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- EMDB-34267: Cryo-EM structure of human Pannexin1 resembling Pannexin2 pore wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-34267
TitleCryo-EM structure of human Pannexin1 resembling Pannexin2 pore with W74R/R75Dmutations
Map datamain map for coordinates
Sample
  • Complex: Pannexin 1 (W74R/R75D)
    • Protein or peptide: Pannexin-1
KeywordsPannexin1 / ATP release / large-pore ion channel. / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHussain N / Penmatsa A
Funding support India, 1 items
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 AP / Sikdar SK / Vinothkumar KR / Penmatsa A
History
DepositionSep 8, 2022-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34267.png

Downloads & links

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Map

FileDownload / File: emd_34267.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map for coordinates
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.9583318 - 1.527624
Average (Standard dev.)0.00041860502 (±0.030946907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map partA

Fileemd_34267_half_map_1.map
Annotationhalf map partA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map part B

Fileemd_34267_half_map_2.map
Annotationhalf map part B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pannexin 1 (W74R/R75D)

EntireName: Pannexin 1 (W74R/R75D)
Components
  • Complex: Pannexin 1 (W74R/R75D)
    • Protein or peptide: Pannexin-1

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Supramolecule #1: Pannexin 1 (W74R/R75D)

SupramoleculeName: Pannexin 1 (W74R/R75D) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: human isoform 1 of Pannexin. Expressed in plasma membranes involved in ATP release
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48 kDa/nm

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Macromolecule #1: Pannexin-1

MacromoleculeName: Pannexin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.127902 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAIAQLATEY VFSDFLLKEP TEPKFKGLRL ELAVDKMVTC IAVGLPLLLI SLAFAQEISI GTQISCFSPS SFSRDQAAFV DSYCWAAVQ QKNSLQSESG NLPLWLHKFF PYILLLFAIL LYLPPLFWRF AAAPHICSDL KFIMEELDKV YNRAIKAAKS A RDLDMRDG ...String:
MAIAQLATEY VFSDFLLKEP TEPKFKGLRL ELAVDKMVTC IAVGLPLLLI SLAFAQEISI GTQISCFSPS SFSRDQAAFV DSYCWAAVQ QKNSLQSESG NLPLWLHKFF PYILLLFAIL LYLPPLFWRF AAAPHICSDL KFIMEELDKV YNRAIKAAKS A RDLDMRDG ACSVPGVTEN LGQSLWEVSE SHFKYPIVEQ YLKTKKNSNN LIIKYISCRL LTLIIILLAC IYLGYYFSLS SL SDEFVCS IKSGILRNDS TVPDQFQCKL IAVGIFQLLS VINLVVYVLL APVVVYTLFV PFRQKTDVLK VYEILPTFDV LHF KSEGYN DLSLYNLFLE ENISEVKSYK CLKVLENIKS SGQGIDPMLL LTNLGMIKMD VVDGKTPMSA EMREEQGNQT AELQ GMNID SETKANNGEK NARQRLLDSS CHHHHHHHH

UniProtKB: Pannexin-1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMTrisTris
100.0 mMKClpotassium chloride
1.0 %Glycerolglycerol
50.0 microMGDNGlycodiosgenin

Details: Fresh solution containing detergent was prepared for every prep.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV / Details: 3.5 s single blot.
DetailsSample is homoheptamer purified to homogeneity.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsPhase plate: OTHER / Spherical aberration corrector: None / Chromatic aberration corrector: None / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV / Details: Gatan k3
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 100.0 K / Max: 100.0 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 15550 / Average electron dose: 39.84 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3869579 / Details: selected through particle picking
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wbf

Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 23 / Avg.num./class: 15000 / Software - Name: cryoSPARC / Software - details: 2D classification
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 23 / Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: non uniform refinement / Number images used: 80029
DetailsImages were screened for ice thickness
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6wbf


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 106.6 / Target criteria: Correlation coeficient
Output model

PDB-8gtt:
Cryo-EM structure of human Pannexin1 resembling Pannexin2 pore with W74R/R75Dmutations

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