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Yorodumi- EMDB-20115: CryoEM structure of PilT4 from Geobacter metallireducens without ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20115 | |||||||||
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Title | CryoEM structure of PilT4 from Geobacter metallireducens without adding nucleotide: C3ocococ conformation | |||||||||
Map data | PilT4 from Geobacter metallireducens | |||||||||
Sample |
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Keywords | ATPase / T4P / type iv pilus / motor / MOTOR PROTEIN | |||||||||
Function / homology | Pilus retraction protein PilT/PilU / : / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / P-loop containing nucleoside triphosphate hydrolase / ATP binding / metal ion binding / Twitching motility pilus retraction ATPase Function and homology information | |||||||||
Biological species | Geobacter metallireducens (bacteria) / Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | McCallum M / Howell PL | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Multiple conformations facilitate PilT function in the type IV pilus. Authors: Matthew McCallum / Samir Benlekbir / Sheryl Nguyen / Stephanie Tammam / John L Rubinstein / Lori L Burrows / P Lynne Howell / Abstract: Type IV pilus-like systems are protein complexes that polymerize pilin fibres. They are critical for virulence in many bacterial pathogens. Pilin polymerization and depolymerization are powered by ...Type IV pilus-like systems are protein complexes that polymerize pilin fibres. They are critical for virulence in many bacterial pathogens. Pilin polymerization and depolymerization are powered by motor ATPases of the PilT/VirB11-like family. This family is thought to operate with C symmetry; however, most of these ATPases crystallize with either C or C symmetric conformations. The relevance of these conformations is unclear. Here, we determine the X-ray structures of PilT in four unique conformations and use these structures to classify the conformation of available PilT/VirB11-like family member structures. Single particle electron cryomicroscopy (cryoEM) structures of PilT reveal condition-dependent preferences for C C, and C conformations. The physiologic importance of these conformations is validated by coevolution analysis and functional studies of point mutants, identifying a rare gain-of-function mutation that favours the C conformation. With these data, we propose a comprehensive model of PilT function with broad implications for PilT/VirB11-like family members. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20115.map.gz | 3.2 MB | EMDB map data format | |
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Header (meta data) | emd-20115-v30.xml emd-20115.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20115_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_20115.png | 51.8 KB | ||
Filedesc metadata | emd-20115.cif.gz | 5.5 KB | ||
Others | emd_20115_additional.map.gz | 31.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20115 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20115 | HTTPS FTP |
-Validation report
Summary document | emd_20115_validation.pdf.gz | 387.5 KB | Display | EMDB validaton report |
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Full document | emd_20115_full_validation.pdf.gz | 387 KB | Display | |
Data in XML | emd_20115_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | emd_20115_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20115 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20115 | HTTPS FTP |
-Related structure data
Related structure data | 6olkMC 6ojxC 6ojyC 6ojzC 6ok2C 6okvC 6oljC 6ollC 6olmC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20115.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PilT4 from Geobacter metallireducens | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: PilT4 from Geobacter metallireducens
File | emd_20115_additional.map | ||||||||||||
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Annotation | PilT4 from Geobacter metallireducens | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PilT Hexamer
Entire | Name: PilT Hexamer |
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Components |
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-Supramolecule #1: PilT Hexamer
Supramolecule | Name: PilT Hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Geobacter metallireducens (bacteria) |
-Macromolecule #1: Twitching motility pilus retraction ATPase
Macromolecule | Name: Twitching motility pilus retraction ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria) Strain: GS-15 / ATCC 53774 / DSM 7210 |
Molecular weight | Theoretical: 42.883379 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MANMHQLLTE LVNRGGSDLH LTTNSPPQIR IDGKLLPLDM PPLNAVDTKQ LCYSILTEQQ KHKFEENNE LDLSFGIKGL SRFRGNVFVQ RGAVAGVFRV IPYKILSFEE LGLPPVVREL AEKPRGLVLV TGPTGSGKST T LAAIIDKI ...String: MGSSHHHHHH SSGLVPRGSH MANMHQLLTE LVNRGGSDLH LTTNSPPQIR IDGKLLPLDM PPLNAVDTKQ LCYSILTEQQ KHKFEENNE LDLSFGIKGL SRFRGNVFVQ RGAVAGVFRV IPYKILSFEE LGLPPVVREL AEKPRGLVLV TGPTGSGKST T LAAIIDKI NTDRHEHIVT VEDPIEYLHP HKSCVVNQRE VGADTKSFKN ALKYILRQDP DVVLVGELRD LETIEAALTL AE TGHLCFA TLHTNSAVQT INRIVDVFPS YQQPQVRAQL SFVLEGVLSQ TLLPKASGTG RVLAIEVMVP NPAIRNLIRE DKI HQIYSQ MQVGQEKFGM MTMNQCLYGL LQKRHITMDV GMGRSPDPDE LKQMLTSGVR PQAPRPPMR UniProtKB: Twitching motility pilus retraction ATPase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Homemade / Material: GOLD |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 42.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Initial fitting in chimera, flexible fitting in Phenix-refine |
Refinement | Protocol: FLEXIBLE FIT / Overall B value: 16.5 |
Output model | PDB-6olk: |