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- PDB-7yds: The structure of the bispecific antibody targeted PD-L1 and 4-1BB -

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Basic information

Entry
Database: PDB / ID: 7yds
TitleThe structure of the bispecific antibody targeted PD-L1 and 4-1BB
Components
  • Anti-PDL1-VH-CH1
  • Anti-PDL1-VL-CL
  • Programmed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / Complex / Checkpoint inhibitors
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 / negative regulation of type II interferon 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 / negative regulation of type II interferon production / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / negative regulation of T cell proliferation / T cell costimulation / positive regulation of T cell proliferation / response to cytokine / recycling endosome membrane / actin cytoskeleton / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / immune response / receptor ligand activity / 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 / Immunoglobulin-like fold / Immunoglobulins / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGao, Y. / Zhu, M. / Liu, W.T. / Cheng, L.S. / Zhu, Z.L. / Niu, L.W.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31621002 China
National Natural Science Foundation of China (NSFC)92153302 China
Ministry of Science and Technology (MoST, China)2017YFA0504903 China
CitationJournal: To Be Published
Title: A bispecific antibody targeted PD-L1 and 4-1BB induces a potent antitumor immune activity in colorectal cancer without systemic toxicity
Authors: Zhu, M. / Gao, Y.
History
DepositionJul 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death 1 ligand 1
B: Anti-PDL1-VH-CH1
C: Anti-PDL1-VL-CL


Theoretical massNumber of molelcules
Total (without water)64,1923
Polymers64,1923
Non-polymers00
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-26 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.076, 94.880, 96.069
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#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: 17080.676 Da / Num. of mol.: 1 / Mutation: N35Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9NZQ7
#2: Antibody Anti-PDL1-VH-CH1


Mass: 23386.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody Anti-PDL1-VL-CL


Mass: 23725.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 18% PEG4000, 0.1M Bis-tris pH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.3→13.14 Å / Num. obs: 29320 / % possible obs: 99.27 % / Redundancy: 2 % / Biso Wilson estimate: 24.45 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.1091 / Rpim(I) all: 0.1091 / Rrim(I) all: 0.1544 / Net I/σ(I): 8.23
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5817 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 2885 / CC1/2: 0.455 / CC star: 0.791 / Rpim(I) all: 0.5817 / Rrim(I) all: 0.8226 / % possible all: 99.55

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
Aimlessdata scaling
MLPHAREphasing
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WKM, 3BIS

6wkm

3bis


Resolution: 2.3→13.14 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 1412 4.82 %
Rwork0.1943 27908 -
obs0.1968 29320 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.39 Å2 / Biso mean: 29.8084 Å2 / Biso min: 7.03 Å2
Refinement stepCycle: final / Resolution: 2.3→13.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 0 398 4623
Biso mean---31.31 -
Num. residues----551
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.380.33661360.289127492885
2.38-2.480.32971580.273127132871
2.48-2.590.31951430.255927572900
2.59-2.720.27191310.238327832914
2.72-2.890.31121160.227227822898
2.89-3.110.2941450.205627892934
3.11-3.420.21081380.18427742912
3.42-3.910.22211430.163727962939
3.91-4.880.19071650.142128142979
4.88-13.140.20381370.164929513088

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