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- EMDB-40196: The Type 9 Secretion System dGldL peak II, NucA substrate bound c... -

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Basic information

Entry
Database: EMDB / ID: EMD-40196
TitleThe Type 9 Secretion System dGldL peak II, NucA substrate bound complex
Map datarefine volume
Sample
  • Complex: Type 9 Secretion System NucA complex
    • Protein or peptide: Endonuclease I
    • Protein or peptide: Protein involved in gliding motility SprA
    • Protein or peptide: Peptidyl-prolyl cis-trans isomeraseProlyl isomerase
    • 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 - NucA Complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / endonuclease activity
Similarity search - Function
Endonuclease I / Endonuclease I / 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 / Lamin tail domain / Lamin Tail Domain ...Endonuclease I / Endonuclease I / 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 / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / His-Me finger superfamily / 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 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold
Similarity search - Domain/homology
Protein involved in gliding motility SprA / Peptidyl-prolyl cis-trans isomerase / Endonuclease I / Type IX secretion system protein PorV domain-containing protein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria) / Flavobacterium johnsoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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 22, 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_40196.png

Downloads & links

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Map

FileDownload / File: emd_40196.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefine volume
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.00927
Minimum - Maximum-0.027897663 - 0.073177196
Average (Standard dev.)0.00005269101 (±0.0023992478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 292.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40196_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_40196_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_40196_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 2

Fileemd_40196_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_40196_half_map_2.map
Annotationhalf map 1
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 NucA complex

EntireName: Type 9 Secretion System NucA complex
Components
  • Complex: Type 9 Secretion System NucA complex
    • Protein or peptide: Endonuclease I
    • Protein or peptide: Protein involved in gliding motility SprA
    • Protein or peptide: Peptidyl-prolyl cis-trans isomeraseProlyl isomerase
    • 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 NucA complex

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

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Macromolecule #1: Endonuclease I

MacromoleculeName: Endonuclease I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 8.454611 KDa
SequenceString:
EIVIFPNPSD GNFNIGLNNF NFPYSLEIFS FTGQKVFEKQ NASDSIISVS YLPSGIYIVK IEKDSKTTIK KIIIN

UniProtKB: Endonuclease I

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Macromolecule #2: Protein involved in gliding motility SprA

MacromoleculeName: Protein involved in gliding motility SprA / type: protein_or_peptide / ID: 2 / 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 #3: Peptidyl-prolyl cis-trans isomerase

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase / type: protein_or_peptide / ID: 3 / 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 #4: Type IX secretion system protein PorV domain-containing protein

MacromoleculeName: Type IX secretion system protein PorV domain-containing protein
type: protein_or_peptide / ID: 4 / 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 #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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 57573
FSC plot (resolution estimation)

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