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Yorodumi- PDB-8wlt: Cryo-EM structure of the membrane-anchored part of the flagellar ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wlt | ||||||||||||
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Title | Cryo-EM structure of the membrane-anchored part of the flagellar motor-hook complex in the CCW state | ||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Flagellar motor / Flagellum | ||||||||||||
Function / homology | Function and homology information bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity ...bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / protein secretion / protein targeting / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Tan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the membrane-anchored part of the flagellar motor-hook complex in the CCW state Authors: Tan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wlt.cif.gz | 8.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8wlt.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8wlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wlt_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 8wlt_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 8wlt_validation.xml.gz | 950.9 KB | Display | |
Data in CIF | 8wlt_validation.cif.gz | 1.4 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/8wlt ftp://data.pdbj.org/pub/pdb/validation_reports/wl/8wlt | HTTPS FTP |
-Related structure data
Related structure data | 37630MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 6 types, 168 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
#1: Protein | Mass: 24726.666 Da / Num. of mol.: 26 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P0A1N8 #2: Protein | Mass: 38194.176 Da / Num. of mol.: 26 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P15930 #4: Protein | Mass: 42233.152 Da / Num. of mol.: 29 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P0A1J1 #6: Protein | Mass: 61295.645 Da / Num. of mol.: 76 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P15928 #10: Protein | Mass: 11087.662 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P26462 #11: Protein | Mass: 15145.061 Da / Num. of mol.: 5 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P16437 |
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-Flagellar basal-body rod protein ... , 3 types, 35 molecules 0123456789ZAZBZCZDZEAFAGAHAIAJAKALAMANAAABACADAEBA...
#3: Protein | Mass: 27784.807 Da / Num. of mol.: 24 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P0A1J3 #5: Protein | Mass: 26121.223 Da / Num. of mol.: 5 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P16323 #12: Protein | Mass: 13991.889 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P0A1I7 |
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-Flagellar biosynthetic protein ... , 3 types, 10 molecules AbAqArAsAtAuAvAwAxAy
#7: Protein | Mass: 9606.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P0A1L5 #8: Protein | | Mass: 28938.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P54702 #9: Protein | Mass: 26801.086 Da / Num. of mol.: 5 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P54700 |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: C ring-containing flagellar motor-hook complex in the CCW state Type: COMPLEX / Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: Blot time: 2 Blot force: -15 Wait time: 60 Blot total: 1 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 22192 / Details: Particles were manually picked using cryoSPARC | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11858 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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