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- EMDB-35141: honeycomb-like structure of human connexin 40.1 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-35141
Titlehoneycomb-like structure of human connexin 40.1
Map datadensity map
Sample
  • Complex: honeycomb-like structure of human connexin 40.1
    • Protein or peptide: human connexin 40.1
Keywordsintercellular gap junction channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of satellite cell activation involved in skeletal muscle regeneration / connexin complex / gap junction channel activity / Gap junction assembly / cell-cell signaling
Similarity search - Function
Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin / Connexins signature 1. / Connexins signature 2. / Connexin homologues / Gap junction channel protein cysteine-rich domain
Similarity search - Domain/homology
Gap junction delta-4 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsZhang H / Wang DP
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900046 China
National Natural Science Foundation of China (NSFC)81972085 China
National Natural Science Foundation of China (NSFC)82172465 China
CitationJournal: To Be Published
Title: honeycomb-like structure of human connexin 40.1
Authors: Zhang H / Wang DP
History
DepositionJan 14, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35141.png

Downloads & links

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Map

FileDownload / File: emd_35141.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdensity map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 512 pix.
= 471.04 Å		0.92 Å/pix.
x 512 pix.
= 471.04 Å		0.92 Å/pix.
x 512 pix.
= 471.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.3087212 - 0.3633943
Average (Standard dev.)0.00091876055 (±0.022320945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 471.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_35141_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_35141_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 : honeycomb-like structure of human connexin 40.1

EntireName: honeycomb-like structure of human connexin 40.1
Components
  • Complex: honeycomb-like structure of human connexin 40.1
    • Protein or peptide: human connexin 40.1

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Supramolecule #1: honeycomb-like structure of human connexin 40.1

SupramoleculeName: honeycomb-like structure of human connexin 40.1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 390 KDa

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Macromolecule #1: human connexin 40.1

MacromoleculeName: human connexin 40.1 / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGVDLLGFL IITLNCNVTM VGKLWFVLTM LLRMLVIVLA GRPVYQDEQE RFVCNTLQPG CANVCYDVF SPVSHLRFWL IQGVCVLLPS AVFSVYVLHR GATLAALGPR RCPDPREPAS G QRRCPRPF GERGGLQVPD FSAGYIIHLL LRTLLEAAFG ALHYFLFGFL ...String:
MEGVDLLGFL IITLNCNVTM VGKLWFVLTM LLRMLVIVLA GRPVYQDEQE RFVCNTLQPG CANVCYDVF SPVSHLRFWL IQGVCVLLPS AVFSVYVLHR GATLAALGPR RCPDPREPAS G QRRCPRPF GERGGLQVPD FSAGYIIHLL LRTLLEAAFG ALHYFLFGFL APKKFPCTRP PC TGVVDCY VSRPTEKSLL MLFLWAVSAL SFLLGLADLV CSLRRRMRRR PGPPTS

UniProtKB: Gap junction delta-4 protein

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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

Concentration4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2547
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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