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- PDB-9zy5: Ca2+ bound gated state Connexin-46 -

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Basic information

Entry
Database: PDB / ID: 9zy5
TitleCa2+ bound gated state Connexin-46
ComponentsGap junction alpha-3 protein
KeywordsMEMBRANE PROTEIN / calcium regulation / channel gating / connexin / cryo-EM / gap junction / large-pore channel
Function / homology
Function and homology information


gap junction-mediated intercellular transport / gap junction hemi-channel activity / connexin complex / visual perception / cell-cell signaling / 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
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Gap junction alpha-3 protein
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsFlores, J.A. / O'Neill, S.E. / Jarodsky, J.M. / Reichow, S.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R35GM124779 United States
National Institutes of Health/National Eye Institute (NIH/NEI)F31EY030409 United States
CitationJournal: Nat Commun / Year: 2026
Title: Calcium induced N-terminal gating and pore collapse in connexin-46/50 gap junctions
Authors: Flores, J.A. / O'Neill, S.E. / Jarodsky, J.M. / Haddad, B.G. / Reichow, S.L.
History
DepositionJan 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)634,635180
Polymers528,39612
Non-polymers106,238168
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 44033.027 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: Q9TU17
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 156 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
Has ligand of interestN
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: Ca2+ bound gated state Connexin-46/50 gap junction / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Ovis aries (sheep)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
22 mMEDTAC10H16N2O81
32 mMEGTAC14H24N2O101
4150 mMSodium chlorideNaCl1
520 mMCalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil Active R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 37 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5750

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4RELIONCTF correction
7UCSF ChimeraXmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 3940202
SymmetryPoint symmetry: D6 (2x6 fold dihedral)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173079 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7jkc

7jkc


Accession code: 7jkc / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0120544
ELECTRON MICROSCOPYf_angle_d0.70827216
ELECTRON MICROSCOPYf_dihedral_angle_d14.0937218
ELECTRON MICROSCOPYf_chiral_restr0.062928
ELECTRON MICROSCOPYf_plane_restr0.0053216

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