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- EMDB-40085: The Type 9 Secretion System Extended Translocon - delta GldL, Pea... -

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Basic information

Entry
Database: EMDB / ID: EMD-40085
TitleThe Type 9 Secretion System Extended Translocon - delta GldL, Peak I, SprE-SkpA-Nterm SprA focused volume
Map datavolume
Sample
  • Complex: Type 9 Secretion System Extended Translocon
    • Protein or peptide: SprE
    • Protein or peptide: SkpA
    • Protein or peptide: SprA
  • Protein or peptide: PPI
  • Protein or peptide: RemZ
  • Protein or peptide: PorV
KeywordsT9SS / type IX secretion system translocon / protein secretion Complex / MEMBRANE PROTEIN
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 15, 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_40085.png

Downloads & links

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Map

FileDownload / File: emd_40085.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationvolume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 448 pix.
= 372.736 Å		0.83 Å/pix.
x 448 pix.
= 372.736 Å		0.83 Å/pix.
x 448 pix.
= 372.736 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0107
Minimum - Maximum-0.01792083 - 0.052595276
Average (Standard dev.)0.00027139785 (±0.0009665558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 372.73602 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40085_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_40085_additional_1.map
Annotationlocal resolution filtered
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: post processed

Fileemd_40085_additional_2.map
Annotationpost processed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_40085_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_40085_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: SprE
    • Protein or peptide: SkpA
    • Protein or peptide: SprA
  • Protein or peptide: PPI
  • Protein or peptide: RemZ
  • Protein or peptide: PorV

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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-#3 / Details: SkpA-SprE-Nterm SprA part of complex
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)

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Macromolecule #1: SprE

MacromoleculeName: SprE / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
SequenceString: MKKNTLKYSF FLIFFLFLIA CSTKNNTFVN RNSHALSTKY NILYNGGLGL EKGLQAIKAN DQDNFWKMLP IEKMQFDENF SEGEKTKNPD FEKAETKATK AIQKHSMNIG GRERNYQIDE AYLMLGKARY YDQRFIPALE AFNYILYKYP NSSNIYTAKI WREKTNMRLG ...String:
MKKNTLKYSF FLIFFLFLIA CSTKNNTFVN RNSHALSTKY NILYNGGLGL EKGLQAIKAN DQDNFWKMLP IEKMQFDENF SEGEKTKNPD FEKAETKATK AIQKHSMNIG GRERNYQIDE AYLMLGKARY YDQRFIPALE AFNYILYKYP NSSNIYTAKI WREKTNMRLG NDAIVVKNIN QLLKKTDLNK QTFSDANALL AEAFLNLEER DSAVAKLRIA EQFSRINEDR ARYKFILGQM YQEVGNKDSA TYYYDGVIHM NRKADRKYMM HAYAKKAQMY DYEKGNDTIF LKTYNKLVAD RENRPYYDVL FYEMGVFYDK KKDKENALKF YNKSLGRKSK DPYLMASAYR NIGNMYFKNT DYTMAAKYYD STLTKLNPKT REFAFIEKNR KNLDNVIKYE GIAKRNDSII KVYGMPDSER KIYFESYIAE LKKKDEAKRI LEEKEKEKLA NVERNNSASS APTAVNPNSL GKPANMDTDG IRPPSGNDAV STFYFYNPTT VAYGKLQFKK MWGNRTIGGN WRLSAIKAAN DAAMLNDSIN EAEANKLKDT VVIEKYTTAF YEKQLPKTQI AIDSIGKERN FAYYQLGLIY KEKFKEYTLA SDKLEQLLRN NPEEKLILPS MYNLYKIYQI TDPAKAEKIK SDITNNYPGS RYAQILNNTN TDDIPSPEKE YQKWYKLFQE EKFDVVLDNI DNLINQYSGD EIVSKFELLK ANTLGKVNGL EAYKKGLENV ADNYPNSDEG KNAREILEKQ VPTLERLNFT TEDNKNWKIL YLISNNDTKT LKQIEEAIRV FLLVENFERL TTSFDKYNRT QSFVAIHGLK SEAYAQDVAG VFRDDKKYKI AQPAIIISTE NYKVVQIKKN LEAYLTPKNP

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Macromolecule #2: SkpA

MacromoleculeName: SkpA / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
SequenceString:
TTRIGYIDME YILENVSDYK EAKSQLELKA QKWKQEIEAK KLNINSLKEG LKTEKALLTK ELIEERETEI KFQENEMLDY QQKQFGADGN LMRQKAALAK PIQDQVFTAV QDIAEAKNYD FIFDKSSDLT MLFSNKRFDI SDQVIRILNR PAMADRQKAL DERRAAREKL IE

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Macromolecule #3: SprA

MacromoleculeName: SprA / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
SequenceString: MRKICIFLLV LFCGNVLRSQ VKPAVQDTTK TQFSVGKMEL ENPPSILSAY KYDPITDRYI YTTSVDGFSI DYPLVLTPKE YEDLLLKESR RDYFRKKMDA IDGKKTGAEA AKKDLLPRYY INSSLFESIF GSNTIDVKPT GSVEMDLGVR YTKQDNPAFS PRNRSSLTFD ...String:
MRKICIFLLV LFCGNVLRSQ VKPAVQDTTK TQFSVGKMEL ENPPSILSAY KYDPITDRYI YTTSVDGFSI DYPLVLTPKE YEDLLLKESR RDYFRKKMDA IDGKKTGAEA AKKDLLPRYY INSSLFESIF GSNTIDVKPT GSVEMDLGVR YTKQDNPAFS PRNRSSLTFD FDQRISMSLM GKIGTRLEVN ANYDTQSTFA FQNLFKLAYT PSEDDIIQKV EVGNVSMPLN STLIRGAQSL FGVKTQLQFG RTTITGVFSE QKSQTKSVVA ENGGTVQNFD LYALDYDNDR HFFLSQYFRN KYDVSLKNYP FIDSRVQITR LEVWVTNKQN RVTTTGGGNN LRNIIALQDL GEAQVSGVPD NEVVVISSTA GFFNNPIDSP TSNTNNKYDP ATIGQAGSFL NSNIREIVTA KSGFNNTNVS EATDYSVLEN ARKLTTNEYT FNPQLGYISL QQRLANDEIL AVAFEYTVGG KVYQVGEFGS DGVDATVVTG NNSSNQAIIT QSLVLKMLKS NLTNVKNPVW NLMMKNVYQI PQAYQIKQDD FRLNILYTDP SPINYITPVQ GSSFPPNPAP DSKVEQTPLL NVFNLDRLNY NNDPQAGGDG FFDYIPGVTV DVQNGRVIFT TKEPFGELIF NKLQTGAGES YNDPTTYNAN QQKYVFRNMY RNTQAGALQD SDKNKFLLRG KYKSSGSNGI PIGAFNVPQG SVVVTAAGRV LVEGIDYSVD YQLGRVQILD PSLQASNTPI EVSLENNSIF GQQTRRFMGF NIEHKISDKF VIGGTYLKMT ERPFTQKSTY GQESVNNTIF GFNGNYSTEV PFLTRLANKL PNIDTDVPSN LSIRGEVAFL RPDAPKASDF QGEATIYVDD FEGSQSTIDM RSAYAWSLAS TPFITSINDN TFNANSNTLE YGFKRAKLSW YTIDPVFYSS KPSGISNDDL SLNTTRRIYS RELYPNTDIA QGQIQVVNTL DLTYYPGERG PYNNNPSFGA SNPSANFGGI MRALNSTNFE QGNVEYIQFW VLDPYVGNGE SPATNAGKIY FNLGEISEDV LKDGRKQYEN GLGPDQVMVN PQPLWGDVPA SQSLIYAFDT NPDNRKNQDV GLDGLPSSRE GSIYTNYAGE ADPAGDDYTY YLNADGGVLE RYKNYNGTEG NSAVSINDPN RGSTTLPDVE DINRDNTMST INAYYEYSID VKPGMQVGEN YITDIREVTN VDLPNGGTTN ARWIQFKIPV SQPQNTIGNI TDFRSIRFMR MFMTGFNSQM TVRFGALDLV RGEWRRYTGT LDANDQNPDD DGVEFDVAAV NIQENGTKCP VNYVMPPGVQ REQLYNNNTV INQNEQALAV RIGGAGLQYQ DSRAVFKNVS VDMRQYKKLK MFLHAESLPN QPTLEDDEMV GFIRFGNDFT QNFYQVEIPL KVTKTGGSCS ISPDLVWMDD NSIDLALDLL TRMKIKAMSI DINSSKRDVN GIYYPDNDPD LEGGDGDGKL TLGIKGNPNF GLVRNLMVGV KSRADHKDIK GEVWFNELRL ADLENKGGMA AILNVDTNMA DFATVSATGR KSTIGFGSLE QGANERDRED VQQYNIVTNL NLGKLLPKKW GINLPFNYAI GEEVITPEYD PFNQDIKLDQ LIRETTDQAE KDNIRTRAID YTKRKSINFI GVRKDRAPEQ KPHVYDIENF TFSQSYNQVE RHDYEVADYE DEQSNSAVNY AYTFQPKEVV PFKSTKFMKK SEYWKLLSDF NFNYLPSNIS FNTNILRQSN RQQFREVEVE GIGLDPLYRR NFAFNYQYGF GFNLTKSLKL NYSATSNNIV RNFLNDDNSP KEDFNIWDDY LDIGTPNQHA QQLVLNYDIP INKIPIFGFV KASYSYTADY MWQRSSTAFS EYEDPNGTVY DLGNTIQNSN SNTLTTTLNM NTLYKYLGLT PGAKKTAKPK TAAPPKPGEK IVNTAKPVVS SSPFYDGLIG VLTSIKNVQI NYTKNSGTVL PGYTPSVGFL GTSKPSLGFV FGSQDDVRYE AAKRGWLTTY QDFNQSFTQV SNKLLKVTAN IDLLPDLKVD LSMDRSYSEN TSEQYSVDPS TNEYKPLSPY TYGMFSISTV MIKTAFSPSD ETQSAAFDDF RSNRLIIANR LAEGHYGSGV AIPRYGDANN PIPAETDPNY AVYTANQGYP IGYTKSNQAV LLPAFLAAYT GSDASSSSTN IFRSFPIPNW SIKYNGLMRY KYFKDKFKRF SLQHNYRASY TINQFRSNFD YNSSPKVQDV NTNFYNEIIM SNVNLVEQFS PLIRMDFELK SSLRVLSEIK KDRALSMSFD NNLLTEVKGM EYIIGLGYRF KDVIFSSRLA DNPTGIIKSD INIKADFSLR NNETLVRYLD YDNNQLAAGQ NIWSLKLTAD YSFSKNLTAI FYYDHSFSKA VISTSFPLTN IRSGFTLRYN FGN

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Macromolecule #4: PPI

MacromoleculeName: PPI / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MKQLLTALLS LTLFISCSKD KDEVKDYTAE NEKEIVDYLA QNNLTAQRTN SGLYYIITKE GSSESEGENP GEEENTGEGE NTEENENDGH PTLNSNITVI YKGYFTNGKV FDESTEGVSY SLRTLIPGWK EGIPLLKSGG EIQLFVPAHL GYGSNGNKTV PGGAVLIFEI TLVSVN

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Macromolecule #5: RemZ

MacromoleculeName: RemZ / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
SequenceString: MDVQAWGGGG AGGGASGAVL DGRAAAGGGG GAYARSNITV AAGATLNASV AGTTTNALVS GAAVNGAAGG SSTILGFETS ILALGGGGGG ANNAGGTPAG GAGGSAASSV GNVSKLDGAA GGNGVTGAIG LLTVSGAGGT AGGGGGAGGA GVASVALGNG PGNAGTAPGG ...String:
MDVQAWGGGG AGGGASGAVL DGRAAAGGGG GAYARSNITV AAGATLNASV AGTTTNALVS GAAVNGAAGG SSTILGFETS ILALGGGGGG ANNAGGTPAG GAGGSAASSV GNVSKLDGAA GGNGVTGAIG LLTVSGAGGT AGGGGGAGGA GVASVALGNG PGNAGTAPGG GGSGAMQSLL GGAQIGGSGA AGRVIITYTC PTYSITGISA ANVCNSVGTT SVVTLTSSGG GLPIGPYVVT YNRSNPSGTG LTAIMNVTTP GTGTFTAAGL NVIGTSNITV TNLTSAACSS NISTNNVASL TVFAATVGGT LAGTATVCSG ATSGTLTLSG QTGSIIKWES SVSPFTVWTT IPNTTNTYTS GALTETSQFR AVIQNGNCAV VNSSIATITV NPLPQGSLSA NGPFCVTGSG QLTFTATAGT GPYTIVYKEN GGADRTAANI SSGVAFPTFT TPVTTTTVYT LVSVTGANTC SRSSGFTNNT ATITVNSRIA TPGFGTVTQP DCVTSTGSVV LTGLPAGSWT ITQSGTASQT YNSSGTTYTI SNLAVGNYTF TVQDAANCPS LATSTLTLIA PVVNIWNGTS WSKGSPPIST DVVRFSGNYS TTGNLSGCSL IVDSGFTVTV NSNHTLTISN AVTNNGGQLI FENNSSLLQT NNVTNVGNIT YKRITPPVRR YDLTYWSSPI TRTPPFTLYD LSPGTLADKY YSYDPVAGWV ISFNGTQQMV PGRGYVVRAP QTNDLNTGAN YLGAFVGVPN NGPISVSLGT AEAFQLLGNP YPSAIYADQF IANNSANLYG TLYFWTHNSL PSSSTPGGAQ YNYDNNDYAV YNLSGSIIVG GMTGQGATTP GNQSAPLGYI AAGQGFFVVS KTAGNAVFTN SMRVAANNTQ FYKTNKSAIE RHRVWINLTN TQGAFKQLLI GYIEGATNFW DHNYDAITAD ANPHLDFYSI NEGQNLVIQG RSLPFNESDV VPLGYRSAIA GEFSISLDHA DGDLTNHAVY LEDKLTNTLH NLQTSNYTFN TAIGTFSDRF VIRYTTATLG TDDFENQTNS FYVSVKDKTI KLNSTEDVMR EVSIFDISGK LLYNNKKVEN TEFQVSNFQS GNQVLIVKVT LDNGNIITKK IVFN

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Macromolecule #6: PorV

MacromoleculeName: PorV / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
SequenceString: MKKISLLLIC LLITTFAKAQ DIERPITTGV PFLLVAADAR AAGLGDQGVA TSSDVFSQQW NPAKYAFAED AQGLSISYTP YLTDLANDIS LGQVTYYNKI NDRSAFAGSF RYFGFGGIEL RQTGDPNEPT REVNPNEFAL DGSYSLKLSE TFSMAVAARY IRSNLKVATE ...String:
MKKISLLLIC LLITTFAKAQ DIERPITTGV PFLLVAADAR AAGLGDQGVA TSSDVFSQQW NPAKYAFAED AQGLSISYTP YLTDLANDIS LGQVTYYNKI NDRSAFAGSF RYFGFGGIEL RQTGDPNEPT REVNPNEFAL DGSYSLKLSE TFSMAVAARY IRSNLKVATE EIDASAAGSF AVDVAGFYQS EEIAYSDFNG RWRAGFNIQN LGPKISYDHD DLSANFLPAN LRVGGGFDFI FDDYNKLGVS LELTKLLVPT PPGPGTPYDA NGDGDFTDPG DISQSQADEA NYKKYKDIGW VSGIFKSFGD APGGFSEELK EITYSAAAEY MYQDAFAMRL GYYHESPMKG AKQFFSLGAG FKYSMIKVDV SYLFSASKVK NPLENTLRFS LTFNFGDKYE TY

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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: 61.2 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 546490
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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