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- PDB-8aok: Complex of PD-L1 with VHH6 -

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Basic information

Entry
Database: PDB / ID: 8aok
TitleComplex of PD-L1 with VHH6
Components
  • Programmed cell death 1 ligand 1
  • VHH 6
KeywordsIMMUNE SYSTEM / Single domain antibody / VHH / programmed cell death 1 ligand 1
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 / adaptive immune response / cellular response to lipopolysaccharide / 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
ACETIC ACID / FORMIC ACID / OXAMIC ACID / DI(HYDROXYETHYL)ETHER / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKang-Pettinger, T. / Hall, G.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Identification, binding, and structural characterization of single domain anti-PD-L1 antibodies inhibitory of immune regulatory proteins PD-1 and CD80.
Authors: Kang-Pettinger, T. / Walker, K. / Brown, R. / Cowan, R. / Wright, H. / Baravalle, R. / Waters, L.C. / Muskett, F.W. / Bowler, M.W. / Sawmynaden, K. / Coombs, P.J. / Carr, M.D. / Hall, G.
History
DepositionAug 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: Programmed cell death 1 ligand 1
B: VHH 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,12611
Polymers27,2952
Non-polymers8329
Water5,603311
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint17 kcal/mol
Surface area11790 Å2
Unit cell
Length a, b, c (Å)99.575, 99.575, 171.515
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-328-

HOH

21A-431-

HOH

31A-445-

HOH

41B-349-

HOH

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#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: 13395.359 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 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): * / References: UniProt: Q9NZQ7
#2: Antibody VHH 6


Mass: 13899.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pET-21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): *

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Non-polymers , 7 types, 320 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES:MOPS, pH 7.5, 0.02 M Ammonium acetate, 0.02 M Potassium sodium tartrate tetrahydrate, 0.02 M Sodium citrate tribasic dihydrate, 0.02 M Sodium formate, 0.02M Sodium oxamate, 10% ...Details: 0.1 M HEPES:MOPS, pH 7.5, 0.02 M Ammonium acetate, 0.02 M Potassium sodium tartrate tetrahydrate, 0.02 M Sodium citrate tribasic dihydrate, 0.02 M Sodium formate, 0.02M Sodium oxamate, 10% (w/v) PEG 20000 and 20% (v/v) PEG 500-MME.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.6→43.1 Å / Num. obs: 56912 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.038 / Rrim(I) all: 0.067 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.76-43.150.0224020.9990.0150.027
1.6-1.635.61.11927910.5360.7771.369

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BIS

3bis


Resolution: 1.6→43.094 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1846 2852 5.014 %
Rwork0.1623 54032 -
all0.163 --
obs-56884 99.83 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.435 Å20 Å20 Å2
2--0.435 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 55 311 2269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132033
X-RAY DIFFRACTIONr_bond_other_d0.0350.0151899
X-RAY DIFFRACTIONr_angle_refined_deg2.1381.6462741
X-RAY DIFFRACTIONr_angle_other_deg2.3911.5834368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0175257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.65421.909110
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg4.944101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3761514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022410
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02494
X-RAY DIFFRACTIONr_nbd_refined0.1930.2343
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2310.21785
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2949
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21019
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.223
X-RAY DIFFRACTIONr_nbd_other0.3210.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3180.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0720.21
X-RAY DIFFRACTIONr_mcbond_it2.4822.301987
X-RAY DIFFRACTIONr_mcbond_other2.4812.306988
X-RAY DIFFRACTIONr_mcangle_it3.3423.4291233
X-RAY DIFFRACTIONr_mcangle_other3.3473.4321234
X-RAY DIFFRACTIONr_scbond_it3.9572.7361046
X-RAY DIFFRACTIONr_scbond_other3.9582.7311045
X-RAY DIFFRACTIONr_scangle_it5.5863.8991500
X-RAY DIFFRACTIONr_scangle_other5.5853.9031501
X-RAY DIFFRACTIONr_lrange_it7.43128.7412330
X-RAY DIFFRACTIONr_lrange_other7.43328.7522331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.3032400.2943910X-RAY DIFFRACTION99.9518
1.642-1.6870.291980.2753879X-RAY DIFFRACTION99.9755
1.687-1.7350.2442040.2463729X-RAY DIFFRACTION100
1.735-1.7890.2452150.2273614X-RAY DIFFRACTION100
1.789-1.8470.2571680.2083550X-RAY DIFFRACTION99.9731
1.847-1.9120.2382030.1913396X-RAY DIFFRACTION99.9722
1.912-1.9840.1961730.173308X-RAY DIFFRACTION99.9139
1.984-2.0650.1891670.1653181X-RAY DIFFRACTION99.9403
2.065-2.1570.1811520.1653069X-RAY DIFFRACTION99.9379
2.157-2.2620.1961480.1552936X-RAY DIFFRACTION100
2.262-2.3850.1461400.1422780X-RAY DIFFRACTION99.6587
2.385-2.5290.1611280.1412662X-RAY DIFFRACTION99.9284
2.529-2.7040.1761290.1412498X-RAY DIFFRACTION100
2.704-2.920.1671180.1442341X-RAY DIFFRACTION100
2.92-3.1980.1691020.1572159X-RAY DIFFRACTION99.6914
3.198-3.5750.181960.1531945X-RAY DIFFRACTION99.174
3.575-4.1270.169830.1381740X-RAY DIFFRACTION99.2919
4.127-5.0520.122860.1251483X-RAY DIFFRACTION99.619
5.052-7.1320.206670.1731164X-RAY DIFFRACTION99.3543
7.132-43.0940.205350.193688X-RAY DIFFRACTION97.047

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