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- EMDB-64747: Human claudin 18.2 in complex with the Fab fragment of Zolbetuximab -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64747
TitleHuman claudin 18.2 in complex with the Fab fragment of Zolbetuximab
Map data
Sample
  • Complex: Human claudin 18.2 in complex with the Fab fragment of Zolbetuximab
    • Complex: Human claudin 18.2
      • Protein or peptide: Isoform A2 of Claudin-18
    • Complex: Fab of Zolbetuximab
      • Protein or peptide: Fab of Zolbetuximab - Heavy chain
      • Protein or peptide: Fab of Zolbetuximab - Light chain
KeywordsCLDN18.2 / tight junction protein / therapeutic antibody / gastric cancer / MEMBRANE PROTEIN/IMMUNE SYSTEM / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang X / Ma H / Fu C / Sun Z / Su Z / Zhou X
Funding support1 items
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, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64747.png

Downloads & links

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Map

FileDownload / File: emd_64747.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.001930743 - 2.012686
Average (Standard dev.)0.0020411764 (±0.0326208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half map B

Fileemd_64747_half_map_1.map
AnnotationEM half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map A

Fileemd_64747_half_map_2.map
AnnotationEM half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human claudin 18.2 in complex with the Fab fragment of Zolbetuximab

EntireName: Human claudin 18.2 in complex with the Fab fragment of Zolbetuximab
Components
  • Complex: Human claudin 18.2 in complex with the Fab fragment of Zolbetuximab
    • Complex: Human claudin 18.2
      • Protein or peptide: Isoform A2 of Claudin-18
    • Complex: Fab of Zolbetuximab
      • Protein or peptide: Fab of Zolbetuximab - Heavy chain
      • Protein or peptide: Fab of Zolbetuximab - Light chain

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Supramolecule #1: Human claudin 18.2 in complex with the Fab fragment of Zolbetuximab

SupramoleculeName: Human claudin 18.2 in complex with the Fab fragment of Zolbetuximab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Human claudin 18.2

SupramoleculeName: Human claudin 18.2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Fab of Zolbetuximab

SupramoleculeName: Fab of Zolbetuximab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Isoform A2 of Claudin-18

MacromoleculeName: Isoform A2 of Claudin-18 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.236254 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MAVTACQGLG FVVSLIGIAG IIAATCMDQW STQDLYNNPV TAVFNYQGLW RSCVRESSGF TECRGYFTLL GLPAMLQAVR ALMIVGIVL GAIGLLVSIF ALKCIRIGSM EDSAKANMTL TSGIMFIVSG LCAIAGVSVF ANMLVTNFWM STANMYTGMG G MVQTVQTR ...String:
MAVTACQGLG FVVSLIGIAG IIAATCMDQW STQDLYNNPV TAVFNYQGLW RSCVRESSGF TECRGYFTLL GLPAMLQAVR ALMIVGIVL GAIGLLVSIF ALKCIRIGSM EDSAKANMTL TSGIMFIVSG LCAIAGVSVF ANMLVTNFWM STANMYTGMG G MVQTVQTR YTFGAALFVG WVAGGLTLIG GVMMCIACRG LAPEETNYKA AAA

UniProtKB: Claudin-18

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Macromolecule #2: Fab of Zolbetuximab - Heavy chain

MacromoleculeName: Fab of Zolbetuximab - Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.299123 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QVQLQQPGAE LVRPGASVKL SCKASGYTFT SYWINWVKQR PGQGLEWIGN IYPSDSYTNY NQKFKDKATL TVDKSSSTAY MQLSSPTSE DSAVYYCTRS WRGNSFDYWG QGTTLTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLQQPGAE LVRPGASVKL SCKASGYTFT SYWINWVKQR PGQGLEWIGN IYPSDSYTNY NQKFKDKATL TVDKSSSTAY MQLSSPTSE DSAVYYCTRS WRGNSFDYWG QGTTLTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSCAAAENLY FQGDYKDDDD KH HHHHHHH HH

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Macromolecule #3: Fab of Zolbetuximab - Light chain

MacromoleculeName: Fab of Zolbetuximab - Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.194826 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DIVMTQSPSS LTVTAGEKVT MSCKSSQSLL NSGNQKNYLT WYQQKPGQPP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVQAEDL AVYYCQNDYS YPFTFGSGTK LEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
DIVMTQSPSS LTVTAGEKVT MSCKSSQSLL NSGNQKNYLT WYQQKPGQPP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVQAEDL AVYYCQNDYS YPFTFGSGTK LEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8.0 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.5 mM DDM
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2-3 s before plunging.
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 57.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -1.8 µm / Nominal defocus min: -1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3415895
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 296899
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot (ver. 0.9.3)
Output model

PDB-9v32:
Human claudin 18.2 in complex with the Fab fragment of Zolbetuximab

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