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Yorodumi- EMDB-34377: Cryo-EM structure of human Pannexin-3 R36S/F40R variant in pre-op... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34377 | |||||||||
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Title | Cryo-EM structure of human Pannexin-3 R36S/F40R variant in pre-open state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Pannexin / ATP / Inner channel lipids / Cell-cell communication / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.68 Å | |||||||||
Authors | Cong Y / Jin X / Kong F / Wu T / Yan C | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Inner channel lipids regulated gating mechanism of human pannexins. Authors: Cong Y / Jin X / Kong F / Wu T / Yan C | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34377.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-34377-v30.xml emd-34377.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_34377.png | 208.7 KB | ||
Masks | emd_34377_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-34377.cif.gz | 5.3 KB | ||
Others | emd_34377_half_map_1.map.gz emd_34377_half_map_2.map.gz | 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34377 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34377 | HTTPS FTP |
-Related structure data
Related structure data | 8gytMC 8gyoC 8gypC 8gyqC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34377.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.843 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34377_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34377_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34377_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pannexin-3 R36S/F40R
Entire | Name: Pannexin-3 R36S/F40R |
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Components |
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-Supramolecule #1: Pannexin-3 R36S/F40R
Supramolecule | Name: Pannexin-3 R36S/F40R / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 350 KDa |
-Macromolecule #1: Pannexin-3
Macromolecule | Name: Pannexin-3 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.674121 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSLAHTAAEY MLSDALLPDR RGPRLKGLRL ELPLDSIVKR VAVGSPLLLM SLAFAQEFSS GSPISCFSPS NFSIRQAAYV DSSCWDSLL HHKQDGPGQD KMKSLWPHKA LPYSLLALAL LMYLPVLLWQ YAAVPALSSD LLFIISELDK SYNRSIRLVQ H MLKIRQKS ...String: MSLAHTAAEY MLSDALLPDR RGPRLKGLRL ELPLDSIVKR 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 |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 7 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.8 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 91298 |