[English] 日本語
Yorodumi
- EMDB-12716: Trimer of dimers TrwK/VirB4unbound C1 at 4.14A - Refinement witho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12716
TitleTrimer of dimers TrwK/VirB4unbound C1 at 4.14A - Refinement without symmetry of TrwK/VirB4unbound trimer of dimers complex (with Hcp1) from the R388 type IV secretion system.
Map dataTrwK/VirB4unbound trimer of dimer with HCP without symmetry sharpened map
Sample
  • Complex: Hexameric complex of Apo-TrwK/VirB4 with Hcp1
    • Protein or peptide: TrwK protein,Protein hcp1
Keywordstype IV secretion system / type 4 secretion system / T4SS / inner membrane complex / inner membrane / R388 plasmid / conjugation / ATPase / bacterial secretion / secretion / secretion system / protein complex / VirB4 / TrwK / Hcp / MEMBRANE PROTEIN
Function / homology
Function and homology information


extracellular region / ATP binding / identical protein binding
Similarity search - Function
CagE, TrbE, VirB component of type IV transporter system, central domain / CagE, TrbE, VirB family, component of type IV transporter system / CagE, TrbE, VirB component of type IV transporter system / TraG, P-loop domain / TraG P-loop domain / : / : / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type IV secretion system protein virB4 / Protein hcp1
Similarity search - Component
Biological speciesSalmonella dublin (bacteria) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsVadakkepat AK / Mace K
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust098302 United Kingdom
Wellcome Trust217089 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Nature / Year: 2022
Title: Cryo-EM structure of a type IV secretion system.
Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong ...Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong / Gabriel Waksman /
Abstract: Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance ...Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance genes spread among bacterial populations. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus-the conjugative type IV secretion system (T4SS)-produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament-the conjugative pilus-that is essential for DNA transfer. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein-protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili.
History
DepositionApr 4, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_12716.png

Downloads & links

-
Map

FileDownload / File: emd_12716.map.gz / Format: CCP4 / Size: 25 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTrwK/VirB4unbound trimer of dimer with HCP without symmetry sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 168 pix.
= 176.064 Å		1.05 Å/pix.
x 201 pix.
= 210.648 Å		1.05 Å/pix.
x 194 pix.
= 203.312 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.5012352 - 1.1692141
Average (Standard dev.)0.022396069 (±0.11088646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin635761
Dimensions201194168
Spacing168201194
CellA: 176.064 Å / B: 210.648 Å / C: 203.312 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: TrwK/VirB4unbound trimer of dimer with HCP without symmetry...

Fileemd_12716_additional_1.map
AnnotationTrwK/VirB4unbound trimer of dimer with HCP without symmetry unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: TrwK/VirB4unbound trimer of dimer - Half-A

Fileemd_12716_half_map_1.map
AnnotationTrwK/VirB4unbound trimer of dimer - Half-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: TrwK/VirB4unbound trimer of dimer - Half-A

Fileemd_12716_half_map_2.map
AnnotationTrwK/VirB4unbound trimer of dimer - Half-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Hexameric complex of Apo-TrwK/VirB4 with Hcp1

EntireName: Hexameric complex of Apo-TrwK/VirB4 with Hcp1
Components
  • Complex: Hexameric complex of Apo-TrwK/VirB4 with Hcp1
    • Protein or peptide: TrwK protein,Protein hcp1

-
Supramolecule #1: Hexameric complex of Apo-TrwK/VirB4 with Hcp1

SupramoleculeName: Hexameric complex of Apo-TrwK/VirB4 with Hcp1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella dublin (bacteria)

-
Macromolecule #1: TrwK protein,Protein hcp1

MacromoleculeName: TrwK protein,Protein hcp1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Molecular weightTheoretical: 111.487844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGAIESRKLL ASETPVGQFI PYSHHVTDTI ISTKNAEYLS VWKIDGRSHQ SASEADVFQW IRELNNTLRG ISSANLSLWT HIVRRRVYE YPDAEFDNVF CRQLDEKYRE SFTGYNLMVN DLYLTVVYRP VSDKVLSFFA KRERETPDQK KHRQESCIKA L EDINRTLG ...String:
MGAIESRKLL ASETPVGQFI PYSHHVTDTI ISTKNAEYLS VWKIDGRSHQ SASEADVFQW IRELNNTLRG ISSANLSLWT HIVRRRVYE YPDAEFDNVF CRQLDEKYRE SFTGYNLMVN DLYLTVVYRP VSDKVLSFFA KRERETPDQK KHRQESCIKA L EDINRTLG QSFKRYGAEL LSVYEKGGHA FSAPLEFLAR LVNGEHIPMP ICRDRFSDYM AVNRPMFSKW GEVGELRSLT GL RRFGMLE IREYDDATEP GQLNVLLESD YEFVLTHSFS VLSRPAAKEY LQRHQKNLID ARDVATDQIE EIDEALNQLI SGH FVMGEH HCTLTVYGET VQQVRDNLAH ASAAMLDVAV LPKPVDLALE AGYWAQLPAN WQWRPRPAPI TSLNFLSFSP FHNF MSGKP TGNPWGPAVT ILKTVSGTPL YFNFHASKEE EDATDKRLLG NTMLIGQSSS GKTVLLGFLL AQAQKFKPTI VAFDK DRGM EISIRAMGGR YLPLKTGEPS GFNPFQLPPT HANLIFLKQF VKKLAAAGGE VTHRDEEEID QAITAMMSDS IDKSLR RLS LLLQFLPNPR SDDMDARPTV HARLVKWCEG GDYGWLFDNP TDALDLSTHQ IYGFDITEFL DNPEARTPVM MYLLYRT ES MIDGRRFMYV FDEFWKPLQD EYFEDLAKNK QKTIRKQNGI FVFATQEPSD ALESNIAKTL IQQCATYIFL ANPKADYE D YTQGFKLTDS EFELVRGLGE FSRRFLIKQG DQSALAEMNL GKFRTIVDGE TVERDFDDEL LVLSGTPDNA EIAESIIAE VGDDPAVWLP IFLDRVKAER SDVGSGSGSA VDMFIKIGDV KGESKDKTHA EEIDVLAWSW GMSQSGSMHM GGGGGAGKVN VQDLSFTKY IDKSTPNLMM ACSSGKHYPQ AKLTIRKAGG ENQVEYLIIT LKEVLVSSVS TGGSGGEDRL TENVTLNFAQ V QVDYQPQK ADGAKDGGPV KYGWNIRQNV QA

UniProtKB: Type IV secretion system protein virB4, Protein hcp1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: CryoSPARC ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 214048
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER / Details: Stochastic gradient descent (SGD)

+
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