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- EMDB-64740: Human claudin 18.2 in complex with the Fab fragment of Osemitamab... -

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Basic information

Entry
Database: EMDB / ID: EMD-64740
TitleHuman claudin 18.2 in complex with the Fab fragment of Osemitamab (TST001)
Map data
Sample
  • Complex: Human claudin 18.2 in complex with the Fab fragment of Osemitamab (TST001)
    • Complex: Human claudin 18.2
      • Protein or peptide: Isoform A2 of Claudin-18
    • Complex: Fab of Osemitamab (TST001)
      • Protein or peptide: Fab of Osemitamab (TST001) - Heavy chain
      • Protein or peptide: Fab of Osemitamab (TST001) - 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: 3.8 Å
AuthorsWang X / Fu C / Ma H / 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 20, 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_64740.png

Downloads & links

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Map

FileDownload / File: emd_64740.map.gz / Format: CCP4 / Size: 91.1 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 288 pix.
= 244.8 Å		0.85 Å/pix.
x 288 pix.
= 244.8 Å		0.85 Å/pix.
x 288 pix.
= 244.8 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: 0.15
Minimum - Maximum-0.0017769486 - 1.7721236
Average (Standard dev.)0.0008422465 (±0.020408358)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_64740_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_64740_half_map_2.map
AnnotationHalf map B
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 Osemitamab...

EntireName: Human claudin 18.2 in complex with the Fab fragment of Osemitamab (TST001)
Components
  • Complex: Human claudin 18.2 in complex with the Fab fragment of Osemitamab (TST001)
    • Complex: Human claudin 18.2
      • Protein or peptide: Isoform A2 of Claudin-18
    • Complex: Fab of Osemitamab (TST001)
      • Protein or peptide: Fab of Osemitamab (TST001) - Heavy chain
      • Protein or peptide: Fab of Osemitamab (TST001) - Light chain

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

SupramoleculeName: Human claudin 18.2 in complex with the Fab fragment of Osemitamab (TST001)
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 Osemitamab (TST001)

SupramoleculeName: Fab of Osemitamab (TST001) / 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 Osemitamab (TST001) - Heavy chain

MacromoleculeName: Fab of Osemitamab (TST001) - Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.096123 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYTFT GYNMNWVRQA PGQGLEWMGN IDPYYGGTSY NQKFKGRVTM TIDKSTSTVY MELSSLRSE DTAVYYCARM YHGNAFDYWG QGTTVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT GYNMNWVRQA PGQGLEWMGN IDPYYGGTSY NQKFKGRVTM TIDKSTSTVY MELSSLRSE DTAVYYCARM YHGNAFDYWG QGTTVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCAAAENLY FQGDYKDDDD KH HHHHHHH HH

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Macromolecule #3: Fab of Osemitamab (TST001) - Light chain

MacromoleculeName: Fab of Osemitamab (TST001) - Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.122812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DIVMTQSPDS LAVSLGERAT INCKSSQSLL NSGNLKNYLT WYQQKPGQPP KLLIYWASTR KSGVPDRFSG SGSGTDFTLT ISSLQAEDV AVYYCQNDYS YPLTFGGGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
DIVMTQSPDS LAVSLGERAT INCKSSQSLL NSGNLKNYLT WYQQKPGQPP KLLIYWASTR KSGVPDRFSG SGSGTDFTLT ISSLQAEDV AVYYCQNDYS YPLTFGGGTK VEIKRTVAAP 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

Concentration11.0 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: 56.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -3.0 µm / Nominal defocus min: -0.1 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: 843125
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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 73763
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
Output model

PDB-9v2u:
Human claudin 18.2 in complex with the Fab fragment of Osemitamab (TST001)

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