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- PDB-8gtt: Cryo-EM structure of human Pannexin1 resembling Pannexin2 pore wi... -

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Basic information

Entry
Database: PDB / ID: 8gtt
TitleCryo-EM structure of human Pannexin1 resembling Pannexin2 pore with W74R/R75Dmutations
ComponentsPannexin-1
KeywordsMEMBRANE PROTEIN / Pannexin1 / ATP release / large-pore ion channel.
Function / homology
Function and homology information


Electric Transmission Across Gap Junctions / leak channel activity / positive regulation of interleukin-1 alpha production / bleb / wide pore channel activity / gap junction channel activity / gap junction / positive regulation of macrophage cytokine production / oogenesis / response to ATP ...Electric Transmission Across Gap Junctions / leak channel activity / positive regulation of interleukin-1 alpha production / bleb / wide pore channel activity / gap junction channel activity / gap junction / positive regulation of macrophage cytokine production / oogenesis / response to ATP / monoatomic cation transport / The NLRP3 inflammasome / positive regulation of interleukin-1 beta production / response to ischemia / calcium channel activity / calcium ion transport / actin filament binding / cell-cell signaling / scaffold protein binding / protease binding / transmembrane transporter binding / signaling receptor binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
Pannexin / Innexin / Innexin / Pannexin family profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHussain, N. / Penmatsa, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)IA/S/22/1/506242 India
CitationJournal: To Be Published
Title: CryoEM structures of Pannexin 1 and 3 reveal channel and pore organization among Pannexin isoforms
Authors: Hussain, N. / Apotikar, A. / Pidathala, S. / Mukherjee, S. / Burada, A.P. / Sikdar, S.K. / Vinothkumar, K.R. / Penmatsa, A.
History
DepositionSep 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pannexin-1
B: Pannexin-1
C: Pannexin-1
D: Pannexin-1
E: Pannexin-1
F: Pannexin-1
G: Pannexin-1


Theoretical massNumber of molelcules
Total (without water)343,8957
Polymers343,8957
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
Pannexin-1 /


Mass: 49127.902 Da / Num. of mol.: 7 / Mutation: W74R, R75D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANX1, MRS1, UNQ2529/PRO6028 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q96RD7

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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: Pannexin 1 (W74R/R75D) / Type: COMPLEX
Details: human isoform 1 of Pannexin. Expressed in plasma membranes involved in ATP release
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 48 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S / Plasmid: pEG Bacmam
Buffer solutionpH: 8
Details: Fresh solution containing detergent was prepared for every prep.
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTrisTris1
2100 mMpotassium chlorideKCl1
31 %glycerolGlycerol1
450 microMGlycodiosgeninGDN1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample is homoheptamer purified to homogeneity.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K / Details: 3.5 s single blot

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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: OTHER
Electron lensMode: OTHER / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 100 K
Image recordingElectron dose: 39.84 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15550
EM imaging opticsEnergyfilter name: GIF Bioquantum / Chromatic aberration corrector: None / Details: Gatan k3 / Energyfilter slit width: 20 eV / Phase plate: OTHER / Spherical aberration corrector: None
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selectionBlobpicker
2EPUimage acquisition
4cryoSPARCv3CTF correctionpatch CTF
7Coot9.03model fitting
11cryoSPARCclassification2D classification
12cryoSPARC3D reconstructionnon uniform refinement
13PHENIXmodel refinementreal space refine
Image processingDetails: Images were screened for ice thickness
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3869579 / Details: selected through particle picking
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80029 / Num. of class averages: 23 / Symmetry type: POINT
Atomic model buildingB value: 106.6 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coeficient
Atomic model buildingPDB-ID: 6WBF

6wbf


Pdb chain-ID: A / Accession code: 6WBF / Source name: PDB / Type: experimental model

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