[English] 日本語
Yorodumi
- EMDB-20116: CryoEM structure of PilT4 from Geobacter metallireducens without ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20116
TitleCryoEM structure of PilT4 from Geobacter metallireducens without adding nucleotide: C2oocooc conformation
Map dataSharpened and z-flipped map
Sample
  • Complex: PilT Hexamer
    • Protein or peptide: Twitching motility pilus retraction ATPase
KeywordsATPase / T4P / type iv pilus / motor / MOTOR PROTEIN
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
Twitching motility pilus retraction ATPase
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria) / Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsMcCallum M / Howell PL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: 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
DepositionApr 16, 2019-
Header (metadata) releaseJun 5, 2019-
Map releaseNov 20, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.41
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.41
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6oll
  • Surface level: 0.41
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20116.png

Downloads & links

-
Map

FileDownload / File: emd_20116.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened and z-flipped map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.41 / Movie #1: 0.41
Minimum - Maximum-1.9166515 - 2.2735968
Average (Standard dev.)0.004868001 (±0.07380414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.360271.360271.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.9172.2740.005

-
Supplemental data

-
Additional map: Original unsharpened and unflipped map

Fileemd_20116_additional.map
AnnotationOriginal unsharpened and unflipped map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PilT Hexamer

EntireName: PilT Hexamer
Components
  • Complex: PilT Hexamer
    • Protein or peptide: Twitching motility pilus retraction ATPase

-
Supramolecule #1: PilT Hexamer

SupramoleculeName: PilT Hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Geobacter metallireducens (bacteria)

-
Macromolecule #1: Twitching motility pilus retraction ATPase

MacromoleculeName: Twitching motility pilus retraction ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Strain: GS-15 / ATCC 53774 / DSM 7210
Molecular weightTheoretical: 42.883379 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
GridModel: Homemade / Material: GOLD
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 42.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsFalcon 3EC
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ojx

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 100786
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6ojx


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial fitting in chimera, flexible fitting in Phenix-refine
RefinementProtocol: FLEXIBLE FIT / Overall B value: 38.4
Output model

PDB-6oll:
CryoEM structure of PilT4 from Geobacter metallireducens without adding nucleotide: C2oocooc conformation

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more