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- EMDB-0134: Structural snapshots of the Type 9 protein translocon Plug-complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0134
TitleStructural snapshots of the Type 9 protein translocon Plug-complex
Map dataSprA-PPI-Plug complex
Sample
  • Complex: Complex of SprA, PPI and Plug
    • Protein or peptide: Protein involved in gliding motility SprA
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase
    • Protein or peptide: Plug
KeywordsType 9 Secretion System Type IX Secretion System T9S folded protein secretion outer membrane protein / PROTEIN TRANSPORT
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Protein of unknown function DUF5103 / Type 9 secretion system plug protein 1st domain / Gliding motility protein SprA N-terminal domain / Cell surface SprA / Motility related/secretion protein / : / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Protein involved in gliding motility SprA / Peptidyl-prolyl cis-trans isomerase / Type 9 secretion system plug protein N-terminal domain-containing protein / SprA
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDeme JC / Lea SM
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust107929/Z/15/Z United Kingdom
Wellcome Trust100298 United Kingdom
CitationJournal: Nature / Year: 2018
Title: Type 9 secretion system structures reveal a new protein transport mechanism.
Authors: Frédéric Lauber / Justin C Deme / Susan M Lea / Ben C Berks /
Abstract: The type 9 secretion system (T9SS) is the protein export pathway of bacteria of the Gram-negative Fibrobacteres-Chlorobi-Bacteroidetes superphylum and is an essential determinant of pathogenicity in ...The type 9 secretion system (T9SS) is the protein export pathway of bacteria of the Gram-negative Fibrobacteres-Chlorobi-Bacteroidetes superphylum and is an essential determinant of pathogenicity in severe periodontal disease. The central element of the T9SS is a so-far uncharacterized protein-conducting translocon located in the bacterial outer membrane. Here, using cryo-electron microscopy, we provide structural evidence that the translocon is the T9SS protein SprA. SprA forms an extremely large (36-strand) single polypeptide transmembrane β-barrel. The barrel pore is capped on the extracellular end, but has a lateral opening to the external membrane surface. Structures of SprA bound to different components of the T9SS show that partner proteins control access to the lateral opening and to the periplasmic end of the pore. Our results identify a protein transporter with a distinctive architecture that uses an alternating access mechanism in which the two ends of the protein-conducting channel are open at different times.
History
DepositionJul 18, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseNov 7, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0874
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0874
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6h3j
  • Surface level: 0.0874
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0134.png

Downloads & links

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Map

FileDownload / File: emd_0134.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSprA-PPI-Plug complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0874 / Movie #1: 0.0874
Minimum - Maximum-0.10104418 - 0.25124836
Average (Standard dev.)0.0015906628 (±0.0132062575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z246.000246.000246.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1010.2510.002

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Supplemental data

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Sample components

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Entire : Complex of SprA, PPI and Plug

EntireName: Complex of SprA, PPI and Plug
Components
  • Complex: Complex of SprA, PPI and Plug
    • Protein or peptide: Protein involved in gliding motility SprA
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase
    • Protein or peptide: Plug

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Supramolecule #1: Complex of SprA, PPI and Plug

SupramoleculeName: Complex of SprA, PPI and Plug / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 335 KDa

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Macromolecule #1: Protein involved in gliding motility SprA

MacromoleculeName: Protein involved in gliding motility SprA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 270.251719 KDa
SequenceString: MRKICIFLLV LFCGNVLRSQ VKPAVQDTTK TQFSVGKMEL ENPPSILSAY KYDPITDRYI YTTSVDGFSI DYPLVLTPKE YEDLLLKES RRDYFRKKMD AIDGKKTGAE AAKKDLLPRY YINSSLFESI FGSNTIDVKP TGSVEMDLGV RYTKQDNPAF S PRNRSSLT ...String:
MRKICIFLLV LFCGNVLRSQ VKPAVQDTTK TQFSVGKMEL ENPPSILSAY KYDPITDRYI YTTSVDGFSI DYPLVLTPKE YEDLLLKES RRDYFRKKMD AIDGKKTGAE AAKKDLLPRY YINSSLFESI FGSNTIDVKP TGSVEMDLGV RYTKQDNPAF S PRNRSSLT FDFDQRISMS LMGKIGTRLE VNANYDTQST FAFQNLFKLA YTPSEDDIIQ KVEVGNVSMP LNSTLIRGAQ SL FGVKTQL QFGRTTITGV FSEQKSQTKS VVAENGGTVQ NFDLYALDYD NDRHFFLSQY FRNKYDVSLK NYPFIDSRVQ ITR LEVWVT NKQNRVTTTG GGNNLRNIIA LQDLGEAQVS GVPDNEVVVI SSTAGFFNNP IDSPTSNTNN KYDPATIGQA GSFL NSNIR EIVTAKSGFN NTNVSEATDY SVLENARKLT TNEYTFNPQL GYISLQQRLA NDEILAVAFE YTVGGKVYQV GEFGS DGVD ATVVTGNNSS NQAIITQSLV LKMLKSNLTN VKNPVWNLMM KNVYQIPQAY QIKQDDFRLN ILYTDPSPIN YITPVQ GSS FPPNPAPDSK VEQTPLLNVF NLDRLNYNND PQAGGDGFFD YIPGVTVDVQ NGRVIFTTKE PFGELIFNKL QTGAGES YN DPTTYNANQQ KYVFRNMYRN TQAGALQDSD KNKFLLRGKY KSSGSNGIPI GAFNVPQGSV VVTAAGRVLV EGIDYSVD Y QLGRVQILDP SLQASNTPIE VSLENNSIFG QQTRRFMGFN IEHKISDKFV IGGTYLKMTE RPFTQKSTYG QESVNNTIF GFNGNYSTEV PFLTRLANKL PNIDTDVPSN LSIRGEVAFL RPDAPKASDF QGEATIYVDD FEGSQSTIDM RSAYAWSLAS TPFITSIND NTFNANSNTL EYGFKRAKLS WYTIDPVFYS SKPSGISNDD LSLNTTRRIY SRELYPNTDI AQGQIQVVNT L DLTYYPGE RGPYNNNPSF GASNPSANFG GIMRALNSTN FEQGNVEYIQ FWVLDPYVGN GESPATNAGK IYFNLGEISE DV LKDGRKQ YENGLGPDQV MVNPQPLWGD VPASQSLIYA FDTNPDNRKN QDVGLDGLPS SREGSIYTNY AGEADPTGDD YTY YLNADG GVLERYKNYN GTEGNSAVSI NDPNRGSTTL PDVEDINRDN TMSTINAYYE YSIDVKPGMQ VGENYITDIR EVTN VDLPN GGTTNARWIQ FKIPVSQPQN TIGNITDFRS IRFMRMFMTG FNSQMTVRFG ALDLVRGEWR RYTGTLDAND QNPDD DGVE FDVAAVNIQE NGTKCPVNYV MPPGVQREQL YNNNTVINQN EQALAVRIGG AGLQYQDSRA VFKNVSVDMR QYKKLK MFL HAESLPNQPT LEDDEMVGFI RFGNDFTQNF YQVEIPLKVT KTGGSCSISP DLVWMDDNSI DLALDLLTRM KIKAMSI DI NSSKRDVNGI YYPDNDPDLE GGDGDGKLTL GIKGNPNFGL VRNLMVGVKS RADHKDIKGE VWFNELRLAD LENKGGMA A ILNVDTNMAD FATVSATGRK STIGFGSLEQ GANERDREDV QQYNIVTNLN LGKLLPKKWG INLPFNYAIG EEVITPEYD PFNQDIKLDQ LIRETTDQAE KDNIRTRAID YTKRKSINFI GVRKDRAPEQ KPHVYDIENF TFSQSYNQVE RHDYEVADYE DEQSNSAVN YAYTFQPKEV VPFKSTKFMK KSEYWKLLSD FNFNYLPSNI SFNTNILRQS NRQQFREVEV EGIGLDPLYR R NFAFNYQY GFGFNLTKSL KLNYSATSNN IVRNFLNDDN SPKEDFNIWD DYLDIGTPNQ HAQQLVLNYD IPINKIPIFG FV KASYSYT ADYMWQRSST AFSEYEDPNG TVYDLGNTIQ NSNSNTLTTT LNMNTLYKYL GLTPGAKKTA KPKTAAPPKP GEK IVNTAK PVVSSSPFYD GLIGVLTSIK NVQINYTKNS GTVLPGYTPS VGFLGTSKPS LGFVFGSQDD VRYEAAKRGW LTTY QDFNQ SFTQVSNKLL KVTANIDLLP DLKVDLSMDR SYSENTSEQY SVDPSTNEYK PLSPYTYGMF SISTVMIKTA FSPSD ETQS AAFDDFRSNR LIIANRLAEG HYGSGVAIPR YGDANNPIPA ETDPNYAVYT ANQGYPIGYT KSNQAVLLPA FLAAYT GSD ASSSSTNIFR SFPIPNWSIK YNGLMRYKYF KDKFKRFSLQ HNYRASYTIN QFRSNFDYNS SPKVQDVNTN FYNEIIM SN VNLVEQFSPL IRMDFELKSS LRVLSEIKKD RALSMSFDNN LLTEVKGMEY IIGLGYRFKD VIFSSRLADN PTGIIKSD I NIKADFSLRN NETLVRYLDY DNNQLAAGQN IWSLKLTADY SFSKNLTAIF YYDHSFSKAV ISTSFPLTNI RSGFTLRYN FGN

UniProtKB: Protein involved in gliding motility SprA

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Macromolecule #2: Peptidyl-prolyl cis-trans isomerase

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Flavobacterium johnsoniae (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101
Molecular weightTheoretical: 19.219141 KDa
SequenceString:
MKQLLTALLS LTLFISCSKD KDEVKDYTAE NEKEIVDYLA QNNLTAQRTN SGLYYIITKE GSSESEGENP GEEENTGEGE NTEENENDG HPTLNSNITV IYKGYFTNGK VFDESTEGVS YSLRTLIPGW KEGIPLLKSG GEIQLFVPAH LGYGSNGNKT V PGGAVLIF EITLVSVN

UniProtKB: Peptidyl-prolyl cis-trans isomerase

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Macromolecule #3: Plug

MacromoleculeName: Plug / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 48.602969 KDa
SequenceString: MPKFLYQSLI ALLIFTSAKA QEIQTEVVPP YNIKTVTFVQ NGNNVVPIFE LNSTFEFQFD DLFGNEANYY FEITHCDYNW KPSDIPKTD YLRGFDGQRI MDYSNSFNTL QVYSHYRLPF PNQFTTQIRL SGNYILKILN EDKEVVLSRK FIVYEEHCTV G AQVKRTRN ...String:
MPKFLYQSLI ALLIFTSAKA QEIQTEVVPP YNIKTVTFVQ NGNNVVPIFE LNSTFEFQFD DLFGNEANYY FEITHCDYNW KPSDIPKTD YLRGFDGQRI MDYSNSFNTL QVYSHYRLPF PNQFTTQIRL SGNYILKILN EDKEVVLSRK FIVYEEHCTV G AQVKRTRN LSNINYKQNL DFTIASNDIT FQTPTQNVKV LLLQNGNFNT AIKNIPPQYT IGNQLVYKYD AETQFWGGNE FL YFENKDI RAANNNVGRI GSNNDIYNAY LYTNAARGNQ IYTNYQDVNG NFVVKNINGA DNSIEADYAW VYFTLSAPAF RMN KDIYIT GIFNNYSLSP EYKMDYNTDK AVFEKAVMIK QGFTNYQYTV ADKKGNIDLE NAIDGNFYQT ENEYTILVYY KESI DRYQR VIGKGNANSI NIVN

UniProtKB: Type 9 secretion system plug protein N-terminal domain-containing protein

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1100000
Startup modelType of model: NONE / Details: ab initio from data
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 150000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE / Target criteria: Correlation
Output model

PDB-6h3j:
Structural snapshots of the Type 9 protein translocon Plug-complex

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