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- EMDB-20117: CryoEM structure of PilT4 from Geobacter metallireducens with add... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20117 | |||||||||
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Title | CryoEM structure of PilT4 from Geobacter metallireducens with added ATP: C6cccccc conformation | |||||||||
![]() | Sharpened map | |||||||||
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![]() | 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![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
![]() | McCallum M / Howell PL | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.4 KB 13.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 106.4 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() | 31.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6olmMC ![]() 6ojxC ![]() 6ojyC ![]() 6ojzC ![]() 6ok2C ![]() 6okvC ![]() 6oljC ![]() 6olkC ![]() 6ollC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Sharpened 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 map
File | emd_20117_additional.map | ||||||||||||
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Annotation | Original unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
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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: #1 |
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Source (natural) | Organism: ![]() |
-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: ![]() Strain: GS-15 / ATCC 53774 / DSM 7210 |
Molecular weight | Theoretical: 42.883379 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Homemade / Material: GOLD |
Vitrification | Cryogen name: ETHANE-PROPANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
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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: 68.8 |
Output model | ![]() PDB-6olm: |