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- 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
TitleStructure of the mycobacterial ESX-5 Type VII Secretion System hexameric pore complex
Map datamap of the complex
Sample
  • Complex: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE
    • Protein or peptide: EccE5
    • Protein or peptide: EccD5
    • Protein or peptide: EccC5
    • Protein or peptide: EccB5
KeywordsMycobacterial 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
Type VII secretion system protein EccE / Putative type VII ESX secretion system translocon, EccE / Type VII secretion system membrane protein EccD / YukD-like / WXG100 protein secretion system (Wss), protein YukD / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain ...Type VII secretion system protein EccE / Putative type VII ESX secretion system translocon, EccE / Type VII secretion system membrane protein EccD / YukD-like / WXG100 protein secretion system (Wss), protein YukD / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system ESX-1, transport TM domain B / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Secretion protein Snm4 / Type VII secretion protein EccE / Type VII secretion protein EccB / FtsK domain-containing protein
Similarity search - Component
Biological speciesMycobacterium xenopi RIVM700367 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChojnowski G / Ritter C
CitationJournal: 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
DepositionDec 14, 2020-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7b9s
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12105.png

Downloads & links

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Map

FileDownload / File: emd_12105.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of the complex
Voxel sizeX=Y=Z: 1.29 Å
Density
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.12
Minimum - Maximum-0.26032734 - 0.68747324
Average (Standard dev.)0.0008209692 (±0.015840963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 580.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.291.291.29
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z580.500580.500580.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.2600.6870.001

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Supplemental data

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Sample components

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Entire : Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, ...

EntireName: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE
Components
  • Complex: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE
    • Protein or peptide: EccE5
    • Protein or peptide: EccD5
    • Protein or peptide: EccC5
    • Protein or peptide: EccB5

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Supramolecule #1: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, ...

SupramoleculeName: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium xenopi RIVM700367 (bacteria) / Location in cell: membrane
Molecular weightTheoretical: 2.142 MDa

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Macromolecule #1: EccE5

MacromoleculeName: EccE5 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium xenopi RIVM700367 (bacteria)
Molecular weightTheoretical: 44.469617 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: 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

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Macromolecule #2: EccD5

MacromoleculeName: EccD5 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium xenopi RIVM700367 (bacteria)
Molecular weightTheoretical: 53.399191 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: 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

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Macromolecule #3: EccC5

MacromoleculeName: EccC5 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium xenopi RIVM700367 (bacteria)
Molecular weightTheoretical: 152.946062 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: 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

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Macromolecule #4: EccB5

MacromoleculeName: EccB5 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium xenopi RIVM700367 (bacteria)
Molecular weightTheoretical: 53.226367 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: 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

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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
Component:
ConcentrationName
20.0 mMTris pH 8.0
150.0 mMNaClSodium chloride
GridModel: 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
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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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 / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm 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

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.14)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.14)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14) / Number images used: 121974

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Atomic model buiding 1

Initial modelPDB ID:

7b9f


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsModel was initially fitted using ChimeraX and then completed manually using Coot and ISOLDE.
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7b9s:
Structure of the mycobacterial ESX-5 Type VII Secretion System hexameric pore complex

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