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- EMDB-0826: Human Cx31.3/GJC3 connexin hemichannel in the presence of calcium -

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Basic information

Entry
Database: EMDB / ID: EMD-0826
TitleHuman Cx31.3/GJC3 connexin hemichannel in the presence of calcium
Map datapostprocess_masked map
Sample
  • Complex: Human Cx31.3/GJC3 connexin hemichannel in the presence of calcium
    • Protein or peptide: Gap junction gamma-3 protein
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: CALCIUM IONCalcium
  • Ligand: water
Function / homology
Function and homology information


connexin complex / gap junction channel activity / myelination / sensory perception of sound / cell-cell signaling / myelin sheath / identical protein binding
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 gamma-3 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsLee HJ / Jeong H / Ryu B / Hyun J / Woo JS
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2018R1C1B6004447 Korea, Republic Of
CitationJournal: Sci Adv / Year: 2020
Title: Cryo-EM structure of human Cx31.3/GJC3 connexin hemichannel.
Authors: Hyuk-Joon Lee / Hyeongseop Jeong / Jaekyung Hyun / Bumhan Ryu / Kunwoong Park / Hyun-Ho Lim / Jejoong Yoo / Jae-Sung Woo /
Abstract: Connexin family proteins assemble into hexameric channels called hemichannels/connexons, which function as transmembrane channels or dock together to form gap junction intercellular channels (GJIChs). ...Connexin family proteins assemble into hexameric channels called hemichannels/connexons, which function as transmembrane channels or dock together to form gap junction intercellular channels (GJIChs). We determined the cryo-electron microscopy structures of human connexin 31.3 (Cx31.3)/GJC3 hemichannels in the presence and absence of calcium ions and with a hearing-loss mutation R15G at 2.3-, 2.5-, and 2.6-Å resolutions, respectively. Compared with available structures of GJICh in open conformation, Cx31.3 hemichannel shows substantial structural changes of highly conserved regions in the connexin family, including opening of calcium ion-binding tunnels, reorganization of salt-bridge networks, exposure of lipid-binding sites, and collocation of amino-terminal helices at the cytoplasmic entrance. We also found that the hemichannel has a pore with a diameter of ~8 Å and selectively transports chloride ions. Our study provides structural insights into the permeant selectivity of Cx31.3 hemichannel.
History
DepositionOct 15, 2019-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l3u
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0826.png

Downloads & links

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Map

FileDownload / File: emd_0826.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocess_masked map
Voxel sizeX=Y=Z: 0.673 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.1646174 - 0.2501305
Average (Standard dev.)0.00020678178 (±0.006566548)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 215.35999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6730.6730.673
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z215.360215.360215.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1650.2500.000

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Supplemental data

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Half map: half map 2

Fileemd_0826_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_0826_half_map_2.map
Annotationhalf map 1
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 Cx31.3/GJC3 connexin hemichannel in the presence of calcium

EntireName: Human Cx31.3/GJC3 connexin hemichannel in the presence of calcium
Components
  • Complex: Human Cx31.3/GJC3 connexin hemichannel in the presence of calcium
    • Protein or peptide: Gap junction gamma-3 protein
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: CALCIUM IONCalcium
  • Ligand: water

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Supramolecule #1: Human Cx31.3/GJC3 connexin hemichannel in the presence of calcium

SupramoleculeName: Human Cx31.3/GJC3 connexin hemichannel in the presence of calcium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Gap junction gamma-3 protein

MacromoleculeName: Gap junction gamma-3 protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.339365 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MCGRFLRRLL AEESRRSTPV GRLLLPVLLG FRLVLLAASG PGVYGDEQSE FVCHTQQPGC KAACFDAFHP LSPLRFWVFQ VILVAVPSA LYMGFTLYHV IWHWELSGKG KEEETLIQGR EGNTDVPGAG SLRLLWAYVA QLGARLVLEG AALGLQYHLY G FQMPSSFA ...String:
MCGRFLRRLL AEESRRSTPV GRLLLPVLLG FRLVLLAASG PGVYGDEQSE FVCHTQQPGC KAACFDAFHP LSPLRFWVFQ VILVAVPSA LYMGFTLYHV IWHWELSGKG KEEETLIQGR EGNTDVPGAG SLRLLWAYVA QLGARLVLEG AALGLQYHLY G FQMPSSFA CRREPCLGSI TCNLSRPSEK TIFLKTMFGV SGFCLLFTFL ELVLLGLGRW WRTWKHKSSS SKYFLTSEST RR HKKATDS LPVVETKEQF QEAVPGRSLA QEKQRPVGPR DA

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Macromolecule #2: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 2 / Number of copies: 6 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 174 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: NONE
Details: Stochastic Gradient Descent (SGD) algorithm in RELION 3.0
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 185517
FSC plot (resolution estimation)

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