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Yorodumi- EMDB-20114: CryoEM structure of PilB from Geobacter metallireducens: C2ccocco... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20114 | |||||||||
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Title | CryoEM structure of PilB from Geobacter metallireducens: C2ccocco conformation | |||||||||
Map data | Sharpened and z-flipped map | |||||||||
Sample |
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Keywords | ATPase / T4P / type iv pilus / motor / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information pilus assembly / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Geobacter metallireducens (bacteria) / Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.8 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_20114.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-20114-v30.xml emd-20114.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20114_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_20114.png | 91.6 KB | ||
Others | emd_20114_additional.map.gz | 31.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20114 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20114 | HTTPS FTP |
-Validation report
Summary document | emd_20114_validation.pdf.gz | 531.4 KB | Display | EMDB validaton report |
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Full document | emd_20114_full_validation.pdf.gz | 530.9 KB | Display | |
Data in XML | emd_20114_validation.xml.gz | 11 KB | Display | |
Data in CIF | emd_20114_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20114 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20114 | HTTPS FTP |
-Related structure data
Related structure data | 6oljMC 6ojxC 6ojyC 6ojzC 6ok2C 6okvC 6olkC 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_20114.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened and z-flipped map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Original unsharpened and unflipped map
File | emd_20114_additional.map | ||||||||||||
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Annotation | Original unsharpened and unflipped map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PilB Hexamer
Entire | Name: PilB Hexamer |
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Components |
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-Supramolecule #1: PilB Hexamer
Supramolecule | Name: PilB Hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Geobacter metallireducens (bacteria) |
-Macromolecule #1: Type IV pilus biogenesis ATPase PilB
Macromolecule | Name: Type IV pilus biogenesis ATPase PilB / 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: 64.899281 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MQASRLGELL VRNNVITKEQ LAKALEEQKS ADGQQRLGSI LIKNGLISEP DLTSFLSKQY GVPSINLSE FEAEQAVVKI IPADVAQKYQ IVPVNRAGST LIIAMADPSN IFAIDDIKFM TGYNVEVVVA SESAIKAAID K YYDQSASL ...String: MGSSHHHHHH SSGLVPRGSH MQASRLGELL VRNNVITKEQ LAKALEEQKS ADGQQRLGSI LIKNGLISEP DLTSFLSKQY GVPSINLSE FEAEQAVVKI IPADVAQKYQ IVPVNRAGST LIIAMADPSN IFAIDDIKFM TGYNVEVVVA SESAIKAAID K YYDQSASL ADVMGDLEMD DLEVIDTDDE VDVSSLERAT EDAPVVKLVN LILTDAIKRK ASDIHIEPYE RSFRVRYRID GV LYEVMKP PLKLKNAITS RIKIMAELDI AERRLPQDGR IKIKLGGGQD MDYRVSVLPT LFGEKVVLRL LDKSNLQLDM TKL GYEPDA LHYFKEAIHK PFGMVLVTGP TGSGKTVSLY SALGELNKTT ENISTAEDPV EFNFAGINQV QMHEDIGLNF AAAL RSFLR QDPDIIMIGE IRDFETAEIA IKAALTGHLV LSTLHTNDAP ATINRLLNMG VEPFLVASAV NLITAQRLAR RVCSE CKQP EEIPIQALID AGVSPDEAPS YVCYKGTGCV KCNNTGYKGR VGFYQVMPML EEIRELILNG ANTAEIKRES MRLGIK TMR QSGLTKLKEG VTSFEEVLRV TVADD UniProtKB: Type IV pilus biogenesis ATPase PilB |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Homemade / Material: GOLD |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.7 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |