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- EMDB-54536: Complex of CADM1 and CD82 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54536
TitleComplex of CADM1 and CD82
Map dataGlobal map of complex of CADM1 and tetraspanin CD82 solubilized in DDM.
Sample
  • Complex: Dimeric complex of tetraspanin CD82 and CADM1
KeywordsTetraspanin / adhesion molecule / DDM / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsLamottke E / Warner H / Deventer S / Schwerdtfeger F / Lanting L / Huizinga EG / Spriel AB / Gros P
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)024.002.009 Netherlands
CitationJournal: To Be Published
Title: Tetraspanin CD82 inhibits the formation of CADM1 oligomers
Authors: Lamottke E / Warner H / Deventer S / Schwerdtfeger F / Lanting L / Huizinga EG / Spriel AB / Gros P
History
DepositionJul 24, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54536.png

Downloads & links

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Map

FileDownload / File: emd_54536.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal map of complex of CADM1 and tetraspanin CD82 solubilized in DDM.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 300 pix.
= 393.6 Å		1.31 Å/pix.
x 300 pix.
= 393.6 Å		1.31 Å/pix.
x 300 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.312 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.107
Minimum - Maximum-0.077758186 - 0.7278462
Average (Standard dev.)-0.00010730099 (±0.012395797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54536_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement on the density outside the micelle.

Fileemd_54536_additional_1.map
AnnotationLocal refinement on the density outside the micelle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened, global map.

Fileemd_54536_additional_2.map
AnnotationSharpened, global map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_54536_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_54536_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 : Dimeric complex of tetraspanin CD82 and CADM1

EntireName: Dimeric complex of tetraspanin CD82 and CADM1
Components
  • Complex: Dimeric complex of tetraspanin CD82 and CADM1

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Supramolecule #1: Dimeric complex of tetraspanin CD82 and CADM1

SupramoleculeName: Dimeric complex of tetraspanin CD82 and CADM1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

Concentration6.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 45730
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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