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- EMDB-3506: cryoEM structure of bacterial holo-translocon -

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Basic information

Entry
Database: EMDB / ID: EMD-3506
TitlecryoEM structure of bacterial holo-translocon
Map datamap of cross-linked HTL
Sample
  • Complex: bacterial holo-translocon (HTL)
    • Protein or peptide: Protein translocase subunit SecY
    • Protein or peptide: Protein translocase subunit SecE
    • Protein or peptide: Protein-export membrane protein SecG
    • Protein or peptide: Protein translocase subunit SecD
    • Protein or peptide: Protein translocase subunit SecF
    • Protein or peptide: Membrane protein insertase YidC
Keywordsholotranslocon / membrane protein insertion machinery / chaperone / protein secretion
Function / homology
Function and homology information


protein insertion into membrane from inner side / membrane insertase activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein insertion into membrane / protein transmembrane transporter activity ...protein insertion into membrane from inner side / membrane insertase activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein insertion into membrane / protein transmembrane transporter activity / protein secretion / protein targeting / intracellular protein transport / protein transport / protein folding / protein-containing complex assembly / membrane / plasma membrane
Similarity search - Function
SecD export protein N-terminal TM domain / SecD export protein N-terminal TM region / Protein-export membrane protein SecF, bacterial / Protein translocase subunit SecD / Protein-export membrane protein SecD/SecF, bacterial / Protein-export membrane protein SecD/SecF/SecDF, conserved site / Protein-export membrane protein SecD/SecF, archaeal and bacterial / : / : / : ...SecD export protein N-terminal TM domain / SecD export protein N-terminal TM region / Protein-export membrane protein SecF, bacterial / Protein translocase subunit SecD / Protein-export membrane protein SecD/SecF, bacterial / Protein-export membrane protein SecD/SecF/SecDF, conserved site / Protein-export membrane protein SecD/SecF, archaeal and bacterial / : / : / : / Protein export membrane protein / SecD/SecF GG Motif / Protein translocase subunit SecDF, P1 domain, N-terminal / SecDF, P1 head subdomain / Membrane insertase YidC, N-terminal / YidC, periplasmic domain superfamily / YidC periplasmic domain / Membrane insertase YidC / : / Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / Membrane insertase YidC/Oxa1, C-terminal / 60Kd inner membrane protein / Membrane insertase YidC/ALB3/OXA1/COX18 / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY
Similarity search - Domain/homology
Protein translocase subunit SecD / Protein translocase subunit SecF / Protein translocase subunit SecE / Protein-export membrane protein SecG / Protein translocase subunit SecY / Membrane protein insertase YidC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsSchaffitzel C / Botte M / Karuppasamy M / Papai G / Schultz P
Funding support Germany, France, United Kingdom, 3 items
OrganizationGrant numberCountry
Baden-Wurttemberg StiftungMeth-P-LS-4 Germany
French National Research AgencyANR- 09-JCJC-0044 France
Biotechnology and Biological Sciences Research CouncilBB/P000940/1 United Kingdom
CitationJournal: Sci Rep / Year: 2016
Title: A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion.
Authors: Mathieu Botte / Nathan R Zaccai / Jelger Lycklama À Nijeholt / Remy Martin / Kèvin Knoops / Gabor Papai / Juan Zou / Aurélien Deniaud / Manikandan Karuppasamy / Qiyang Jiang / Abhishek ...Authors: Mathieu Botte / Nathan R Zaccai / Jelger Lycklama À Nijeholt / Remy Martin / Kèvin Knoops / Gabor Papai / Juan Zou / Aurélien Deniaud / Manikandan Karuppasamy / Qiyang Jiang / Abhishek Singha Roy / Klaus Schulten / Patrick Schultz / Juri Rappsilber / Giuseppe Zaccai / Imre Berger / Ian Collinson / Christiane Schaffitzel /
Abstract: The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein ...The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein insertion. By employing an integrative approach combining small-angle neutron scattering (SANS), low-resolution electron microscopy and biophysical analyses we determined the arrangement of the proteins and lipids within the super-complex. The results guided the placement of X-ray structures of individual HTL components and allowed the proposal of a model of the functional translocon. Their arrangement around a central lipid-containing pool conveys an unexpected, but compelling mechanism for membrane-protein insertion. The periplasmic domains of YidC and SecD are poised at the protein-channel exit-site of SecY, presumably to aid the emergence of translocating polypeptides. The SecY lateral gate for membrane-insertion is adjacent to the membrane 'insertase' YidC. Absolute-scale SANS employing a novel contrast-match-point analysis revealed a dynamic complex adopting open and compact configurations around an adaptable central lipid-filled chamber, wherein polytopic membrane-proteins could fold, sheltered from aggregation and proteolysis.
History
DepositionNov 20, 2016-
Header (metadata) releaseDec 28, 2016-
Map releaseDec 28, 2016-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 8.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5mg3
  • Surface level: 8.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3506.png

Downloads & links

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Map

FileDownload / File: emd_3506.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of cross-linked HTL
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 140 pix.
= 190.4 Å		1.36 Å/pix.
x 140 pix.
= 190.4 Å		1.36 Å/pix.
x 140 pix.
= 190.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.5 / Movie #1: 8.5
Minimum - Maximum-63.992626000000001 - 153.928089999999997
Average (Standard dev.)1.7283827 (±15.463875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 190.40001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z190.400190.400190.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-63.993153.9281.728

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Supplemental data

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Sample components

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Entire : bacterial holo-translocon (HTL)

EntireName: bacterial holo-translocon (HTL)
Components
  • Complex: bacterial holo-translocon (HTL)
    • Protein or peptide: Protein translocase subunit SecY
    • Protein or peptide: Protein translocase subunit SecE
    • Protein or peptide: Protein-export membrane protein SecG
    • Protein or peptide: Protein translocase subunit SecD
    • Protein or peptide: Protein translocase subunit SecF
    • Protein or peptide: Membrane protein insertase YidC

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Supramolecule #1: bacterial holo-translocon (HTL)

SupramoleculeName: bacterial holo-translocon (HTL) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Membrane Protein Complex consisting of SecYEG-SecDFYajC-YidC
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Protein translocase subunit SecY

MacromoleculeName: Protein translocase subunit SecY / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 50.410523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VWNCERITIS HRKQTMAKQP GLDFQSAKGG LGELKRRLLF VIGALIVFRI GSFIPIPGID AAVLAKLLEQ QRGTIIEMFN MFSGGALSR ASIFALGIMP YISASIIIQL LTVVHPTLAE IKKEGESGRR KISQYTRYGT LVLAIFQSIG IATGLPNMPG M QGLVINPG ...String:
VWNCERITIS HRKQTMAKQP GLDFQSAKGG LGELKRRLLF VIGALIVFRI GSFIPIPGID AAVLAKLLEQ QRGTIIEMFN MFSGGALSR ASIFALGIMP YISASIIIQL LTVVHPTLAE IKKEGESGRR KISQYTRYGT LVLAIFQSIG IATGLPNMPG M QGLVINPG FAFYFTAVVS LVTGTMFLMW LGEQITERGI GNGISIIIFA GIVAGLPPAI AHTIEQARQG DLHFLVLLLV AV LVFAVTF FVVFVERGQR RIVVNYAKRQ QGRRVYAAQS THLPLKVNMA GVIPAIFASS IILFPATIAS WFGGGTGWNW LTT ISLYLQ PGQPLYVLLY ASAIIFFCFF YTALVFNPRE TADNLKKSGA FVPGIRPGEQ TAKYIDKVMT RLTLVGALYI TFIC LIPEF MRDAMKVPFY FGGTSLLIVV VVIMDFMAQV QTLMMSSQYE SALKKANLKG YGR

UniProtKB: Protein translocase subunit SecY

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Macromolecule #2: Protein translocase subunit SecE

MacromoleculeName: Protein translocase subunit SecE / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.248021 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHDDD DKAMGANTEA QGSGRGLEAM KWVVVVALLL VAIVGNYLYR DIMLPLRALA VVILIAAAGG VALLTTKGKA TVAFAREAR TEVRKVIWPT RQETLHTTLI VAAVTAVMSL ILWGLDGILV RLVSFITGLR F

UniProtKB: Protein translocase subunit SecE

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Macromolecule #3: Protein-export membrane protein SecG

MacromoleculeName: Protein-export membrane protein SecG / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.326448 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VGTGWYSGSP GILYHWPEVL RIQELIMYEA LLVVFLIVAI GLVGLIMLQQ GKGADMGASF GAGASATLFG SSGSGNFMTR MTALLATLF FIISLVLGNI NSNKTNKGSE WENLSAPAKT EQTQPAAPAK PTSDIPN

UniProtKB: Protein-export membrane protein SecG

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Macromolecule #4: Protein translocase subunit SecD

MacromoleculeName: Protein translocase subunit SecD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 67.687984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHMLN RYPLWKYVML IVVIVIGLLY ALPNLFGEDP AVQITGARGV AASEQTLIQV QKTLQEEKIT AKSVALEEGA ILARFDSTD TQLRAREALM GVMGDKYVVA LNLAPATPRW LAAIHAEPMK LGLDLRGGVH FLMEVDMDTV LGKLQEQNID S LRSDLREK ...String:
MHHHHHHMLN RYPLWKYVML IVVIVIGLLY ALPNLFGEDP AVQITGARGV AASEQTLIQV QKTLQEEKIT AKSVALEEGA ILARFDSTD TQLRAREALM GVMGDKYVVA LNLAPATPRW LAAIHAEPMK LGLDLRGGVH FLMEVDMDTV LGKLQEQNID S LRSDLREK GIPYTTVRKE NNYGLSITFR DAKARDEAIA YLSKRHPDLV ISSQGSNQLR AVMSDARLSE AREYAVQQNI NI LRNRVNQ LGVAEPVVQR QGADRIVVEL PGIQDTARAK EILGATATLE FRLVNTNVDQ AAAASGRVPG DSEVKQTREG QPV VLYKRV ILTGDHITDS TSSQDEYNQP QVNISLDSAG GNIMSNFTKD NIGKPMATLF VEYKDSGKKD ANGRAVLVKQ EEVI NIANI QSRLGNSFRI TGINNPNEAR QLSLLLRAGA LIAPIQIVEE RTIGPTLGMQ NIEQGLEACL AGLLVSILFM IIFYK KFGL IATSALIANL ILIVGIMSLL PGATLSMPGI AGIVLTLAVA VDANVLINER IKEELSNGRT VQQAIDEGYR GAFSSI FDA NITTLIKVII LYAVGTGAIK GFAITTGIGV ATSMFTAIVG TRAIVNLLYG GKRVKKLSI

UniProtKB: Protein translocase subunit SecD

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Macromolecule #5: Protein translocase subunit SecF

MacromoleculeName: Protein translocase subunit SecF / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 35.41325 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAQEYTVEQL NHGRKVYDFM RWDYWAFGIS GLLLIAAIVI MGVRGFNWGL DFTGGTVIEI TLEKPAEIDV MRDALQKAGF EEPMLQNFG SSHDIMVRMP PAEGETGGQV LGSQVLKVIN ESTNQNAAVK RIEFVGPSVG ADLAQTGAMA LMAALLSILV Y VGFRFEWR ...String:
MAQEYTVEQL NHGRKVYDFM RWDYWAFGIS GLLLIAAIVI MGVRGFNWGL DFTGGTVIEI TLEKPAEIDV MRDALQKAGF EEPMLQNFG SSHDIMVRMP PAEGETGGQV LGSQVLKVIN ESTNQNAAVK RIEFVGPSVG ADLAQTGAMA LMAALLSILV Y VGFRFEWR LAAGVVIALA HDVIITLGIL SLFHIEIDLT IVASLMSVIG YSLNDSIVVS DRIRENFRKI RRGTPYEIFN VS LTQTLHR TLITSGTTLM VILMLYLFGG PVLEGFSLTM LIGVSIGTAS SIYVASALAL KLGMKREHML QQKVEKEGAD QPS ILP

UniProtKB: Protein translocase subunit SecF

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Macromolecule #6: Membrane protein insertase YidC

MacromoleculeName: Membrane protein insertase YidC / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 62.658582 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDPSSRDSQR NLLVIALLFV SFMIWQAWEQ DKNPQPQAQQ TTQTTTTAAG SAADQGVPAS GQGKLISVKT DVLDLTINTR GGDVEQALL PAYPKELNST QPFQLLETSP QFIYQAQSGL TGRDGPDNPA NGPRPLYNVE KDAYVLAEGQ NELQVPMTYT D AAGNTFTK ...String:
MDPSSRDSQR NLLVIALLFV SFMIWQAWEQ DKNPQPQAQQ TTQTTTTAAG SAADQGVPAS GQGKLISVKT DVLDLTINTR GGDVEQALL PAYPKELNST QPFQLLETSP QFIYQAQSGL TGRDGPDNPA NGPRPLYNVE KDAYVLAEGQ NELQVPMTYT D AAGNTFTK TFVLKRGDYA VNVNYNVQNA GEKPLEISSF GQLKQSITLP PHLDTGSSNF ALHTFRGAAY STPDAAYAAY AF DTIADNE NLNISSKGGW VAMLQQYFAT AWIPHNDGTN NFYTANLGNG IAAIGYKSQP VLVQPGQTGA MNSTLWVGPE IQD KMAAVA PHLDLTVDYG WLWFISQPLF KLLKWIHSFV GNWGFSIIII TFIVRGIMYP LTKAQYTSMA KMRMLQPKIQ AMRE RLGDD KQRISQEMMA LYKAEKVNPL GGCFPLLIQM PIFLALYYML MGSVELRQAP FALWIHDLSA QDPYYILPIL MGVTM FFIQ KMSPTTVTDP MQQKIMTFMP VIFTVFFLWF PSGLVLYYIV SNLVTIIQQQ LIYRGLEKRG LHSREKKKSH HHHHH

UniProtKB: Membrane protein insertase YidC

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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 / Chamber humidity: 100 % / Chamber temperature: 5 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 84732
Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 53648
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER
FSC plot (resolution estimation)

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