+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3985 | |||||||||
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Title | PilQ from Thermus thermophilus | |||||||||
Map data | None | |||||||||
Sample |
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Biological species | Thermus thermophilus HB27 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.4 Å | |||||||||
Authors | D'Imprima E / Vonck J / Sanchez R | |||||||||
Citation | Journal: Elife / Year: 2017 Title: Cryo-EM structure of the bifunctional secretin complex of . Authors: Edoardo D'Imprima / Ralf Salzer / Ramachandra M Bhaskara / Ricardo Sánchez / Ilona Rose / Lennart Kirchner / Gerhard Hummer / Werner Kühlbrandt / Janet Vonck / Beate Averhoff / Abstract: Secretins form multimeric channels across the outer membrane of Gram-negative bacteria that mediate the import or export of substrates and/or extrusion of type IV pili. The secretin complex of is an ...Secretins form multimeric channels across the outer membrane of Gram-negative bacteria that mediate the import or export of substrates and/or extrusion of type IV pili. The secretin complex of is an oligomer of the 757-residue PilQ protein, essential for DNA uptake and pilus extrusion. Here, we present the cryo-EM structure of this bifunctional complex at a resolution of ~7 Å using a new reconstruction protocol. Thirteen protomers form a large periplasmic domain of six stacked rings and a secretin domain in the outer membrane. A homology model of the PilQ protein was fitted into the cryo-EM map. A crown-like structure outside the outer membrane capping the secretin was found not to be part of PilQ. Mutations in the secretin domain disrupted the crown and abolished DNA uptake, suggesting a central role of the crown in natural transformation. | |||||||||
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_3985.map.gz | 11.6 MB | EMDB map data format | |
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Header (meta data) | emd-3985-v30.xml emd-3985.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_3985.png | 38.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3985 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3985 | HTTPS FTP |
-Validation report
Summary document | emd_3985_validation.pdf.gz | 203.8 KB | Display | EMDB validaton report |
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Full document | emd_3985_full_validation.pdf.gz | 202.9 KB | Display | |
Data in XML | emd_3985_validation.xml.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3985 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3985 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3985.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.63 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PilQ complex with 13-fold symmetry
Entire | Name: PilQ complex with 13-fold symmetry |
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Components |
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-Supramolecule #1: PilQ complex with 13-fold symmetry
Supramolecule | Name: PilQ complex with 13-fold symmetry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Thermus thermophilus HB27 (bacteria) |
Molecular weight | Theoretical: 1 MDa |
-Macromolecule #1: PilQ
Macromolecule | Name: PilQ / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermus thermophilus HB27 (bacteria) |
Sequence | String: MKSAWIRAAV IALAGLGAFA LAGSFPEEPR FQAPVNLKVS ESQVKAGQTL PLDVVLEALA RSVGLQPLI YRAYDPSGDP ATAQPPLPNV KLDFQGKPFR EVWDLLFATY GNQYSLDYLF L PPDVVVVA PTQVITALVD APSRTGAMER RPYIVGVPEI AYKRTETDAQ ...String: MKSAWIRAAV IALAGLGAFA LAGSFPEEPR FQAPVNLKVS ESQVKAGQTL PLDVVLEALA RSVGLQPLI YRAYDPSGDP ATAQPPLPNV KLDFQGKPFR EVWDLLFATY GNQYSLDYLF L PPDVVVVA PTQVITALVD APSRTGAMER RPYIVGVPEI AYKRTETDAQ GQPRTVVNIE GA KAWVQND LLPFLSREAA GLNVNWIVVE EGGRLKAVLS VLATPEQHAR FSDILQRAGI DFR PLPALA QPKPRVEKTY TLTYATFPDL LAFLQSRLPE AQIGVVPTNP QRAIVLATEE DHAR LSELL KTADVPKTVR RVYTLQNLTF AEAQERLKPL LEKDLKGARL ESLPGNPKAL LLEAP EAEH ALFAEILKAL DVPPQAPQAP QEATLRRLYP LHYANAEQVA PFLAREVPGI VVQTVP GQP LLSVRGTEAQ LREVESLLAQ IDRPPEQGPP VFQRAYQLSN AKAVELAQVL QEALKAR QA QNQGQQNQAP PTREATVVAD PRTNTLIVTG TQEDLALVEG LIPKLDQPVP QVNLRVRI Q EVQSNLTRSL GLKWNSIAGG NVAASILDSG LSLIFDSTRS LAALNIMATL DALQQQGLS RALRDVNQTV LNNQTARLQS GETFFIRRVV NDQVERVPFD VGLIVEVTPQ ITADGQILLN IKAEVSGNV QRNPVDGDVD RFTKQVVTTT LRVKDGETVV LGGLTSQESN QSQQGVPLLM D IPLIGELF KQRTNESTDK ELLVVITADI LKEAASANP |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blotting for 8-10 seconds. |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Lower energy threshold: 18 eV / Energy filter - Upper energy threshold: 18 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-45 / Average exposure time: 9.0 sec. / Average electron dose: 33.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 30675 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm / Nominal magnification: 20000 |
Sample stage | Specimen holder model: JEOL / Cooling holder cryogen: NITROGEN |