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- EMDB-19488: Stalk-Arches-IMC at 4.33A - Refinement without symmetry of the St... -

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Basic information

Entry
Database: EMDB / ID: EMD-19488
TitleStalk-Arches-IMC at 4.33A - Refinement without symmetry of the Stalk-Arches-IMC from the fully-assembled R388 type IV secretion.
Map dataSTALK-ARCHES-IMC _ Unsharpened
Sample
  • Complex: Stalk-Arches-IMC complex from the fully-assembled R388 type IV secretion system
    • Protein or peptide: TrwJ protein
    • Protein or peptide: TrwG protein
    • Protein or peptide: TrwE protein
    • Protein or peptide: TrwI protein
    • Protein or peptide: TrwM protein
    • Protein or peptide: Type IV secretion system protein virB4
Keywordstype IV secretion system type 4 secretion system T4SS Arches Stalk inner membrane complex IMC R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB3 VirB4 VirB5 VirB6 VirB8 VirB10 TrwM TrwK TrwJ TrwI TrwG TrwE / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein secretion by the type IV secretion system / ATP binding / membrane / plasma membrane
Similarity search - Function
Type IV secretion system, VirB5 / Type IV secretion system, VirB5-domain / Type IV secretion system proteins / Plasmid conjugal transfer TrbL/VirB6 / Type IV secretion system, VirB3 / TrbD / AvhB / TrbL/VirB6 plasmid conjugal transfer protein / Type IV secretory pathway, VirB3-like protein / 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 ...Type IV secretion system, VirB5 / Type IV secretion system, VirB5-domain / Type IV secretion system proteins / Plasmid conjugal transfer TrbL/VirB6 / Type IV secretion system, VirB3 / TrbD / AvhB / TrbL/VirB6 plasmid conjugal transfer protein / Type IV secretory pathway, VirB3-like protein / 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 IV secretion system protein VirB8/PtlE / : / Bacterial virulence protein VirB8 / VirB8 protein / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / NTF2-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TrwM protein / Type IV secretion system protein virB4 / TrwJ protein / TrwI protein / TrwG protein / TrwE protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.33 Å
AuthorsMace K / Waksman G
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: EMBO J / Year: 2024
Title: Cryo-EM structure of a conjugative type IV secretion system suggests a molecular switch regulating pilus biogenesis.
Authors: Kévin Macé / Gabriel Waksman /
Abstract: Conjugative type IV secretion systems (T4SS) mediate bacterial conjugation, a process that enables the unidirectional exchange of genetic materials between a donor and a recipient bacterial cell. ...Conjugative type IV secretion systems (T4SS) mediate bacterial conjugation, a process that enables the unidirectional exchange of genetic materials between a donor and a recipient bacterial cell. Bacterial conjugation is the primary means by which antibiotic resistance genes spread among bacterial populations (Barlow 2009; Virolle et al, 2020). Conjugative T4SSs form pili: long extracellular filaments that connect with recipient cells. Previously, we solved the cryo-electron microscopy (cryo-EM) structure of a conjugative T4SS. In this article, based on additional data, we present a more complete T4SS cryo-EM structure than that published earlier. Novel structural features include details of the mismatch symmetry within the OMCC, the presence of a fourth VirB8 subunit in the asymmetric unit of both the arches and the inner membrane complex (IMC), and a hydrophobic VirB5 tip in the distal end of the stalk. Additionally, we provide previously undescribed structural insights into the protein VirB10 and identify a novel regulation mechanism of T4SS-mediated pilus biogenesis by this protein, that we believe is a key checkpoint for this process.
History
DepositionJan 25, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19488.png

Downloads & links

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Map

FileDownload / File: emd_19488.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSTALK-ARCHES-IMC _ Unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 546.304 Å		1.07 Å/pix.
x 512 pix.
= 546.304 Å		1.07 Å/pix.
x 512 pix.
= 546.304 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-0.71761763 - 1.9973441
Average (Standard dev.)0.027171923 (±0.09129263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 546.304 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19488_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: STALK-ARCHES-IMC Sharpened-deepEMhancer

Fileemd_19488_additional_1.map
AnnotationSTALK-ARCHES-IMC _ Sharpened-deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-B

Fileemd_19488_half_map_1.map
AnnotationHalf-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-A

Fileemd_19488_half_map_2.map
AnnotationHalf-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Stalk-Arches-IMC complex from the fully-assembled R388 type IV se...

EntireName: Stalk-Arches-IMC complex from the fully-assembled R388 type IV secretion system
Components
  • Complex: Stalk-Arches-IMC complex from the fully-assembled R388 type IV secretion system
    • Protein or peptide: TrwJ protein
    • Protein or peptide: TrwG protein
    • Protein or peptide: TrwE protein
    • Protein or peptide: TrwI protein
    • Protein or peptide: TrwM protein
    • Protein or peptide: Type IV secretion system protein virB4

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Supramolecule #1: Stalk-Arches-IMC complex from the fully-assembled R388 type IV se...

SupramoleculeName: Stalk-Arches-IMC complex from the fully-assembled R388 type IV secretion system
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: TrwJ protein

MacromoleculeName: TrwJ protein / type: protein_or_peptide / ID: 1 / Details: Sequence from conjugative plasmid R388 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.190461 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKLVMTAAV AAILGAASPV MAQGIPVFDG TRALDFVQQF ARMKEQLDTA KDQLAEAQRM YEAVTGGRGL GDLMRNAQLR EYLPDDLRT VYDSANGGGY SGISGSINDI LRDERLNGSV ADMRRSIEER SRTAAATDKA VGLRAYEGAQ QRLAQIEGLM D EISRTQDQ ...String:
MKKLVMTAAV AAILGAASPV MAQGIPVFDG TRALDFVQQF ARMKEQLDTA KDQLAEAQRM YEAVTGGRGL GDLMRNAQLR EYLPDDLRT VYDSANGGGY SGISGSINDI LRDERLNGSV ADMRRSIEER SRTAAATDKA VGLRAYEGAQ QRLAQIEGLM D EISRTQDQ KAIEELQARI AGEQAAIQNE TTKLQMIAQL RQAEQALISE QRRERNMRIL SSGNQGMPTI Q

UniProtKB: TrwJ protein

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Macromolecule #2: TrwG protein

MacromoleculeName: TrwG protein / type: protein_or_peptide / ID: 2 / Details: Sequence from conjugative plasmid R388 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.799994 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKKQPKPVK AEQLKSYYEE SRGLERDLIG EFVKSRKTAW RVATASGLFG LLGMVCGIVG FSQPAPAPLV LRVDNATGAV DVVTTLREH ESSYGEVVDT YWLNQYVLNR EAYDYNTIQM NYDTTALLSA PAVQQDYYKL FDGSNARDRV LGNKARITVR V RSIQPNGR ...String:
MSKKQPKPVK AEQLKSYYEE SRGLERDLIG EFVKSRKTAW RVATASGLFG LLGMVCGIVG FSQPAPAPLV LRVDNATGAV DVVTTLREH ESSYGEVVDT YWLNQYVLNR EAYDYNTIQM NYDTTALLSA PAVQQDYYKL FDGSNARDRV LGNKARITVR V RSIQPNGR GQATVRFTTQ QHNSNGTVEA PQHQIATIGY TYIGAPMRSS DRLLNPLGFQ VTSYRADPEI LNN

UniProtKB: TrwG protein

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Macromolecule #3: TrwE protein

MacromoleculeName: TrwE protein / type: protein_or_peptide / ID: 3 / Details: Sequence from conjugative plasmid R388 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42.443785 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFGRKKGDVI DAGAELERAE QERIEGEYGA SELASERRPH TPGARTLLMV LLCVIAVVLV TLSYKAYKVR GVVEDDDAQP QQVVRQVIP GYTPRPIRPE PENVPEPPQP TTSVPAIQPA PVTQPVRPQP TGPREKTPYE LARERMLRSG LTAGSGGGED L PRPQGGDV ...String:
MFGRKKGDVI DAGAELERAE QERIEGEYGA SELASERRPH TPGARTLLMV LLCVIAVVLV TLSYKAYKVR GVVEDDDAQP QQVVRQVIP GYTPRPIRPE PENVPEPPQP TTSVPAIQPA PVTQPVRPQP TGPREKTPYE LARERMLRSG LTAGSGGGED L PRPQGGDV PAGGLMGGGG GGGELAEKLQ PMRLSGSSAG RLGNRDMLIT QGTQLDCVLE TRLVTTQPGM TTCHLTRDVY ST SGRVVLL DRGSKVVGFY QGGLRQGQAR IFVQWSRIET PSGVVINLDS PGTGPLGEAG LGGWIDRHFW ERFGGAIMIS LIG DLGDWA SRQGSRQGDN SIQFSNTANG VESAAAEALR NSINIPPTLY KNQGERVNIL VARDLDFSDV YSLESIPTK

UniProtKB: TrwE protein

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Macromolecule #4: TrwI protein

MacromoleculeName: TrwI protein / type: protein_or_peptide / ID: 4 / Details: Sequence from conjugative plasmid R388 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 35.324172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAFELFTPLF NKIDQTTATY VTDISSRAIA AITPVVSVGL TLGFITYGWL IIRGAVEMPV AEFLNRCLRI GIIVSIALAG GLYQGEIAN AITTVPDELA SALLGNPTQG ASAAALVDQS AQQGFDRASE AFEEAGFFSS DGLLYGLFGI IILLATGLLA A IGGAFLLL ...String:
MAFELFTPLF NKIDQTTATY VTDISSRAIA AITPVVSVGL TLGFITYGWL IIRGAVEMPV AEFLNRCLRI GIIVSIALAG GLYQGEIAN AITTVPDELA SALLGNPTQG ASAAALVDQS AQQGFDRASE AFEEAGFFSS DGLLYGLFGI IILLATGLLA A IGGAFLLL AKIALALLAG LGPLFILALI WQPTHRFFDQ WAQQVLNYGL LIVLFAAVFG LLMQIFGSYM ADLRFDGAQN VA YAIGGSV ILSIVSIVLL MQLPSIASGL AGGIGLGYMW ELRSMRSGAG AAMRGGRAMA RGARAAPGAA RGAAVGAANM AKT VATGGA GVARAAAGYF RGRKAG

UniProtKB: TrwI protein

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Macromolecule #5: TrwM protein

MacromoleculeName: TrwM protein / type: protein_or_peptide / ID: 5 / Details: Sequence from conjugative plasmid R388 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.292585 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKPPQQQHEA FPLFKGATRL PTIWGVPMIP LMAMVMGVAV IALTVSIWWW ALVPPLWFIM AQITKNDDKA FRIWWLWIDT KFRNRNKGF WGASSYSPAN YRKRR

UniProtKB: TrwM protein

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Macromolecule #6: Type IV secretion system protein virB4

MacromoleculeName: Type IV secretion system protein virB4 / type: protein_or_peptide / ID: 6 / Details: Sequence from conjugative plasmid R388 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 93.76993 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 SDV

UniProtKB: Type IV secretion system protein virB4

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65173
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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