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- PDB-9w43: Structure of the complex of human PD-1 and a PD-1-directed antibody -

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Basic information

Entry
Database: PDB / ID: 9w43
TitleStructure of the complex of human PD-1 and a PD-1-directed antibody
Components
  • Heavy chain of 1C4 Fab fragment
  • Light chain of 1C4 Fab fragment
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / PD-1 / PD-1-directed antibody / antigen-antibody complex
Function / homology
Function and homology information


regulatory T cell apoptotic process / negative regulation of tolerance induction / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / negative regulation of T cell activation / humoral immune response / Co-inhibition by PD-1 ...regulatory T cell apoptotic process / negative regulation of tolerance induction / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / negative regulation of T cell activation / humoral immune response / Co-inhibition by PD-1 / negative regulation of T cell receptor signaling pathway / regulation of immune response / negative regulation of inflammatory response / transmembrane signaling receptor activity / signaling receptor activity / Potential therapeutics for SARS / adaptive immune response / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / Immunoglobulin V-Type / 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 protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsJiang, W.B. / Xu, J.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2026
Title: Dual agonism and selective T-cell depletion activity of a PD-1-directed antibody for treating autoimmune diseases.
Authors: Jiang, W. / Li, L. / Xue, W. / He, X. / Chu, X. / Song, L. / Li, X. / Zhao, R. / Yuan, X. / Jin, X. / Fan, L. / Sun, T. / Zhu, A. / Zhou, L. / Gu, F. / Xu, Q. / Ma, G. / Wang, S. / Jin, L. / Xu, J.L.
History
DepositionJul 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 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: Heavy chain of 1C4 Fab fragment
B: Light chain of 1C4 Fab fragment
C: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)58,9403
Polymers58,9403
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody Heavy chain of 1C4 Fab fragment


Mass: 22857.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Light chain of 1C4 Fab fragment


Mass: 23194.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Programmed cell death protein 1 / Protein PD-1 / hPD-1


Mass: 12887.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Homo sapiens (human) / References: UniProt: Q15116
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: PD1-fab complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
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: 59 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179370 / Symmetry type: POINT

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