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- PDB-5jdr: Structure of PD-L1 -

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Basic information

Entry
Database: PDB / ID: 5jdr
TitleStructure of PD-L1
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / immunosuppression
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 / T cell costimulation / negative regulation of T cell proliferation / 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 ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhou, A. / Wei, H.
CitationJournal: Cell Discov / Year: 2017
Title: Structural basis of a novel PD-L1 nanobody for immune checkpoint blockade.
Authors: Zhang, F. / Wei, H. / Wang, X. / Bai, Y. / Wang, P. / Wu, J. / Jiang, X. / Wang, Y. / Cai, H. / Xu, T. / Zhou, A.
History
DepositionApr 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
Revision 1.2Nov 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


Theoretical massNumber of molelcules
Total (without water)54,3402
Polymers54,3402
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.240, 91.510, 141.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A19 - 131
2114B19 - 131
1124A132 - 168
2124B132 - 168
1224A176 - 228
2224B176 - 228
1326A169 - 175
2326B169 - 175

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.919523, -0.175797, -0.351528), (0.270907, 0.364509, -0.890923), (0.284757, -0.914456, -0.287549)47.28728, 19.90837, 16.50082

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Components

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


Mass: 27169.791 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 18-239
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 295 K / Method: liquid diffusion / Details: 0.2 M Ammonium Acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→70.92 Å / Num. obs: 13282 / % possible obs: 99.9 % / Redundancy: 6.7 % / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4z18

4z18


Resolution: 2.7→70.92 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.894 / SU B: 42.071 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27558 683 5.2 %RANDOM
Rwork0.22745 ---
obs0.22998 12575 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.349 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2---3.2 Å2-0 Å2
3---1.99 Å2
Refinement stepCycle: 1 / Resolution: 2.7→70.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 0 7 3372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193440
X-RAY DIFFRACTIONr_bond_other_d0.0010.023291
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9534668
X-RAY DIFFRACTIONr_angle_other_deg0.83137580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14824.817164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32915622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5221520
X-RAY DIFFRACTIONr_chiral_restr0.0710.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02766
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8493.8851675
X-RAY DIFFRACTIONr_mcbond_other0.8493.8851674
X-RAY DIFFRACTIONr_mcangle_it1.5585.8252092
X-RAY DIFFRACTIONr_mcangle_other1.5585.8252093
X-RAY DIFFRACTIONr_scbond_it0.5943.951765
X-RAY DIFFRACTIONr_scbond_other0.5943.951766
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1245.8782577
X-RAY DIFFRACTIONr_long_range_B_refined2.80828.9373364
X-RAY DIFFRACTIONr_long_range_B_other2.80828.9373364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1747medium positional0.440.5
22A1406medium positional0.510.5
22A102loose positional0.895
11B1747medium thermal4.392
22B1406medium thermal9.582
22B102loose thermal15.4210
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 42 -
Rwork0.346 934 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 28.219 Å / Origin y: 5.519 Å / Origin z: 16.648 Å
111213212223313233
T0.3654 Å20.0373 Å20.0347 Å2-0.0562 Å20.0591 Å2--0.076 Å2
L1.371 °20.1801 °2-0.3327 °2-1.405 °2-0.3944 °2--0.6992 °2
S0.1539 Å °0.2722 Å °0.2884 Å °-0.2552 Å °0.0089 Å °0.132 Å °-0.1364 Å °-0.0871 Å °-0.1629 Å °

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