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- PDB-8rpb: Structure of S79 Fab in complex with IgV domain of human PD-L1 -

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Basic information

Entry
Database: PDB / ID: 8rpb
TitleStructure of S79 Fab in complex with IgV domain of human PD-L1
Components
  • Programmed cell death 1 ligand 1
  • heavy chain of S79 fab
  • light chain of S79 fab
KeywordsIMMUNE SYSTEM / Fab
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.794 Å
AuthorsSvensson, A. / Kelpsas, V. / Laursen, M. / Rose, N.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Mabs / Year: 2024
Title: Structural analysis of light chain-driven bispecific antibodies targeting CD47 and PD-L1.
Authors: Malinge, P. / Chauchet, X. / Bourguignon, J. / Bosson, N. / Calloud, S. / Bautzova, T. / Borlet, M. / Laursen, M. / Kelpsas, V. / Rose, N. / Gueneau, F. / Ravn, U. / Magistrelli, G. / Fischer, N.
History
DepositionJan 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: heavy chain of S79 fab
L: light chain of S79 fab
P: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,61713
Polymers60,7293
Non-polymers88810
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-110 kcal/mol
Surface area24430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.852, 185.852, 110.237
Angle α, β, γ (deg.)90, 90, 120
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11H-306-

SO4

21H-306-

SO4

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Components

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Protein , 1 types, 1 molecules P

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


Mass: 14335.406 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7

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Antibody , 2 types, 2 molecules HL

#1: Antibody heavy chain of S79 fab


Mass: 23468.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody light chain of S79 fab


Mass: 22925.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 27 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 4.21 Å3/Da / Density % sol: 70.82 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.0, 1.6M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.79→48.24 Å / Num. obs: 28276 / % possible obs: 99.7 % / Redundancy: 24 % / CC1/2: 0.995 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.043 / Net I/σ(I): 11.8
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 23.9 % / Rmerge(I) obs: 3.089 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3987 / CC1/2: 0.622 / Rpim(I) all: 0.637 / % possible all: 98.1

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.794→48.24 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.385 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.383 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.269
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 1385 -RANDOM
Rwork0.2289 ---
obs0.23 28249 99.8 %-
Displacement parametersBiso mean: 119.06 Å2
Baniso -1Baniso -2Baniso -3
1--3.0203 Å20 Å20 Å2
2---3.0203 Å20 Å2
3---6.0406 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.794→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 49 17 4190
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074263HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.965799HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1397SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes703HARMONIC5
X-RAY DIFFRACTIONt_it4263HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion558SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2908SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion16.79
LS refinement shellResolution: 2.794→2.81 Å
RfactorNum. reflection% reflection
Rfree0.3519 24 -
Rwork0.3414 --
obs--90.51 %
Refinement TLS params.

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)
16.4416-0.0740.94852.05230.74042.6844-0.397-0.1112-0.3155-0.1112-0.03550.5856-0.31550.58560.4326-0.24570.1743-0.19320.1993-0.02560.1313-17.4374-74.7604-9.3984
26.8902-0.8761.30218.322.25085.0447-1.21151.5701-0.4341.57011.191-0.2982-0.434-0.29820.02050.02840.8038-0.36640.5367-0.5064-0.2772-40.2809-60.958412.792
311.6712-2.53931.62826.8222-2.34298.8733-0.6184-0.6389-0.7085-0.6389-0.27012.4728-0.70852.47280.8885-0.7768-0.1817-0.04741.11640.8076-0.37122.3222-71.1313-29.0013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|1 - H|116 L|1 - L|113 }H1 - 116
2X-RAY DIFFRACTION1{ H|1 - H|116 L|1 - L|113 }L1 - 113
3X-RAY DIFFRACTION2{ H|117 - H|218 L|114 - L|215 }H117 - 218
4X-RAY DIFFRACTION2{ H|117 - H|218 L|114 - L|215 }L114 - 215
5X-RAY DIFFRACTION3{ P|* }P18 - 131

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