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- EMDB-10074: SecA in complex with ribosome nascent chain -

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Basic information

Entry
Database: EMDB / ID: EMD-10074
TitleSecA in complex with ribosome nascent chain
Map dataSecA bound to translating ribosome (with focused refined)
Sample
  • Complex: ribosome nascent chain in complex with SecA
    • Protein or peptide: SecA
Function / homology
Function and homology information


protein-secreting ATPase / intracellular protein transmembrane transport / protein import / protein targeting / helicase activity / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
SEC-C motif / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily ...SEC-C motif / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein translocase subunit SecA
Similarity search - Component
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsJomaa A / Shuai W / Shan S / Ban N
Funding support Switzerland, United States, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
National Institutes of Health/National Center for Research Resources United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: The molecular mechanism of cotranslational membrane protein recognition and targeting by SecA.
Authors: Shuai Wang / Ahmad Jomaa / Mateusz Jaskolowski / Chien-I Yang / Nenad Ban / Shu-Ou Shan /
Abstract: Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent ...Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent membrane proteins to the SecYEG translocase at the plasma membrane. The molecular mechanism of this pathway remains unclear. Here we use biochemical and cryoelectron microscopy analyses to show that the amino-terminal amphipathic helix of SecA and the ribosomal protein uL23 form a composite binding site for the transmembrane domain (TMD) on the nascent protein. This binding mode further enables recognition of charged residues flanking the nascent TMD and thus explains the specificity of SecA recognition. Finally, we show that membrane-embedded SecYEG promotes handover of the translating ribosome from SecA to the translocase via a concerted mechanism. Our work provides a molecular description of the SecA-mediated cotranslational targeting pathway and demonstrates an unprecedented role of the ribosome in shielding nascent TMDs.
History
DepositionJun 17, 2019-
Header (metadata) releaseOct 9, 2019-
Map releaseOct 9, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10074.png

Downloads & links

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Map

FileDownload / File: emd_10074.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSecA bound to translating ribosome (with focused refined)
Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.10420957 - 0.186529
Average (Standard dev.)0.00029363655 (±0.010255728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 166.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z166.800166.800166.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-420-29
NX/NY/NZ887886
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.1040.1870.000

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Supplemental data

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Sample components

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Entire : ribosome nascent chain in complex with SecA

EntireName: ribosome nascent chain in complex with SecA
Components
  • Complex: ribosome nascent chain in complex with SecA
    • Protein or peptide: SecA

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Supramolecule #1: ribosome nascent chain in complex with SecA

SupramoleculeName: ribosome nascent chain in complex with SecA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35
Molecular weightTheoretical: 2.6 MDa

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Macromolecule #1: SecA

MacromoleculeName: SecA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: QGHMMLIKLL TKVFGCRNDR TLRRMRKVVN IINAMEPEMM KLSDEELKGK TAEFRARLEK GEVLENLIPE AFAVVREASK RVFGMRHFDV QLLGGMVLNE RCIAEMRTGE GKTLTATLPA YLNALTGKGV HVVTVNDYLA QRDAENNRPL FEFLGLTVGI NLPGMPAPAK ...String:
QGHMMLIKLL TKVFGCRNDR TLRRMRKVVN IINAMEPEMM KLSDEELKGK TAEFRARLEK GEVLENLIPE AFAVVREASK RVFGMRHFDV QLLGGMVLNE RCIAEMRTGE GKTLTATLPA YLNALTGKGV HVVTVNDYLA QRDAENNRPL FEFLGLTVGI NLPGMPAPAK REAYAADITY GTNNEYGFDY LRDNMAFSPE ERVQRKLHYA LVDEVDSILI DEARTPLIIS GPAEDSSEMY KRVNKIIPHL IRQEKEDSET FQGEGHFSVD EKSRQVNLTE RGLVLIEELL VKEGIMDEGE SLYSPANIML MHHVTAALRA HALFTRDVDY IVKDGEVIIV DEHTGRTMQG RRWSDGLHQA VEAKEGVQIQ NENQTLASIT FQNYFRLYEK LAGMTGTADT EAFEFSSIYK LDTVVVPTNR PMIRKDLPDL VYMTEAEKIQ AIIEDIKERT AKGQPVLVGT ISIEKSELVS NELTKAGIKH NVLNAKFHAN EAAIVAQAGY PAAVTIATNM AGRGTDIVLG GSWQAEVAAL ENPTAEQIEK IKADWQVRHD AVLEAGGLHI IGTERHESRR IDNQLRGRSG RQGDAGSSRF YLSMEDALMR IFASDRVSGM MRKLGMKPGE AIEHPWVTKA IANAQRKVES RNFDIRKQLL EYDDVANDQR RAIYSQRNEL LDVSDVSETI NSIREDVFKA TIDAYIPPQS LEEMWDIPGL QERLKNDFDL DLPIAEWLDK EPELHEETLR ERILAQSIEV YQRKEEVVGA EMMRHFEKGV MLQTLDSLWK EHLAAMDYLR QGIHLRGYAQ KDPKQEYKRE SFSMFAAMLE SLKYEVISTL SKVQVRMP

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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: 7.4
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailsprepared using in-vitro translation system

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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
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: 70S ribosome
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 37334

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Atomic model buiding 1

Initial modelPDB ID:

5gag

RefinementProtocol: RIGID BODY FIT

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