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- PDB-3bo0: Ribosome-SecY complex -

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Basic information

Entry
Database: PDB / ID: 3bo0
TitleRibosome-SecY complex
Components
  • (23S RIBOSOMAL ...) x 4
  • (PREPROTEIN TRANSLOCASE ...) x 3
KeywordsRIBOSOME / Ribosome-SecY complex / protein translocation
Function / homology
Function and homology information


intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting / protein transport / plasma membrane
Similarity search - Function
Preprotein translocase subunit SecG / Protein translocase subunit SecY / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secY signature 1. / Protein secY signature 2. ...Preprotein translocase subunit SecG / Protein translocase subunit SecY / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / 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
: / RNA / RNA (> 10) / Preprotein translocase subunit SecG / Protein translocase subunit SecE / Protein translocase subunit SecY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsAkey, C.W. / Menetret, J.F.
CitationJournal: Mol Cell / Year: 2007
Title: Ribosome binding of a single copy of the SecY complex: implications for protein translocation.
Authors: Jean-François Ménétret / Julia Schaletzky / William M Clemons / Andrew R Osborne / Sigrid S Skånland / Carilee Denison / Steven P Gygi / Don S Kirkpatrick / Eunyong Park / Steven J ...Authors: Jean-François Ménétret / Julia Schaletzky / William M Clemons / Andrew R Osborne / Sigrid S Skånland / Carilee Denison / Steven P Gygi / Don S Kirkpatrick / Eunyong Park / Steven J Ludtke / Tom A Rapoport / Christopher W Akey /
Abstract: The SecY complex associates with the ribosome to form a protein translocation channel in the bacterial plasma membrane. We have used cryo-electron microscopy and quantitative mass spectrometry to ...The SecY complex associates with the ribosome to form a protein translocation channel in the bacterial plasma membrane. We have used cryo-electron microscopy and quantitative mass spectrometry to show that a nontranslating E. coli ribosome binds to a single SecY complex. The crystal structure of an archaeal SecY complex was then docked into the electron density maps. In the resulting model, two cytoplasmic loops of SecY extend into the exit tunnel near proteins L23, L29, and L24. The loop between transmembrane helices 8 and 9 interacts with helices H59 and H50 in the large subunit RNA, while the 6/7 loop interacts with H7. We also show that point mutations of basic residues within either loop abolish ribosome binding. We suggest that SecY binds to this primary site on the ribosome and subsequently captures and translocates the nascent chain.
History
DepositionDec 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_image_scans / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
D: 23S RIBOSOMAL RNA
E: 23S RIBOSOMAL RNA
F: 23S RIBOSOMAL RNA
G: 23S RIBOSOMAL RNA
A: PREPROTEIN TRANSLOCASE SecY SUBUNIT
B: PREPROTEIN TRANSLOCASE SecE SUBUNIT
C: Preprotein translocase secG subunit


Theoretical massNumber of molelcules
Total (without water)93,1227
Polymers93,1227
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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23S RIBOSOMAL ... , 4 types, 4 molecules DEFG

#1: RNA chain 23S RIBOSOMAL RNA /


Mass: 8698.224 Da / Num. of mol.: 1 / Fragment: GB residues 79-105 / Source method: isolated from a natural source / Details: helix 7 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 33357927
#2: RNA chain 23S RIBOSOMAL RNA /


Mass: 8860.439 Da / Num. of mol.: 1 / Fragment: GB residues 478-504 / Source method: isolated from a natural source / Details: helix 24 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 33357927
#3: RNA chain 23S RIBOSOMAL RNA /


Mass: 6024.601 Da / Num. of mol.: 1 / Fragment: GB residues 1385-1403 / Source method: isolated from a natural source / Details: helix 47 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 33357927
#4: RNA chain 23S RIBOSOMAL RNA /


Mass: 10382.260 Da / Num. of mol.: 1 / Fragment: GB residues 1518-1549 / Source method: isolated from a natural source / Details: helix 59 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 33357927

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PREPROTEIN TRANSLOCASE ... , 3 types, 3 molecules ABC

#5: Protein PREPROTEIN TRANSLOCASE SecY SUBUNIT


Mass: 48367.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q60175*PLUS
#6: Protein PREPROTEIN TRANSLOCASE SecE SUBUNIT / PROTEIN TRANSPORT PROTEIN SEC61 GAMMA SUBUNIT


Mass: 7149.573 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q57817*PLUS
#7: Protein/peptide Preprotein translocase secG subunit / Protein transport protein SEC61 subunit beta homolog


Mass: 3639.310 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P60460*PLUS

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Details

Sequence detailsTHIS PDB FILE WAS OBTAINED UPON RIGID BODY REFINEMENT OF A STARTING PDB FILE INTO A CRYO-EM MAP. ...THIS PDB FILE WAS OBTAINED UPON RIGID BODY REFINEMENT OF A STARTING PDB FILE INTO A CRYO-EM MAP. THE E. COLI RIBOSOMES ARE OBTAINED NATURALLY, BUT FOR THE MODELING OF THE PROTEINS INTO THE EM MAP, AUTHORS SOMETIMES DID NOT MODEL IN THE ENTIRE PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ribosome-SecY complex / Type: RIBOSOME / Details: in DDM
Buffer solutionName: 50 mM HEPES- KOH pH 7.5, 100 mM KOAc, 10 mM Mg(OAc)2, 0.05% DDM
pH: 7.5
Details: 50 mM HEPES- KOH pH 7.5, 100 mM KOAc, 10 mM Mg(OAc)2, 0.05% DDM
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Solid carbon on a holey film, 400 mesh Cu grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: The specimens were plunge frozen in liquid ethane at 4 degrees C at an RH of ~90-95%.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Details: Gatan DH626 cold holder
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 51000 X / Nominal defocus max: -3000 nm / Nominal defocus min: -700 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

CTF correctionDetails: EMAN- phase flipping of particles form the same micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Projection matching in EMAN / Resolution: 9.6 Å / Num. of particles: 39000 / Actual pixel size: 2.73 Å / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: visual fit in O and Chimera
Details: REFINEMENT PROTOCOL--rigid body, followed by manual rebuilding and extension of the loops
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11RHZ11RHZ1PDBexperimental model
22I2T

2i2t
PDB Unreleased entry

12I2T2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms4169 2263 0 0 6432

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