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- PDB-9v31: Human claudin 18.2 (dimer form) in complex with the Fab fragment ... -

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Basic information

Entry
Database: PDB / ID: 9v31
TitleHuman claudin 18.2 (dimer form) in complex with the Fab fragment of Osemitamab (TST001)
Components
  • Fab of Osemitamab (TST001) - Heavy chain
  • Fab of Osemitamab (TST001) - Light chain
  • Isoform A2 of Claudin-18
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / CLDN18.2 / tight junction protein / therapeutic antibody / gastric cancer / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


calcium-independent cell-cell adhesion / tight junction organization / Tight junction interactions / epithelial fluid transport / negative regulation of osteoclast development / bicellular tight junction assembly / negative regulation of bone resorption / digestive tract development / organ growth / negative regulation of protein localization to nucleus ...calcium-independent cell-cell adhesion / tight junction organization / Tight junction interactions / epithelial fluid transport / negative regulation of osteoclast development / bicellular tight junction assembly / negative regulation of bone resorption / digestive tract development / organ growth / negative regulation of protein localization to nucleus / lung alveolus development / cellular response to estrogen stimulus / lateral plasma membrane / bicellular tight junction / negative regulation of tumor necrosis factor-mediated signaling pathway / protein localization to nucleus / epithelial cell proliferation / cell-cell junction / response to ethanol / cell adhesion / structural molecule activity / identical protein binding / plasma membrane
Similarity search - Function
Claudin-18 / Claudin / Claudin, conserved site / Claudin family signature. / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsWang, X. / Ma, H. / Fu, C. / Sun, Z. / Su, Z. / Zhou, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Recognition of human claudin 18.2 by therapeutic antibodies
Authors: Wang, X. / Fu, C. / Ma, H. / Yang, P. / Sun, Z. / Su, Z. / Zhou, X.
History
DepositionMay 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 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: Isoform A2 of Claudin-18
H: Fab of Osemitamab (TST001) - Heavy chain
L: Fab of Osemitamab (TST001) - Light chain
C: Fab of Osemitamab (TST001) - Heavy chain
D: Fab of Osemitamab (TST001) - Light chain
B: Isoform A2 of Claudin-18


Theoretical massNumber of molelcules
Total (without water)146,9106
Polymers146,9106
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Isoform A2 of Claudin-18


Mass: 22236.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLDN18, UNQ778/PRO1572 / Production host: Komagataella pastoris (fungus) / References: UniProt: P56856
#2: Antibody Fab of Osemitamab (TST001) - Heavy chain


Mass: 27096.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab of Osemitamab (TST001) - Light chain


Mass: 24122.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
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

Component
IDNameTypeEntity IDParent-IDSource
1Human claudin 18.2 (dimer form) in complex with the Fab fragment of Osemitamab (TST001)COMPLEXall0MULTIPLE SOURCES
2Human claudin 18.2COMPLEX#11RECOMBINANT
3Fab of Osemitamab (TST001)COMPLEX#2-#31RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Komagataella pastoris (fungus)4922
22Komagataella pastoris (fungus)4922
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.5 / Details: 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.5 mM DDM
SpecimenConc.: 8.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K / Details: blot for 2-3 s before plunging

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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: -1800 nm / Nominal defocus min: -1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 57.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7Coot0.9.3model fitting
9RELION5initial Euler assignment
10RELION5final Euler assignment
11RELION5classification
12cryoSPARC4.43D reconstruction
13PHENIX1.19.1_4122:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1379077
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66529 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039028
ELECTRON MICROSCOPYf_angle_d0.63212256
ELECTRON MICROSCOPYf_dihedral_angle_d4.4181235
ELECTRON MICROSCOPYf_chiral_restr0.0411403
ELECTRON MICROSCOPYf_plane_restr0.0041536

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