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- PDB-7zxp: cryo-EM structure of Connexin 32 R22G mutation gap junction channel -

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Basic information

Entry
Database: PDB / ID: 7zxp
Titlecryo-EM structure of Connexin 32 R22G mutation gap junction channel
ComponentsGap junction beta-1 protein
KeywordsMEMBRANE PROTEIN / connexin / gap junction channel / cell communication
Function / homology
Function and homology information


purine ribonucleotide transport / epididymis development / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / Gap junction assembly / gap junction channel activity / lateral plasma membrane / cell-cell signaling ...purine ribonucleotide transport / epididymis development / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / Gap junction assembly / gap junction channel activity / lateral plasma membrane / cell-cell signaling / nervous system development / endoplasmic reticulum membrane / identical protein binding
Similarity search - Function
Gap junction beta-1 protein (Cx32) / 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 beta-1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsQi, C. / Korkhov, V.M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation184951 Switzerland
CitationJournal: Sci Adv / Year: 2023
Title: Structures of wild-type and selected CMT1X mutant connexin 32 gap junction channels and hemichannels.
Authors: Chao Qi / Pia Lavriha / Erva Bayraktar / Anand Vaithia / Dina Schuster / Micaela Pannella / Valentina Sala / Paola Picotti / Mario Bortolozzi / Volodymyr M Korkhov /
Abstract: In myelinating Schwann cells, connection between myelin layers is mediated by gap junction channels (GJCs) formed by docked connexin 32 (Cx32) hemichannels (HCs). Mutations in Cx32 cause the X-linked ...In myelinating Schwann cells, connection between myelin layers is mediated by gap junction channels (GJCs) formed by docked connexin 32 (Cx32) hemichannels (HCs). Mutations in Cx32 cause the X-linked Charcot-Marie-Tooth disease (CMT1X), a degenerative neuropathy without a cure. A molecular link between Cx32 dysfunction and CMT1X pathogenesis is still missing. Here, we describe the high-resolution cryo-electron cryo-myography (cryo-EM) structures of the Cx32 GJC and HC, along with two CMT1X-linked mutants, W3S and R22G. While the structures of wild-type and mutant GJCs are virtually identical, the HCs show a major difference: In the W3S and R22G mutant HCs, the amino-terminal gating helix partially occludes the pore, consistent with a diminished HC activity. Our results suggest that HC dysfunction may be involved in the pathogenesis of CMT1X.
History
DepositionMay 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gap junction beta-1 protein
B: Gap junction beta-1 protein
C: Gap junction beta-1 protein
D: Gap junction beta-1 protein
E: Gap junction beta-1 protein
F: Gap junction beta-1 protein
G: Gap junction beta-1 protein
H: Gap junction beta-1 protein
I: Gap junction beta-1 protein
J: Gap junction beta-1 protein
K: Gap junction beta-1 protein
L: Gap junction beta-1 protein


Theoretical massNumber of molelcules
Total (without water)383,58512
Polymers383,58512
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Gap junction beta-1 protein / Connexin-32 / Cx32 / GAP junction 28 kDa liver protein


Mass: 31965.393 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GJB1, CX32 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P08034

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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: Connexin32 R22G mutation gap junction channel complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 32 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70675 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00218924
ELECTRON MICROSCOPYf_angle_d0.43125776
ELECTRON MICROSCOPYf_dihedral_angle_d3.3762484
ELECTRON MICROSCOPYf_chiral_restr0.0393048
ELECTRON MICROSCOPYf_plane_restr0.0033084

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