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- PDB-3bis: Crystal Structure of the PD-L1 -

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Basic information

Entry
Database: PDB / ID: 3bis
TitleCrystal Structure of the PD-L1
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / CO-STIMULATION / IMMUNOGLOBULIN-LIKE BETA-SANDWICH / T CELL / B CELL / PROGRAMMED DEATH / TRANSMEMBRANE / INHIBITORY RECEPTOR / Glycoprotein / Immunoglobulin domain
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 / positive regulation of interleukin-10 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 / 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 / receptor ligand activity / 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 ...: / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / MAD / Resolution: 2.64 Å
AuthorsLin, D.Y. / Tanaka, Y. / Iwasaki, M. / Gittis, A.G. / Su, H.P. / Mikami, B. / Okazaki, T. / Honjo, T. / Minato, N. / Garboczi, D.N.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors.
Authors: Lin, D.Y. / Tanaka, Y. / Iwasaki, M. / Gittis, A.G. / Su, H.P. / Mikami, B. / Okazaki, T. / Honjo, T. / Minato, N. / Garboczi, D.N.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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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 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)50,7942
Polymers50,7942
Non-polymers00
Water81145
1
A: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)25,3971
Polymers25,3971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)25,3971
Polymers25,3971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.08, 92.70, 141.72
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-266-

HOH

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Components

#1: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / PD-L1 / PDCD1 ligand 1 / B7 homolog 1 / B7-H1 / CD274 antigen


Mass: 25396.779 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 (DE3) / References: UniProt: Q9NZQ7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.1 M NaCacodylate, 0.2 M ammonium formate or ammonium fluoride, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0722, 0.97948, 1.54
DetectorType: SBC-3 / Detector: CCD / Date: Dec 8, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07221
20.979481
31.541
ReflectionResolution: 2.64→50 Å / Num. obs: 14169 / % possible obs: 95.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.8
Reflection shellResolution: 2.64→2.73 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.272

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.64→19.84 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 30.871 / SU ML: 0.327 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.292 700 5 %RANDOM
Rwork0.217 ---
obs0.22 13406 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.64→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 0 45 3457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223481
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9594729
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.13224.819166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.07515626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9591520
X-RAY DIFFRACTIONr_chiral_restr0.110.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022600
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.21178
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22228
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8111.52187
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11723466
X-RAY DIFFRACTIONr_scbond_it1.69931471
X-RAY DIFFRACTIONr_scangle_it2.6124.51263
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.64→2.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5 34 -
Rwork0.384 700 -
obs--69.97 %
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)
13.3033-1.30331.37423.5499-0.86572.14780.1415-0.0182-0.1233-0.1094-0.11850.1844-0.0595-0.0421-0.05750.1126-0.01690.01070.1359-0.00150.1657-12.0616.973-33.413
23.9277-0.00531.75114.9149-4.200810.24870.14490.3369-0.4818-0.4355-0.36890.21590.2301-0.4711-0.54050.1640.08340.02160.15480.15750.1514-4.279-16.768-1.858
32.32811.75450.462313.0841-1.67822.2620.0968-0.25170.1548-0.25910.07250.62311.1918-0.0425-0.05820.18190.0350.11180.1204-0.02350.188-21.23523.954-24.4
43.4650.5513-1.93026.3896-2.59216.09890.6055-0.0354-0.5701-0.1398-0.1930.8604-0.1609-0.38480.41520.176-0.15640.04340.18220.03370.2483-27.565-15.083-13.828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA133 - 230116 - 213
2X-RAY DIFFRACTION2AA19 - 1292 - 112
3X-RAY DIFFRACTION3BB133 - 229116 - 212
4X-RAY DIFFRACTION4BB18 - 1291 - 112

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