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- PDB-7czd: Crystal structure of PD-L1 in complex with a VHH -

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Basic information

Entry
Database: PDB / ID: 7czd
TitleCrystal structure of PD-L1 in complex with a VHH
Components
  • Programmed cell death 1 ligand 1
  • anti-PD-L1 VHH
KeywordsIMMUNE SYSTEM / antibody / Complex / VHH
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
DI(HYDROXYETHYL)ETHER / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsWang, C.
CitationJournal: J Immunother Cancer / Year: 2021
Title: Generation of a safe and efficacious llama single-domain antibody fragment (vHH) targeting the membrane-proximal region of 4-1BB for engineering therapeutic bispecific antibodies for cancer.
Authors: Zhai, T. / Wang, C. / Xu, Y. / Huang, W. / Yuan, Z. / Wang, T. / Dai, S. / Peng, S. / Pang, T. / Jiang, W. / Huang, Y. / Zou, Y. / Xu, Y. / Sun, J. / Gong, X. / Zhang, J. / Tsun, A. / Li, B. / Miao, X.
History
DepositionSep 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: anti-PD-L1 VHH
B: Programmed cell death 1 ligand 1
C: anti-PD-L1 VHH
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,70311
Polymers52,2254
Non-polymers4797
Water10,557586
1
A: anti-PD-L1 VHH
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2995
Polymers26,1122
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-5 kcal/mol
Surface area11180 Å2
MethodPISA
2
C: anti-PD-L1 VHH
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4056
Polymers26,1122
Non-polymers2924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-1 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.620, 97.990, 67.520
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody anti-PD-L1 VHH


Mass: 12657.917 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
#2: Protein Programmed cell death 1 ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 13454.492 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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.614
11-h,-k,l20.386
ReflectionResolution: 1.64→39.65 Å / Num. obs: 51992 / % possible obs: 94.6 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.031 / Net I/σ(I): 15
Reflection shellResolution: 1.64→1.67 Å / Rmerge(I) obs: 0.441 / Num. unique obs: 2495 / CC1/2: 0.796 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JDS, 5M2J

5jds

5m2j


Resolution: 1.64→39.65 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.496 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 2586 5 %RANDOM
Rwork0.1496 ---
obs0.1513 49377 94.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.04 Å2 / Biso mean: 19.532 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1-9.65 Å20 Å25.88 Å2
2---9.61 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.64→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3650 0 31 586 4267
Biso mean--38.25 30.65 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133882
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173572
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.6425267
X-RAY DIFFRACTIONr_angle_other_deg1.2211.5798335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3915508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69322.857196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8315690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9611521
X-RAY DIFFRACTIONr_chiral_restr0.0510.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02821
LS refinement shellResolution: 1.64→1.682 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 173 -
Rwork0.24 3529 -
all-3702 -
obs--92.02 %

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