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- PDB-6mhq: Structure of connexin-46 intercellular gap junction channel at 3.... -

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Basic information

Entry
Database: PDB / ID: 6mhq
TitleStructure of connexin-46 intercellular gap junction channel at 3.4 angstrom resolution by cryoEM
ComponentsGap junction alpha-3 protein, connexin-46
KeywordsMEMBRANE PROTEIN / ion channel / gap junction / cell communication / connexin
Function / homology
Function and homology information


gap junction hemi-channel activity / gap junction-mediated intercellular transport / cell communication / connexin complex / visual perception / plasma membrane
Similarity search - Function
Gap junction alpha-3 protein (Cx46) / Connexin, C-terminal / 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. ...Gap junction alpha-3 protein (Cx46) / Connexin, C-terminal / 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 alpha-3 protein
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMyers, J.B. / Reichow, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM124779 United States
CitationJournal: Nature / Year: 2018
Title: Structure of native lens connexin 46/50 intercellular channels by cryo-EM.
Authors: Janette B Myers / Bassam G Haddad / Susan E O'Neill / Dror S Chorev / Craig C Yoshioka / Carol V Robinson / Daniel M Zuckerman / Steve L Reichow /
Abstract: Gap junctions establish direct pathways for cell-to-cell communication through the assembly of twelve connexin subunits that form intercellular channels connecting neighbouring cells. Co-assembly of ...Gap junctions establish direct pathways for cell-to-cell communication through the assembly of twelve connexin subunits that form intercellular channels connecting neighbouring cells. Co-assembly of different connexin isoforms produces channels with unique properties and enables communication across cell types. Here we used single-particle cryo-electron microscopy to investigate the structural basis of connexin co-assembly in native lens gap junction channels composed of connexin 46 and connexin 50 (Cx46/50). We provide the first comparative analysis to connexin 26 (Cx26), which-together with computational studies-elucidates key energetic features governing gap junction permselectivity. Cx46/50 adopts an open-state conformation that is distinct from the Cx26 crystal structure, yet it appears to be stabilized by a conserved set of hydrophobic anchoring residues. 'Hot spots' of genetic mutations linked to hereditary cataract formation map to the core structural-functional elements identified in Cx46/50, suggesting explanations for many of the disease-causing effects.
History
DepositionSep 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.pdbx_description
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Gap junction alpha-3 protein, connexin-46
B: Gap junction alpha-3 protein, connexin-46
C: Gap junction alpha-3 protein, connexin-46
D: Gap junction alpha-3 protein, connexin-46
E: Gap junction alpha-3 protein, connexin-46
F: Gap junction alpha-3 protein, connexin-46
G: Gap junction alpha-3 protein, connexin-46
H: Gap junction alpha-3 protein, connexin-46
I: Gap junction alpha-3 protein, connexin-46
J: Gap junction alpha-3 protein, connexin-46
K: Gap junction alpha-3 protein, connexin-46
L: Gap junction alpha-3 protein, connexin-46


Theoretical massNumber of molelcules
Total (without water)455,62212
Polymers455,62212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Gap junction alpha-3 protein, connexin-46 / Connexin-44 / Cx44


Mass: 37968.516 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Eye
Plasmid details: C-terminal truncated version isolated from lens core
Tissue: Lens / References: UniProt: Q9TU17
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Connexin-46 gap junction / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.45 MDa / Experimental value: NO
Source (natural)Organism: Ovis aries (sheep)
Cellular location: C-terminal truncated version isolated from lens core
Organ: Eye / Tissue: Lens
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHepes1
2150 mMNaCl1
32 mMEDTA1
42 mMEGTA1
SpecimenConc.: 2.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K
Details: 10 sec wait before blotting, 4.0 second blot before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Image recordingAverage exposure time: 10 sec. / Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter slit width: 30 eV
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1DoG Pickerparticle selection
2SerialEMimage acquisition
4Gctf1.06CTF correction
7Cootmodel fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 398066
SymmetryPoint symmetry: D6 (2x6 fold dihedral)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30128 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 2ZW3

2zw3


Pdb chain-ID: A / Accession code: 2ZW3 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01433180
ELECTRON MICROSCOPYf_angle_d0.959280
ELECTRON MICROSCOPYf_dihedral_angle_d10.81813824
ELECTRON MICROSCOPYf_chiral_restr0.0762784
ELECTRON MICROSCOPYf_plane_restr0.0035016

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