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- EMDB-34265: CryoEM structure of human Pannexin isoform 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-34265
TitleCryoEM structure of human Pannexin isoform 3
Map dataMain Map of Pannexin 3
Sample
  • Organelle or cellular component: Pannexin 3
    • Protein or peptide: Pannexin-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PHOSPHATIDYLETHANOLAMINE
KeywordsPannexins / large pore ion-channels / MEMBRANE PROTEIN
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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.91 Å
AuthorsHussain N / Penmatsa A
Funding support India, 1 items
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 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_34265.png

Downloads & links

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Map

FileDownload / File: emd_34265.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain Map of Pannexin 3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 383.4 Å		1.07 Å/pix.
x 360 pix.
= 383.4 Å		1.07 Å/pix.
x 360 pix.
= 383.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-1.618716 - 3.105998
Average (Standard dev.)0.011120179 (±0.06648128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 383.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Panx3 halfmapB

Fileemd_34265_half_map_1.map
AnnotationPanx3_halfmapB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Panx3 halfmapA

Fileemd_34265_half_map_2.map
AnnotationPanx3_halfmapA
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 3

EntireName: Pannexin 3
Components
  • Organelle or cellular component: Pannexin 3
    • Protein or peptide: Pannexin-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PHOSPHATIDYLETHANOLAMINE

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Supramolecule #1: Pannexin 3

SupramoleculeName: Pannexin 3 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: human isoform 3 of Pannexin. Expressed in ER and Plasma membranes involved in calcium and ATP regulation
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.68 kDa/nm

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Macromolecule #1: Pannexin-3

MacromoleculeName: Pannexin-3 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.734219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLAHTAAEY MLSDALLPDR RGPRLKGLRL ELPLDRIVKF VAVGSPLLLM SLAFAQEFSS GSPISCFSPS NFSIRQAAYV DSSCWDSLL HHKQDGPGQD KMKSLWPHKA LPYSLLALAL LMYLPVLLWQ YAAVPALSSD LLFIISELDK SYNRSIRLVQ H MLKIRQKS ...String:
MSLAHTAAEY MLSDALLPDR RGPRLKGLRL ELPLDRIVKF VAVGSPLLLM SLAFAQEFSS GSPISCFSPS NFSIRQAAYV DSSCWDSLL HHKQDGPGQD KMKSLWPHKA LPYSLLALAL LMYLPVLLWQ YAAVPALSSD LLFIISELDK SYNRSIRLVQ H MLKIRQKS SDPYVFWNEL EKARKERYFE FPLLERYLAC KQRSHSLVAT YLLRNSLLLI FTSATYLYLG HFHLDVFFQE EF SCSIKTG LLSDETHVPN LITCRLTSLS IFQIVSLSSV AIYTILVPVI IYNLTRLCRW DKRLLSVYEM LPAFDLLSRK MLG CPINDL NVILLFLRAN ISELISFSWL SVLCVLKDTT TQKHNIDTVV DFMTLLAGLE PSKPKHLTNS ACDEHP

UniProtKB: Pannexin-3

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 7 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

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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

Concentration5 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. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV / Details: blotted for 3.5 seconds.
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: 3.3000000000000003 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 130000
Specialist opticsPhase plate: OTHER / Spherical aberration corrector: None / Chromatic aberration corrector: None / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV / Details: Bioquantum with K2 camera
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 K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 1122 / Average electron dose: 48.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 411263
Startup modelType of model: OTHER / Details: AlphaFold2 model
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 34 / Avg.num./class: 926 / Software - Name: cryoSPARC / Software - details: 2D classification
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: non uniform refinement / Number images used: 31517
DetailsImages were screened for ice thickness
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 143.6 / Target criteria: Correlation coeficient
Output model

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

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