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- EMDB-34156: structure of human connexin 40.1 intercellular gap junction chann... -

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Basic information

Entry
Database: EMDB / ID: EMD-34156
Titlestructure of human connexin 40.1 intercellular gap junction channel by cryoEM
Map datadensity map
Sample
  • Complex: decameric structure of human connexin 40.1 intercellular gap junction channel
    • Protein or peptide: Gap junction delta-4 protein
  • Ligand: CHOLESTEROL
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
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: 3.0 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: structure of human connexin 40.1 intercellular gap junction channel by cryoEM
Authors: Zhang H / Wang DP
History
DepositionAug 23, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34156.png

Downloads & links

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Map

FileDownload / File: emd_34156.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 353.28 Å		0.92 Å/pix.
x 384 pix.
= 353.28 Å		0.92 Å/pix.
x 384 pix.
= 353.28 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: 0.21
Minimum - Maximum-2.5861459 - 4.208074
Average (Standard dev.)0.004773354 (±0.103142716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_34156_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_34156_half_map_2.map
Annotationhalf 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 : decameric structure of human connexin 40.1 intercellular gap junc...

EntireName: decameric structure of human connexin 40.1 intercellular gap junction channel
Components
  • Complex: decameric structure of human connexin 40.1 intercellular gap junction channel
    • Protein or peptide: Gap junction delta-4 protein
  • Ligand: CHOLESTEROL
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: decameric structure of human connexin 40.1 intercellular gap junc...

SupramoleculeName: decameric structure of human connexin 40.1 intercellular gap junction channel
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 260 KDa

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Macromolecule #1: Gap junction delta-4 protein

MacromoleculeName: Gap junction delta-4 protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.030973 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGVDLLGFL IITLNCNVTM VGKLWFVLTM LLRMLVIVLA GRPVYQDEQE RFVCNTLQPG CANVCYDVFS PVSHLRFWLI QGVCVLLPS AVFSVYVLHR GATLAALGPR RCPDPREPAS GQRRCPRPFG ERGGLQVPDF SAGYIIHLLL RTLLEAAFGA L HYFLFGFL ...String:
MEGVDLLGFL IITLNCNVTM VGKLWFVLTM LLRMLVIVLA GRPVYQDEQE RFVCNTLQPG CANVCYDVFS PVSHLRFWLI QGVCVLLPS AVFSVYVLHR GATLAALGPR RCPDPREPAS GQRRCPRPFG ERGGLQVPDF SAGYIIHLLL RTLLEAAFGA L HYFLFGFL APKKFPCTRP PCTGVVDCYV SRPTEKSLLM LFLWAVSALS FLLGLADLVC SLRRRMRRRP GPPTS

UniProtKB: Gap junction delta-4 protein

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 30 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 10 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #4: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 4 / Number of copies: 10 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41530
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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