationJournal: To Be Published
Title: Crystal strucutre of PD-L1 and 2IC6 protein
Authors: Liu, K.F. / Xu, Z.P. / Han, P. / Gao, G.F. / Chai, Y. / Tan, S.G.
History
DepositionMar 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 1 ligand 1
C: 2IC6
D: 2IC6


Theoretical massNumber of molelcules
Total (without water)73,9834
Polymers73,9834
Non-polymers00
Water00
1
A: Programmed cell death 1 ligand 1
D: 2IC6


Theoretical massNumber of molelcules
Total (without water)36,9912
Polymers36,9912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-9 kcal/mol
Surface area17350 Å2
MethodPISA
2
B: Programmed cell death 1 ligand 1
C: 2IC6


Theoretical massNumber of molelcules
Total (without water)36,9912
Polymers36,9912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-9 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.079, 103.079, 173.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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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: 27482.363 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#2: Protein 2IC6


Mass: 9509.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) chemical production metagenome (others)
Production host: Escherichia coli (E. coli)
Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 16% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3.43→50 Å / Num. obs: 12131 / % possible obs: 82.5 % / Redundancy: 13.7 % / Biso Wilson estimate: 23.47 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 18.797
Reflection shellResolution: 3.43→3.55 Å / Rmerge(I) obs: 2.045 / Num. unique obs: 12131

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13-2998refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRQ

3rrq


Resolution: 3.44→44.56 Å / SU ML: 0.4187 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.2662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2617 486 4.88 %
Rwork0.2481 9467 -
obs0.2488 9953 82.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.47 Å2
Refinement stepCycle: LAST / Resolution: 3.44→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 0 0 4616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254688
X-RAY DIFFRACTIONf_angle_d0.64276349
X-RAY DIFFRACTIONf_chiral_restr0.0448752
X-RAY DIFFRACTIONf_plane_restr0.0051809
X-RAY DIFFRACTIONf_dihedral_angle_d16.26531777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.44-3.930.26541020.28191799X-RAY DIFFRACTION47.55
3.93-4.950.29441910.2443817X-RAY DIFFRACTION100
4.96-44.560.22561930.23553851X-RAY DIFFRACTION99.73
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)
10.007531196245380.01136019259940.00354918405034-0.00131272222556-0.05972128058280.00186454929605-0.0564231779344-0.05219238771510.07489467818590.0698933931440.14198604714-0.07703649686190.02923768016570.1279789000110.1169215971070.08484406754180.01905694998980.09398331275850.2942038093150.6866837349180.039075030882515.298147298-23.1772834782-13.7558800958
20.00860784568144-0.002994057716-0.003032274888980.00351356705849-0.0425247425698-0.00160936738051-0.0664266091210.0307610618622-0.026916720949-0.0825875133520.104438596129-0.0818072555797-0.01447768984980.1053777947910.08392242643860.09827840270880.0268299644283-0.1013197033580.2877064743830.6740994929290.09518620709915.2606385237-28.3599395559-29.9351937944
30.0362982422771-0.03917156276160.01299302380350.0402084437420.0002317471356740.0510771006741-0.07876680728920.008913972512030.01464962500270.0359184382705-0.05189481885530.003874645556940.0170289402983-0.0149572108322-0.133044724956-0.03292503200950.00679659745781-0.06216522827380.1603753270760.1477468889140.208694215285-33.2012941838-31.1414667174-33.3865511424
40.111558437785-0.009779886210180.03224004749030.06072742686380.06653936970260.148597840797-0.0747658490230.005180266243740.0156683890538-0.0261571163517-0.05770448213310.0392792523827-0.0291645244774-0.0678057770144-0.08372568548770.02270082786580.02319003971320.0279351939680.1826028053190.1030119484220.268374285758-33.2181392621-20.4413140015-10.3189115222
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA18 - 2291 - 212
22chain BBB18 - 2291 - 212
33chain CCC3 - 791 - 77
44chain DDD3 - 791 - 77

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