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- PDB-8gtr: CryoEM structure of human Pannexin isoform 3 -

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Basic information

Entry
Database: PDB / ID: 8gtr
TitleCryoEM structure of human Pannexin isoform 3
ComponentsPannexin-3
KeywordsMEMBRANE PROTEIN / Pannexins / large pore ion-channels
Function / homology
Function and homology information


wide pore channel activity / positive regulation of interleukin-1 production / gap junction / monoatomic cation transport / monoatomic ion transmembrane transport / cell-cell signaling / structural molecule activity / plasma membrane
Similarity search - Function
Pannexin / Innexin / Innexin / Pannexin family profile.
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / Pannexin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.91 Å
AuthorsHussain, N. / Penmatsa, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)IA/I/15/2/502063 India
CitationJournal: To Be Published
Title: Structural insights into pore dynamics of human 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-3
B: Pannexin-3
C: Pannexin-3
D: Pannexin-3
E: Pannexin-3
F: Pannexin-3
G: Pannexin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,82621
Polymers313,1407
Non-polymers6,68714
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Pannexin-3 /


Mass: 44734.219 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANX3 / Plasmid: pEG Bacmam / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q96QZ0
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
Has ligand of interestN

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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 3 / Type: ORGANELLE OR CELLULAR COMPONENT
Details: human isoform 3 of Pannexin. Expressed in ER and Plasma membranes involved in calcium and ATP regulation
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 44.68 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.: 5 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: blotted for 3.5 seconds

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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: 130000 X / Nominal defocus max: 3300 nm / Nominal defocus min: 1800 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: 48.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1122
EM imaging opticsEnergyfilter name: GIF Bioquantum / Chromatic aberration corrector: None / Details: Bioquantum with K2 camera / 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: 411263
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31517 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 143.6 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coeficient

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