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Yorodumi- EMDB-12105: Structure of the mycobacterial ESX-5 Type VII Secretion System he... -
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-Basic information
Entry | Database: EMDB / ID: EMD-12105 | |||||||||
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Title | Structure of the mycobacterial ESX-5 Type VII Secretion System hexameric pore complex | |||||||||
Map data | map of the complex | |||||||||
Sample |
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Keywords | Mycobacterial ESX-5 Type VII Secretion System / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycobacterium xenopi RIVM700367 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Chojnowski G / Ritter C | |||||||||
Citation | Journal: Sci Adv / Year: 2021 Title: Structure of the mycobacterial ESX-5 type VII secretion system pore complex. Authors: Katherine S H Beckham / Christina Ritter / Grzegorz Chojnowski / Daniel S Ziemianowicz / Edukondalu Mullapudi / Mandy Rettel / Mikhail M Savitski / Simon A Mortensen / Jan Kosinski / Matthias Wilmanns / Abstract: The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation ...The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation machinery and the composition of the central secretion pore have remained unknown. Here, we present the high-resolution structure of the 2.1-megadalton ESX-5 core complex. Our structure captured a dynamic, secretion-competent conformation of the pore within a well-defined transmembrane section, sandwiched between two flexible protein layers at the cytosolic entrance and the periplasmic exit. We propose that this flexibility endows the ESX-5 machinery with large conformational plasticity required to accommodate targeted protein secretion. Compared to known secretion systems, a highly dynamic state of the pore may represent a fundamental principle of bacterial secretion machineries. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12105.map.gz | 312.1 MB | EMDB map data format | |
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Header (meta data) | emd-12105-v30.xml emd-12105.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_12105.png | 187.9 KB | ||
Filedesc metadata | emd-12105.cif.gz | 7.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12105 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12105 | HTTPS FTP |
-Related structure data
Related structure data | 7b9sMC 7b7jC 7b9fC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12105.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | map of the complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, ...
Entire | Name: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE |
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Components |
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-Supramolecule #1: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, ...
Supramolecule | Name: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycobacterium xenopi RIVM700367 (bacteria) / Location in cell: membrane |
Molecular weight | Theoretical: 2.142 MDa |
-Macromolecule #1: EccE5
Macromolecule | Name: EccE5 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium xenopi RIVM700367 (bacteria) |
Molecular weight | Theoretical: 44.469617 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: MRAQRRFGLD LSWPRLTGVF LIDVAVLALV SHLPDAWQAN HIAWWTGVGV AVLVTIVAVV TYRRTPLACA LVARVLDRFV DPEMTLTEG CTPALDHQRR FGHDVVGIRE YQGQLVAVVT VEGHEEAPSG RHRNRDAAPA WLPVEAVAAR LRQFDVRLDA I DIVSVGTR ...String: MRAQRRFGLD LSWPRLTGVF LIDVAVLALV SHLPDAWQAN HIAWWTGVGV AVLVTIVAVV TYRRTPLACA LVARVLDRFV DPEMTLTEG CTPALDHQRR FGHDVVGIRE YQGQLVAVVT VEGHEEAPSG RHRNRDAAPA WLPVEAVAAR LRQFDVRLDA I DIVSVGTR RTSGRDDVSD VGVDDTGPVD ARQPLDEHHT WLVLRMDPQR NVAAVAARDS VAATLAAATE RLAHDLNGRR WT ARPLTSS EIDDMDATVL AGLQPAHVRP RRRRLKYKQP EGYKEFVTSF WVSPRDITSE TLERLWLPDT EATAVTVRLR PRH GGVEVS AWVRYHSSRR LRRSVWGGLN RLTGRQLDAV CASMPVPTRR PRLVVPAREL HDGEELAVLV GQAPAPSPSP AAAR UniProtKB: Type VII secretion protein EccE |
-Macromolecule #2: EccD5
Macromolecule | Name: EccD5 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium xenopi RIVM700367 (bacteria) |
Molecular weight | Theoretical: 53.399191 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: MTAIVEAPQP GAEAIASPQA AVVAIMAADV QIAVVLDAHA PISVMIDPLL KVVNTRLREL GVAPLEAKGR GRWMLCLVDG TPLRPNLSL TEQEVYDGDR LWLKFLEDTE HRSEVIEHIS TAVATNLSKR FAPIDPVVAV QVGATMVAVG VLLGSALLGW W RWQHESWL ...String: MTAIVEAPQP GAEAIASPQA AVVAIMAADV QIAVVLDAHA PISVMIDPLL KVVNTRLREL GVAPLEAKGR GRWMLCLVDG TPLRPNLSL TEQEVYDGDR LWLKFLEDTE HRSEVIEHIS TAVATNLSKR FAPIDPVVAV QVGATMVAVG VLLGSALLGW W RWQHESWL PAPFAAVIAV LVLTVATMIL ARSKTVPDRR VGDILLLSGL VPLAVAIAAT APGPVGAPHA VLGFGVFGVA AM LVMRFTG RRLGVYTALV TLCAAATAAG LARMVLLTSA VTLLTCVLLA CVLMYHGAPA LSRWLSGIRL PVFPSATSRW VFE ARPDLP TTVVVSGGGQ PTLEGPASVR DVLLRAERAR SFLTGLLVGL GVLTVVCLAG LCDPHAGRRW LPLLLAAFTF GFLI LRGRS YVDRWQAITL AATAVLIIAA VAVRYVLVSG SPAVLSAGVA VLVLLPAAGL TAAAVVPNTI YSPLFRKIVE WIEYL CLMP IFPLALWLMN VYEAIRYR UniProtKB: Secretion protein Snm4 |
-Macromolecule #3: EccC5
Macromolecule | Name: EccC5 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium xenopi RIVM700367 (bacteria) |
Molecular weight | Theoretical: 152.946062 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: MKQGFARPTP ERAPVVKPEN IVLPTPLSVP PPEGKPWWLV VVGVLVVGLL VGMVGMTVAS GSRLFLGAGA IFPIFMIGGV AMMMFGGRF GGQQQMSRPK LDAMRAQFML MLDMLRETAQ ESADSMDANY RWFHPAPTTL AAAVGSSRMW ERQPDGKDLN F GVVRVGVG ...String: MKQGFARPTP ERAPVVKPEN IVLPTPLSVP PPEGKPWWLV VVGVLVVGLL VGMVGMTVAS GSRLFLGAGA IFPIFMIGGV AMMMFGGRF GGQQQMSRPK LDAMRAQFML MLDMLRETAQ ESADSMDANY RWFHPAPTTL AAAVGSSRMW ERQPDGKDLN F GVVRVGVG MTRPEVTWGE PQNMPTDIEL EPVTGKALQE FGRYQSVVYN LPKMVSLLVE PWYSLVGERE QVLGLTRAII CQ LAFSHGP DHVQMIVVTS DPDRWDWVKW IPHFGDPRRR DAAGNARMVY TSVREFATEQ AELFAGRGSF TPRHASSSAE TPT PHHVII SDIEDPQWEY VISSEGVDGV TFFDLTGSPL WTGAPQRVLR FTDSAGVIET LPRDRDTWMV IDDNAWFFAL ADQM SEADA EQFAHQMAHW RLAEAYEEIG QRVVQLGARD ILSYYGIDDA GEIDFNTLWS GSGRRDLLSR SRLRIPFGNR ADNGE LLFL DMKSLDEGGD GPHGVMSGTT GSGKSSLVRT VIASLMLAHP PEELQFVLAD LKGGSAVKPF DGVPHVSRII TDLEDD QAL MERFLEAMWG EIARRKEICF SAGVDGAKEY NELRARMKAR GEDMPPLPML VVVIDEFYEW FRIMPTAVDV LDSIGRQ GR AYWVHLMMAS QTIESRAEKL MENMGYRLVL KAQTAGAAQA AGVPNAVNLP SQAGLGYFRK SGDEIIRFQA EYLWRDYR R GSSYDGEEQA PLTHSVDYIR PQLFTTAFAP LEVSVSGPDG QSALPQVVDG EAVNGHRGGD DVDEEEEALR TPKVGTVII DQLRQIDFEP YRLWHPPLDV PVPIDELVNR FLGRPWQQDY GTAKNLVFPI GIIDRPYKHD QPPWTVDTSG AGANVLILGA GGAGKTTAL QTLICAAALT HTPEQVQFYC LAYSGTALTT VANLPHVGGV SGPTDPYGVR RTVAEVLGLV RDRKRSFLEY D VPSMEVFR RRKFGGEPGG VPDDGFGDVY LVIDNYRALA EENEVLIEQV NQIINQGPSF GVHVVATADR ESELRPPVRS GF GSRVELR LAAVEDAKLV RSRFAKDVPP KPGRGMVAVN YVRLDSDPQA GLHTLVARPA LGSTPDAVFE SDSVAAAVRQ VAA GEARPV RRLPARFGLD QLRQVAAADR RQGVGAGGIA WAISELDLQP VYLNFADNAH LMVTGRRECG RTTTLATIMS EIGR IYAPG ASTAPPTSRP SAQVWLVDPR RQLLTVLGSD YVEKFAYNLD GVAAMMDDLA AALARREPPP GLSAEELLSR SWWSG PEIF LIIDDIQQLP PGFDSPLHKA APWVTRAADV GLHVFVTRTF GGWSSAGSDP ILRALHQANA PLLVMDADPD EGFIRG KMK GGPLPRGRGL LMAEDTGVFV QVAATDLRR UniProtKB: FtsK domain-containing protein |
-Macromolecule #4: EccB5
Macromolecule | Name: EccB5 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium xenopi RIVM700367 (bacteria) |
Molecular weight | Theoretical: 53.226367 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: MPSEQRGQHR SGYGLGLSTR TQVTGYQFLA RRTAMALTRW RVRMEVEPGR RQVLAVVASV SAAGVICLGA LLWSFISPSG QMGESPIIA DRDSGALYVR VGDTLYPALN LASARLIAGR AENPHKVRSS QIAEQPHGPM VGIPGAPSDI SPTSPASSSW L VCDAVTAA ...String: MPSEQRGQHR SGYGLGLSTR TQVTGYQFLA RRTAMALTRW RVRMEVEPGR RQVLAVVASV SAAGVICLGA LLWSFISPSG QMGESPIIA DRDSGALYVR VGDTLYPALN LASARLIAGR AENPHKVRSS QIAEQPHGPM VGIPGAPSDI SPTSPASSSW L VCDAVTAA QGVGAPASVT VTVIDGTPDL SGRRHVLSGS DAVVLRYGND TWVIRQGRRS RIDAANRAVL LPLGLTPEQV KQ ASPMSRA LYDALPVGPE LAVPKVPDAG KPANFPGAPA PVGAVLVTPQ ISGPQQYSVV LPDGVQTISP IVAQILQNAG TPA GSMPVV VAPATLARMP VVHGLDLSAY PDSPLNVVNM KENPATCWWW EKTAGEERAR TQVVSGPTVP IATSDTNKVV SLVK ADNTG READRVYYGP NYANFVVVTG NDPAASTAES LWLLSKSGVR FGVDNSREAR TALGLTSTPS PAPWVALRLL APGPM LSRA DALVRHDTLP TDTNPAELAV PK UniProtKB: Type VII secretion protein EccB |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE | ||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-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 / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 27873 / Average electron dose: 49.34 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 2.14) |
Final angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 2.14) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14) / Number images used: 121974 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Model was initially fitted using ChimeraX and then completed manually using Coot and ISOLDE. |
Refinement | Space: REAL / Protocol: OTHER |
Output model | PDB-7b9s: |