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- EMDB-40191: The Type 9 Secretion System in vitro assembled, RemA-CTD substrat... -

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Basic information

Entry
Database: EMDB / ID: EMD-40191
TitleThe Type 9 Secretion System in vitro assembled, RemA-CTD substrate bound complex
Map datarefined volume
Sample
  • Complex: Type 9 Secretion System Extended Translocon
    • Protein or peptide: Protein involved in gliding motility SprA
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase
    • Protein or peptide: RemA
  • Protein or peptide: Type IX secretion system protein PorV domain-containing protein
  • Ligand: Lauryl Maltose Neopentyl Glycol
KeywordsT9SS / Type IX Secretion System Translocon / Protein Secretion PorV - SprA - PPI - RemA Complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / carbohydrate binding
Similarity search - Function
Type IX secretion system protein PorV / : / Type IX secretion system protein PorV / Gliding motility protein SprA N-terminal domain / Cell surface SprA / Motility related/secretion protein / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / : ...Type IX secretion system protein PorV / : / Type IX secretion system protein PorV / Gliding motility protein SprA N-terminal domain / Cell surface SprA / Motility related/secretion protein / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / : / 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 IX secretion system protein PorV domain-containing protein / RemA
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria) / Flavobacterium johnsoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDeme JC / Lea SM
Funding support United Kingdom, European Union, United States, 6 items
OrganizationGrant numberCountry
Wellcome Trust219477/Z/19/Z United Kingdom
Wellcome Trust107929/Z/15/Z United Kingdom
European Research Council (ERC)833713European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007474/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S021264/1 United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
CitationJournal: Nat Microbiol / Year: 2024
Title: The Type 9 Secretion System caught in the act of transport
Authors: Lauber F / Deme JC / Liu X / Kjaer A / Miller HL / Alcock F / Lea SM / Berks BC
History
DepositionMar 21, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40191.png

Downloads & links

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Map

FileDownload / File: emd_40191.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefined volume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246.6 Å		0.82 Å/pix.
x 300 pix.
= 246.6 Å		0.82 Å/pix.
x 300 pix.
= 246.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0136
Minimum - Maximum-0.023097146 - 0.05512726
Average (Standard dev.)0.000015007674 (±0.002412703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40191_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: local resolution filtered

Fileemd_40191_additional_1.map
Annotationlocal resolution filtered
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: postprocessed volume

Fileemd_40191_additional_2.map
Annotationpostprocessed volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_40191_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_40191_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Type 9 Secretion System Extended Translocon

EntireName: Type 9 Secretion System Extended Translocon
Components
  • Complex: Type 9 Secretion System Extended Translocon
    • Protein or peptide: Protein involved in gliding motility SprA
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase
    • Protein or peptide: RemA
  • Protein or peptide: Type IX secretion system protein PorV domain-containing protein
  • Ligand: Lauryl Maltose Neopentyl Glycol

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Supramolecule #1: Type 9 Secretion System Extended Translocon

SupramoleculeName: Type 9 Secretion System Extended Translocon / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)

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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: 270.221688 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 AGEADPAGDD 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
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
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: Type IX secretion system protein PorV domain-containing protein

MacromoleculeName: Type IX secretion system protein PorV domain-containing protein
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 44.210043 KDa
SequenceString: MKKISLLLIC LLITTFAKAQ DIERPITTGV PFLLVAADAR AAGLGDQGVA TSSDVFSQQW NPAKYAFAED AQGLSISYTP YLTDLANDI SLGQVTYYNK INDRSAFAGS FRYFGFGGIE LRQTGDPNEP TREVNPNEFA LDGSYSLKLS ETFSMAVAAR Y IRSNLKVA ...String:
MKKISLLLIC LLITTFAKAQ DIERPITTGV PFLLVAADAR AAGLGDQGVA TSSDVFSQQW NPAKYAFAED AQGLSISYTP YLTDLANDI SLGQVTYYNK INDRSAFAGS FRYFGFGGIE LRQTGDPNEP TREVNPNEFA LDGSYSLKLS ETFSMAVAAR Y IRSNLKVA TEEIDASAAG SFAVDVAGFY QSEEIAYSDF NGRWRAGFNI QNLGPKISYD HDDLSANFLP ANLRVGGGFD FI FDDYNKL GVSLELTKLL VPTPPGPGTP YDANGDGDFT DPGDISQSQA DEANYKKYKD IGWVSGIFKS FGDAPGGFSE ELK EITYSA AAEYMYQDAF AMRLGYYHES PMKGAKQFFS LGAGFKYSMI KVDVSYLFSA SKVKNPLENT LRFSLTFNFG DKYE TY

UniProtKB: Type IX secretion system protein PorV domain-containing protein

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Macromolecule #4: RemA

MacromoleculeName: RemA / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 154.116562 KDa
SequenceString: MIRKLLLLII LFIQYLSFGQ SANNYCFSSS TSTYSNLTGA TAFPGMPTNG NNDDVISSFS TLPFTFNFAG INYTQIKISE NGWLSFANV NNAYFDNSAA NANNAKPILF PFWDDMVYSS VPRYRIDTVS GSRILKIEWI QQYFYNGNNG NAISFQVWLY E GSNKIEYR ...String:
MIRKLLLLII LFIQYLSFGQ SANNYCFSSS TSTYSNLTGA TAFPGMPTNG NNDDVISSFS TLPFTFNFAG INYTQIKISE NGWLSFANV NNAYFDNSAA NANNAKPILF PFWDDMVYSS VPRYRIDTVS GSRILKIEWI QQYFYNGNNG NAISFQVWLY E GSNKIEYR YSRGNNNSGN ISASIGIYDA NGNYITLNDS GSNPTGQVDT FTTSINARPA TNQVYTFTPP PAQPTPTQAG SL YTFCIDN SNTQTNTVSN GQYSLVNVIQ GYNYTFSVDN IFAGAENLTL LDNSNNNLSP SVVSSGTSGA TVTWTATFSG QVR VLLTGN CGETNSGTMT LRLNSAANTL DSQTTAGANN TWIGHVYNSV GAAPSPFTNA NYAGYYTIGT ENFDTDFGGD YTCF PVFSN GVQRASMYTE GFAVRYRMQS TRPAGCYLIR IIGDDGVRLS INNGGYILDR WVEQGATTYS NILVNVPANP IFTLE YYEN AGANRVAFNI TPFDAALNTI TAPATVNFCN GGDPAVIDGS LQYNSADPNA ANPYINFQWQ IQTDGGGFSN IPGATG RTY DPPAMAANGT ANDIVYQYRR LATSNVAGTG TACDFTASTP VTITNSPTSV GGTASANQSI CYGTQPANIT LSGYRGN IQ WQASIDNTNF NNIDGATTAV LAGSQIGTLT KTTYYRATTS GTCNTATSTV VTITVRAGNN IISYSNGTSG TVCMQPVE N AVGSLTAPAG TYFNNVSFAS YGTPTGTACG SFVINPFCHA ATSQSVVESA LLGNSNTILI AATNGNFTDP CVGTTKRLY ITASYSQSIC AGNLPGTITG SIPTGNDTYT YLWESSTTSN TTGFSAASGT NNGQNYTPGT LTQDTWFRRT AYDGACSSVS AVVLVKVIA KVWNGNTNTD WNTASNWTPN GVPTASDCVV IPNTTNKPII NGTNTNSYAN TLSVNNLGAL TVNSTNTLNI T NTIAVNTT GSLTFNNNSS LLQTNTGTNI NSGNITYRRD TQPVRRYDFT YWSTPVTSTP AFTLANLSPA TLLDKYYSYD PA AGWIISF NGILPMAKGS GYIVRSPQTF DITIPAVYPA SFVGVPNNGN VTVNVVPNSF NLIGNPYPSA VNAFQLLSAN STI GSLYFW MHNAPPSDAV SGDATYNYAS SDYAVFNSSG GVTTSNAAQT PAGYIAAGQA FFTNNGAGNS ILFTNNMRAS GNNS QFYKT TGTDNIERNR IWLNFANKEG AFKQLLVGYI DGATNNWDIQ YDAETMDANT YTDFYSINQN MSLTIQGRGL PFENS DVIP LGYKTTIAGD FTISIDHVDG LFDKQNVYLE DKTTGTVSDL KAQDYTFKTE AGTFTDRFAL RYTNKTLGTG DFENVK DGL LISVKDKTIK VTSAKENIKE VNIFDITGKL IYNKKKVGNT ELSISNLQSA DQVLLVKVNL ENNAQITRKV IFK

UniProtKB: RemA

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Macromolecule #5: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 5 / Number of copies: 1 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 37140
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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