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- PDB-8gn8: structure of human connexin 40.1 pentameric hemichannel by cryoEM -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8gn8
Titlestructure of human connexin 40.1 pentameric hemichannel by cryoEM
ComponentsGap junction delta-4 protein
KeywordsMEMBRANE PROTEIN / connexin hemichannel
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang, H. / Wang, D.P.
Funding support China, 3items
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, D.P.
History
DepositionAug 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Gap junction delta-4 protein
A: Gap junction delta-4 protein
B: Gap junction delta-4 protein
C: Gap junction delta-4 protein
E: Gap junction delta-4 protein


Theoretical massNumber of molelcules
Total (without water)130,1555
Polymers130,1555
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area16790 Å2
ΔGint-111 kcal/mol
Surface area49750 Å2

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Components

#1: Protein
Gap junction delta-4 protein / Connexin-40.1 / Cx40.1


Mass: 26030.973 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GJD4, CX40.1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q96KN9
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: structure of human connexin 40.1 pentameric hemichannel
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.13 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 4 mg/ml / Embedding 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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62658 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 90.75 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00238120
ELECTRON MICROSCOPYf_angle_d0.603311050
ELECTRON MICROSCOPYf_chiral_restr0.03941310
ELECTRON MICROSCOPYf_plane_restr0.00561360
ELECTRON MICROSCOPYf_dihedral_angle_d4.73091100

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