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- PDB-9ly6: antibody 20G5 (Fab')2 in complex with human B7-H3 -

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Basic information

Entry
Database: PDB / ID: 9ly6
Titleantibody 20G5 (Fab')2 in complex with human B7-H3
Components
  • CD276 antigen
  • antibody 20G5 Fab heavy chain
  • antibody 20G5 Fab light chain
KeywordsANTITUMOR PROTEIN/IMMUNE SYSTEM / B7-H3 / antibody / complex / ANTITUMOR PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of immune response / regulation of cytokine production / positive regulation of T cell proliferation / T cell activation / positive regulation of type II interferon production / T cell receptor signaling pathway / signaling receptor binding / external side of plasma membrane / membrane
Similarity search - Function
: / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...: / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsLi, B. / Zhou, S. / He, K.
Funding support China, 1items
OrganizationGrant numberCountry
Other private China
CitationJournal: To Be Published
Title: B7-H3-mediated cis-inhibition of EGFR by a tumor-selective bispecific antibody enhances anti-tumor efficacy and minimizes on-target toxicities
Authors: Bin, L. / Shuaixiang, Z. / Kaijie, H.
History
DepositionFeb 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD276 antigen
B: antibody 20G5 Fab heavy chain
C: antibody 20G5 Fab light chain
D: antibody 20G5 Fab heavy chain
E: antibody 20G5 Fab light chain


Theoretical massNumber of molelcules
Total (without water)143,6825
Polymers143,6825
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CD276 antigen / 4Ig-B7-H3 / B7 homolog 3 / B7-H3 / Costimulatory molecule


Mass: 46544.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD276, B7H3, PSEC0249, UNQ309/PRO352 / Production host: Homo sapiens (human) / References: UniProt: Q5ZPR3
#2: Antibody antibody 20G5 Fab heavy chain


Mass: 25274.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody antibody 20G5 Fab light chain


Mass: 23293.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: antibody 20G5 (Fab')2 in complex with human B7-H3 / Type: COMPLEX / Entity ID: #2-#3, #1 / Source: RECOMBINANT
Molecular weightValue: 145 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.0particle selection
13cryoSPARC4.4.03D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109088 / Symmetry type: POINT

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