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Yorodumi- EMDB-29911: The Type 9 Secretion System Extended Translocon - delta GldL, Pea... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29911 | |||||||||||||||||||||
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Title | The Type 9 Secretion System Extended Translocon - delta GldL, Peak I, SprA-PorV-RemZ-PPI focused volume | |||||||||||||||||||||
Map data | unsharpened volume | |||||||||||||||||||||
Sample |
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Keywords | T9SS / type IX secretion system translocon / protein secretion Complex / MEMBRANE PROTEIN | |||||||||||||||||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding Similarity search - Function | |||||||||||||||||||||
Biological species | Flavobacterium johnsoniae UW101 (bacteria) / Flavobacterium johnsoniae (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||||||||||||||
Authors | Deme JC / Lea SM | |||||||||||||||||||||
Funding support | United Kingdom, European Union, United States, 6 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29911.map.gz | 273.3 MB | EMDB map data format | |
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Header (meta data) | emd-29911-v30.xml emd-29911.xml | 27.5 KB 27.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29911_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_29911.png | 66.2 KB | ||
Masks | emd_29911_msk_1.map | 343 MB | Mask map | |
Filedesc metadata | emd-29911.cif.gz | 8.2 KB | ||
Others | emd_29911_additional_1.map.gz emd_29911_additional_2.map.gz emd_29911_half_map_1.map.gz emd_29911_half_map_2.map.gz | 199.9 MB 26.8 MB 273.8 MB 273.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29911 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29911 | HTTPS FTP |
-Related structure data
Related structure data | 8gl6C 8gl8C 8gljC 8glkC 8glmC 8glnC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29911.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | unsharpened volume | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29911_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: local resolution filtered volume
File | emd_29911_additional_1.map | ||||||||||||
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Annotation | local resolution filtered volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: sharpened volume
File | emd_29911_additional_2.map | ||||||||||||
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Annotation | sharpened volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_29911_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_29911_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Type 9 Secretion System Extended Translocon
Entire | Name: Type 9 Secretion System Extended Translocon |
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Components |
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-Supramolecule #1: Type 9 Secretion System Extended Translocon
Supramolecule | Name: Type 9 Secretion System Extended Translocon / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Flavobacterium johnsoniae UW101 (bacteria) |
-Macromolecule #1: SprA
Macromolecule | Name: SprA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Flavobacterium johnsoniae (bacteria) |
Sequence | String: 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 UniProtKB: UNIPROTKB: Q516C7 |
-Macromolecule #2: PorV
Macromolecule | Name: PorV / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Flavobacterium johnsoniae (bacteria) |
Sequence | String: 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 UniProtKB: Type IX secretion system protein PorV domain-containing protein |
-Macromolecule #3: PPI
Macromolecule | Name: PPI / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Flavobacterium johnsoniae (bacteria) |
Sequence | String: MKQLLTALLS LTLFISCSKD KDEVKDYTAE NEKEIVDYLA QNNLTAQRTN SGLYYIITKE GSSESEGENP GEEENTGEGE NTEENENDGH PTLNSNITVI YKGYFTNGKV FDESTEGVSY SLRTLIPGWK EGIPLLKSGG EIQLFVPAHL GYGSNGNKTV PGGAVLIFEI TLVSVN UniProtKB: Peptidyl-prolyl cis-trans isomerase |
-Macromolecule #4: SprE
Macromolecule | Name: SprE / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Flavobacterium johnsoniae (bacteria) |
Sequence | String: 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 UniProtKB: SprE |
-Macromolecule #5: RemZ
Macromolecule | Name: RemZ / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Flavobacterium johnsoniae (bacteria) |
Sequence | String: 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 UniProtKB: T9SS sorting signal type C domain-containing protein |
-Macromolecule #6: SkpA
Macromolecule | Name: SkpA / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Flavobacterium johnsoniae (bacteria) |
Sequence | String: MRKQFLFIFL ALIVANTSQA QGKTTRIGYI DMEYILENVS DYKEAKSQLE LKAQKWKQEI EAKKLNINSL KEGLKTEKAL LTKELIEERE TEIKFQENEM LDYQQKQFGA DGNLMRQKAA LAKPIQDQVF TAVQDIAEAK NYDFIFDKSS DLTMLFSNKR FDISDQVIRI ...String: MRKQFLFIFL ALIVANTSQA QGKTTRIGYI DMEYILENVS DYKEAKSQLE LKAQKWKQEI EAKKLNINSL KEGLKTEKAL LTKELIEERE TEIKFQENEM LDYQQKQFGA DGNLMRQKAA LAKPIQDQVF TAVQDIAEAK NYDFIFDKSS DLTMLFSNKR FDISDQVIRI LNRTDKREQL NKKQLKEQEA KENRENEIDE NPAMADRQKA LDERRAAREK LIEDRRLEQE AKKKEYDDRR KAMQAERDAK KNGTVSETAK TTEAAKTTEA VKTDATAKPA STTETTTTPA ETAASKAEER QKLYEQRKKE LEERRKKILE EREAAKKAKE AETQKTNTTN N UniProtKB: Outer membrane chaperone Skp (OmpH) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.2 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |