[English] 日本語
Yorodumi
- EMDB-8953: Handover mechanism of the growing pilus by the bacterial outer me... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8953
TitleHandover mechanism of the growing pilus by the bacterial outer membrane usher FimD
Map dataFimDCFGH tip complex
Sample
  • Complex: FimDCFGH tip complex
    • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin
    • Protein or peptide: Fimbrial biogenesis outer membrane usher protein
    • Protein or peptide: Protein FimF
    • Protein or peptide: Protein FimG
    • Protein or peptide: Chaperone protein FimC
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / mannose binding / host cell membrane / chaperone-mediated protein folding ...fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / mannose binding / host cell membrane / chaperone-mediated protein folding / protein folding chaperone / cell wall organization / cell outer membrane / outer membrane-bounded periplasmic space / cell adhesion
Similarity search - Function
Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. ...Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Fimbrial biogenesis outer membrane usher protein / Protein FimF / Protein FimG / Type 1 fimbrin D-mannose specific adhesin / Outer membrane usher protein FimD / Chaperone protein FimC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsDu M / Yuan Z / Yu H / Henderson N / Sarowar S / Zhao G / Werneburg GT / Thanassi DG / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM062987 United States
CitationJournal: Nature / Year: 2018
Title: Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimD.
Authors: Minge Du / Zuanning Yuan / Hongjun Yu / Nadine Henderson / Samema Sarowar / Gongpu Zhao / Glenn T Werneburg / David G Thanassi / Huilin Li /
Abstract: Pathogenic bacteria such as Escherichia coli assemble surface structures termed pili, or fimbriae, to mediate binding to host-cell receptors. Type 1 pili are assembled via the conserved chaperone- ...Pathogenic bacteria such as Escherichia coli assemble surface structures termed pili, or fimbriae, to mediate binding to host-cell receptors. Type 1 pili are assembled via the conserved chaperone-usher pathway. The outer-membrane usher FimD recruits pilus subunits bound by the chaperone FimC via the periplasmic N-terminal domain of the usher. Subunit translocation through the β-barrel channel of the usher occurs at the two C-terminal domains (which we label CTD1 and CTD2) of this protein. How the chaperone-subunit complex bound to the N-terminal domain is handed over to the C-terminal domains, as well as the timing of subunit polymerization into the growing pilus, have previously been unclear. Here we use cryo-electron microscopy to capture a pilus assembly intermediate (FimD-FimC-FimF-FimG-FimH) in a conformation in which FimD is in the process of handing over the chaperone-bound end of the growing pilus to the C-terminal domains. In this structure, FimF has already polymerized with FimG, and the N-terminal domain of FimD swings over to bind CTD2; the N-terminal domain maintains contact with FimC-FimF, while at the same time permitting access to the C-terminal domains. FimD has an intrinsically disordered N-terminal tail that precedes the N-terminal domain. This N-terminal tail folds into a helical motif upon recruiting the FimC-subunit complex, but reorganizes into a loop to bind CTD2 during handover. Because both the N-terminal and C-terminal domains of FimD are bound to the end of the growing pilus, the structure further suggests a mechanism for stabilizing the assembly intermediate to prevent the pilus fibre diffusing away during the incorporation of thousands of subunits.
History
DepositionJul 9, 2018-
Header (metadata) releaseAug 8, 2018-
Map releaseOct 17, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.047
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.047
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6e14
  • Surface level: 0.047
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8953.png

Downloads & links

-
Map

FileDownload / File: emd_8953.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFimDCFGH tip complex
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.047 / Movie #1: 0.047
Minimum - Maximum-0.25662112 - 0.45568055
Average (Standard dev.)0.0007922393 (±0.009751722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 218.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z218.000218.000218.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2570.4560.001

-
Supplemental data

-
Sample components

-
Entire : FimDCFGH tip complex

EntireName: FimDCFGH tip complex
Components
  • Complex: FimDCFGH tip complex
    • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin
    • Protein or peptide: Fimbrial biogenesis outer membrane usher protein
    • Protein or peptide: Protein FimF
    • Protein or peptide: Protein FimG
    • Protein or peptide: Chaperone protein FimC

-
Supramolecule #1: FimDCFGH tip complex

SupramoleculeName: FimDCFGH tip complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 180 KDa

-
Macromolecule #1: Type 1 fimbrin D-mannose specific adhesin

MacromoleculeName: Type 1 fimbrin D-mannose specific adhesin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 31.48826 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDYP ETITDYVTLQ RGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR TDKPWPVALY LTPVSSAGGV AIKAGSLIAV LILRQTNNYN S DDFQFVWN ...String:
MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDYP ETITDYVTLQ RGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR TDKPWPVALY LTPVSSAGGV AIKAGSLIAV LILRQTNNYN S DDFQFVWN IYANNDVVVP TGGCDVSARD VTVTLPDYPG SVPIPLTVYC AKSQNLGYYL SGTTADAGNS IFTNTASFSP AQ GVGVQLT RNGTIIPANN TVSLGAVGTS AVSLGLTANY ARTGGQVTAG NVQSIIGVTF VYQ

-
Macromolecule #2: Fimbrial biogenesis outer membrane usher protein

MacromoleculeName: Fimbrial biogenesis outer membrane usher protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 96.705109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSYLNLRLYQ RNTQCLHIRK HRLAGFFVRL FVACAFAAQA SLSSAELYFN PRFLADDPQA VADLSRFENG QELPPGTYRV DIYLNNGYM ATRDVTFNTG DSEQGIVPCL TRAQLASMGL NTASVAGMNL LADDACVPLT TMVQDATAHL DVGQQRLNLT I PQAFMSNR ...String:
MSYLNLRLYQ RNTQCLHIRK HRLAGFFVRL FVACAFAAQA SLSSAELYFN PRFLADDPQA VADLSRFENG QELPPGTYRV DIYLNNGYM ATRDVTFNTG DSEQGIVPCL TRAQLASMGL NTASVAGMNL LADDACVPLT TMVQDATAHL DVGQQRLNLT I PQAFMSNR ARGYIPPELW DPGINAGLLN YNFSGNSVQN RIGGNSHYAY LNLQSGLNIG AWRLRDNTTW SYNSSDRSSG SK NKWQHIN TWLERDIIPL RSRLTLGDGY TQGDIFDGIN FRGAQLASDD NMLPDSQRGF APVIHGIARG TAQVTIKQNG YDI YNSTVP PGPFTINDIY AAGNSGDLQV TIKEADGSTQ IFTVPYSSVP LLQREGHTRY SITAGEYRSG NAQQEKPRFF QSTL LHGLP AGWTIYGGTQ LADRYRAFNF GIGKNMGALG ALSVDMTQAN STLPDDSQHD GQSVRFLYNK SLNESGTNIQ LVGYR YSTS GYFNFADTTY SRMNGYNIET QDGVIQVKPK FTDYYNLAYN KRGKLQLTVT QQLGRTSTLY LSGSHQTYWG TSNVDE QFQ AGLNTAFEDI NWTLSYSLTK NAWQKGRDQM LALNVNIPFS HWLRSDSKSQ WRHASASYSM SHDLNGRMTN LAGVYGT LL EDNNLSYSVQ TGYAGGGDGN SGSTGYATLN YRGGYGNANI GYSHSDDIKQ LYYGVSGGVL AHANGVTLGQ PLNDTVVL V KAPGAKDAKV ENQTGVRTDW RGYAVLPYAT EYRENRVALD TNTLADNVDL DNAVANVVPT RGAIVRAEFK ARVGIKLLM TLTHNNKPLP FGAMVTSESS QSSGIVADNG QVYLSGMPLA GKVQVKWGEE ENAHCVANYQ LPPESQQQLL TQLSAECRS

-
Macromolecule #3: Protein FimF

MacromoleculeName: Protein FimF / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.379371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAADSTITIR GYVRDNGCSV AAESTNFTVD LMENAAKQFN NIGATTPVVP FRILLSPCGN AVSAVKVGFT GVADSHNANL LALENTVSA ASGLGIQLLN EQQNQIPLNA PSSALSWTTL TPGKPNTLNF YARLMATQVP VTAGHINATA TFTLEYQ

-
Macromolecule #4: Protein FimG

MacromoleculeName: Protein FimG / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.190834 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAAILALASA TIQAADVTIT VNGKVVAKPC TVSTTNATVD LGDLYSFSLM SAGAASAWHD VALELTNCPV GTSRVTASFS GAADSTGYY KNQGTAQNIQ LELQDDSGNT LNTGATKTVQ VDDSSQSAHF PLQVRALTVN GGATQGTIQA VISITYTYS

-
Macromolecule #5: Chaperone protein FimC

MacromoleculeName: Chaperone protein FimC / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.716869 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNKNVNVRK SQEITFCLLA GILMFMAMMV AGRAEAGVAL GATRVIYPAG QKQEQLAVTN NDENSTYLIQ SWVENADGVK DGRFIVTPP LFAMKGKKEN TLRILDATNN QLPQDRESLF WMNVKAIPSM DKSKLTENTL QLAIISRIKL YYRPAKLALP P DQAAEKLR ...String:
MSNKNVNVRK SQEITFCLLA GILMFMAMMV AGRAEAGVAL GATRVIYPAG QKQEQLAVTN NDENSTYLIQ SWVENADGVK DGRFIVTPP LFAMKGKKEN TLRILDATNN QLPQDRESLF WMNVKAIPSM DKSKLTENTL QLAIISRIKL YYRPAKLALP P DQAAEKLR FRRSANSLTL INPTPYYLTV TELNAGTRVL ENALVPPMGE STVKLPSDAG SNITYRTIND YGALTPKMTG VM E

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 250370

+
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