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- PDB-8aom: Complex of PD-L1 with VHH1 -

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Basic information

Entry
Database: PDB / ID: 8aom
TitleComplex of PD-L1 with VHH1
Components
  • Programmed cell death 1 ligand 1
  • VHH6
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 / cellular response to lipopolysaccharide / adaptive immune response / 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
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 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

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Assembly

Deposited unit
A: Programmed cell death 1 ligand 1
V: VHH6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5213
Polymers38,4962
Non-polymers241
Water82946
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-13 kcal/mol
Surface area17560 Å2
Unit cell
Length a, b, c (Å)149.512, 149.512, 149.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Programmed cell death 1 ligand 1


Mass: 25456.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): * / References: UniProt: Q9NZQ7
#2: Antibody VHH6


Mass: 13039.438 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): *
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
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: 3.63 Å3/Da / Density % sol: 66.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M MOPS, pH 7.5, and 12% (w/v) PEG 8000

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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 S 1M / Detector: PIXEL / Date: Sep 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.2→47.324 Å / Num. obs: 28213 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.039 / Rrim(I) all: 0.083 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.08-47.287.40.0434360.9780.0220.049
2.2-2.277.11.9324240.2871.1162.244

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZQK

4zqk


Resolution: 2.202→47.324 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: FREE R-VALUE / ESU R: 0.19 / ESU R Free: 0.173
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2447 1417 5.023 %
Rwork0.208 26795 -
all0.21 --
obs-28212 99.862 %
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: 70.154 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.202→47.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 1 46 2683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132691
X-RAY DIFFRACTIONr_bond_other_d0.0350.0152509
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.6463654
X-RAY DIFFRACTIONr_angle_other_deg2.3681.585772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6845331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1322.535142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.32515457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8151517
X-RAY DIFFRACTIONr_chiral_restr0.070.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023056
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02622
X-RAY DIFFRACTIONr_nbd_refined0.1870.2378
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2330.22216
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21234
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21340
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.219
X-RAY DIFFRACTIONr_nbd_other0.3550.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0510.24
X-RAY DIFFRACTIONr_mcbond_it5.9387.071333
X-RAY DIFFRACTIONr_mcbond_other5.8737.0671332
X-RAY DIFFRACTIONr_mcangle_it8.10810.5931661
X-RAY DIFFRACTIONr_mcangle_other8.10810.5971662
X-RAY DIFFRACTIONr_scbond_it6.8537.8451358
X-RAY DIFFRACTIONr_scbond_other6.8367.8421357
X-RAY DIFFRACTIONr_scangle_it9.94211.4551993
X-RAY DIFFRACTIONr_scangle_other9.93911.4571993
X-RAY DIFFRACTIONr_lrange_it12.43879.1262724
X-RAY DIFFRACTIONr_lrange_other12.45579.1532722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.202-2.2590.3761000.3651975X-RAY DIFFRACTION100
2.259-2.3210.37870.3511912X-RAY DIFFRACTION100
2.321-2.3880.397950.3341868X-RAY DIFFRACTION100
2.388-2.4610.3351100.311786X-RAY DIFFRACTION100
2.461-2.5420.364810.3121794X-RAY DIFFRACTION99.9467
2.542-2.6310.332790.2811716X-RAY DIFFRACTION100
2.631-2.730.304940.2511611X-RAY DIFFRACTION100
2.73-2.8420.284960.2261572X-RAY DIFFRACTION100
2.842-2.9680.294850.2271514X-RAY DIFFRACTION100
2.968-3.1130.297790.2261454X-RAY DIFFRACTION100
3.113-3.2810.265700.2291387X-RAY DIFFRACTION100
3.281-3.480.28680.2261316X-RAY DIFFRACTION99.8557
3.48-3.720.234600.2191241X-RAY DIFFRACTION99.9232
3.72-4.0170.27520.2131161X-RAY DIFFRACTION99.5895
4.017-4.40.198650.1681045X-RAY DIFFRACTION99.8201
4.4-4.9190.177590.142963X-RAY DIFFRACTION99.6101
4.919-5.6770.222570.163841X-RAY DIFFRACTION99.4463
5.677-6.9480.193390.186725X-RAY DIFFRACTION99.3498
6.948-9.8050.255260.176583X-RAY DIFFRACTION99.8361
9.805-47.3240.187150.235331X-RAY DIFFRACTION96.648

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