[English] 日本語
Yorodumi
- EMDB-34157: structure of human connexin 40.1 pentameric hemichannel by cryoEM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34157
Titlestructure of human connexin 40.1 pentameric hemichannel by cryoEM
Map data
Sample
  • Complex: structure of human connexin 40.1 pentameric hemichannel
    • Protein or peptide: Gap junction delta-4 protein
Keywordsconnexin hemichannel / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of satellite cell activation involved in skeletal muscle regeneration / connexin complex / Gap junction assembly / gap junction channel activity / 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: 3.5 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-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_34157.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.)
0.92 Å/pix.
x 256 pix.
= 235.52 Å
0.92 Å/pix.
x 256 pix.
= 235.52 Å
0.92 Å/pix.
x 256 pix.
= 235.52 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
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-2.2875934 - 3.6305711
Average (Standard dev.)0.005808034 (±0.11637206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 235.52 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_34157_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #2

Fileemd_34157_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire : structure of human connexin 40.1 pentameric hemichannel

EntireName: structure of human connexin 40.1 pentameric hemichannel
Components
  • Complex: structure of human connexin 40.1 pentameric hemichannel
    • Protein or peptide: Gap junction delta-4 protein

-
Supramolecule #1: structure of human connexin 40.1 pentameric hemichannel

SupramoleculeName: structure of human connexin 40.1 pentameric hemichannel
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 130 KDa

-
Macromolecule #1: Gap junction delta-4 protein

MacromoleculeName: Gap junction delta-4 protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62658
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more