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- PDB-2wwa: Cryo-EM structure of idle yeast Ssh1 complex bound to the yeast 8... -

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Entry
Database: PDB / ID: 2wwa
TitleCryo-EM structure of idle yeast Ssh1 complex bound to the yeast 80S ribosome
Components
  • (25S RRNA) x 4
  • (60S RIBOSOMAL PROTEIN ...) x 8
  • (PROTEIN TRANSPORT PROTEIN ...Protein targeting) x 2
  • SEC SIXTY-ONE PROTEIN HOMOLOG
KeywordsRIBOSOME / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / TRANSMEMBRANE / PHOSPHOPROTEIN / SIGNAL SEQUENCE / MEMBRANE / TRANSPORT / RNA-BINDING / RRNA-BINDING / TRANSLOCATION / PROTEIN CONDUCTING CHANNEL / PROTEIN EXIT TUNNEL / ENDOPLASMIC RETICULUM / COTRANSLATIONAL PROTEIN TRANSLOCATION / ISOPEPTIDE BOND / PROTEIN TRANSPORT
Function / homology
Function and homology information


translocon complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane / post-translational protein targeting to membrane, translocation / nuclear inner membrane ...translocon complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane / post-translational protein targeting to membrane, translocation / nuclear inner membrane / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / protein transmembrane transporter activity / regulation of translational fidelity / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / guanyl-nucleotide exchange factor activity / ribosomal large subunit assembly / ribosome binding / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / mRNA binding / structural molecule activity / endoplasmic reticulum membrane / endoplasmic reticulum / RNA binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein transport Sec61-beta/Sbh / 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 secE/sec61-gamma signature. / Protein secY signature 1. / SecE/Sec61-gamma subunits of protein translocation complex ...Protein transport Sec61-beta/Sbh / 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 secE/sec61-gamma signature. / Protein secY signature 1. / 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 / Ribosomal protein L23/L25, N-terminal / 60S ribosomal protein L35 / Ribosomal protein L23, N-terminal domain / Ribosomal protein L31e, conserved site / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e, conserved site / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L19e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal_L31e / 60S ribosomal protein L19 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L31e / Ribosomal protein L39e / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L39e domain superfamily / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L19e / Ribosomal L39 protein / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L31e signature. / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L1e signature. / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L22/L17, conserved site / Ribosomal L29 protein / Ribosomal protein L24/L26, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L25/L23 / Ribosomal protein L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L24 signature. / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L4/L1 family / Ribosomal protein L23/L15e core domain superfamily / KOW / KOW motif / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / 60S ribosomal protein L19-A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A ...RNA / RNA (> 10) / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / 60S ribosomal protein L19-A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Protein transport protein SSS1 / Sec sixty-one protein homolog / 60S ribosomal protein L35-A / Large ribosomal subunit protein uL4B / Protein transport protein SBH2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsBecker, T. / Mandon, E. / Bhushan, S. / Jarasch, A. / Armache, J.P. / Funes, S. / Jossinet, F. / Gumbart, J. / Mielke, T. / Berninghausen, O. ...Becker, T. / Mandon, E. / Bhushan, S. / Jarasch, A. / Armache, J.P. / Funes, S. / Jossinet, F. / Gumbart, J. / Mielke, T. / Berninghausen, O. / Schulten, K. / Westhof, E. / Gilmore, R. / Beckmann, R.
CitationJournal: Science / Year: 2009
Title: Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome.
Authors: Thomas Becker / Shashi Bhushan / Alexander Jarasch / Jean-Paul Armache / Soledad Funes / Fabrice Jossinet / James Gumbart / Thorsten Mielke / Otto Berninghausen / Klaus Schulten / Eric ...Authors: Thomas Becker / Shashi Bhushan / Alexander Jarasch / Jean-Paul Armache / Soledad Funes / Fabrice Jossinet / James Gumbart / Thorsten Mielke / Otto Berninghausen / Klaus Schulten / Eric Westhof / Reid Gilmore / Elisabet C Mandon / Roland Beckmann /
Abstract: The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. Although Sec complexes can form oligomers, it has been suggested that a single copy may ...The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. Although Sec complexes can form oligomers, it has been suggested that a single copy may serve as an active PCC. We determined subnanometer-resolution cryo-electron microscopy structures of eukaryotic ribosome-Sec61 complexes. In combination with biochemical data, we found that in both idle and active states, the Sec complex is not oligomeric and interacts mainly via two cytoplasmic loops with the universal ribosomal adaptor site. In the active state, the ribosomal tunnel and a central pore of the monomeric PCC were occupied by the nascent chain, contacting loop 6 of the Sec complex. This provides a structural basis for the activity of a solitary Sec complex in cotranslational protein translocation.
History
DepositionOct 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Structure summary
Revision 1.2Oct 21, 2015Group: Other
Revision 1.3Apr 19, 2017Group: Other
Revision 2.0Oct 3, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / em_software ...atom_site / em_software / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_software.image_processing_id / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.i_auth_seq_id / _ndb_struct_na_base_pair.i_label_comp_id / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair.j_auth_seq_id / _ndb_struct_na_base_pair.j_label_comp_id / _ndb_struct_na_base_pair.j_label_seq_id / _ndb_struct_na_base_pair.pair_name / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.i_auth_seq_id_1 / _ndb_struct_na_base_pair_step.i_auth_seq_id_2 / _ndb_struct_na_base_pair_step.i_label_comp_id_1 / _ndb_struct_na_base_pair_step.i_label_comp_id_2 / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.j_auth_seq_id_1 / _ndb_struct_na_base_pair_step.j_auth_seq_id_2 / _ndb_struct_na_base_pair_step.j_label_comp_id_1 / _ndb_struct_na_base_pair_step.j_label_comp_id_2 / _ndb_struct_na_base_pair_step.j_label_seq_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_2 / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.step_name / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement

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Structure visualization

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  • Simplified surface model + fitted atomic model
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Assembly

Deposited unit
A: SEC SIXTY-ONE PROTEIN HOMOLOG
B: PROTEIN TRANSPORT PROTEIN SSS1
C: PROTEIN TRANSPORT PROTEIN SEB2
D: 25S RRNA
E: 25S RRNA
F: 25S RRNA
G: 25S RRNA
H: 60S RIBOSOMAL PROTEIN L4-B
I: 60S RIBOSOMAL PROTEIN L17-A
J: 60S RIBOSOMAL PROTEIN L19
K: 60S RIBOSOMAL PROTEIN L25
L: 60S RIBOSOMAL PROTEIN L26-A
M: 60S RIBOSOMAL PROTEIN L31-A
N: 60S RIBOSOMAL PROTEIN L35
O: 60S RIBOSOMAL PROTEIN L39


Theoretical massNumber of molelcules
Total (without water)261,77615
Polymers261,77615
Non-polymers00
Water0
1


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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SEC SIXTY-ONE PROTEIN HOMOLOG / SSH1P / SSH1 COMPLEX SUBUNIT SSH1 / SSH1 COMPLEX SUBUNIT ALPHA


Mass: 53350.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38353

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PROTEIN TRANSPORT PROTEIN ... , 2 types, 2 molecules BC

#2: Protein PROTEIN TRANSPORT PROTEIN SSS1 / Protein targeting / SSS1P / SEC61 COMPLEX SUBUNIT SSS1 / SEC61 COMPLEX SUBUNIT GAMMA / SSH1 COMPLEX SUBUNIT SSS1 / SSH1 ...SSS1P / SEC61 COMPLEX SUBUNIT SSS1 / SEC61 COMPLEX SUBUNIT GAMMA / SSH1 COMPLEX SUBUNIT SSS1 / SSH1 COMPLEX SUBUNIT GAMMA


Mass: 8958.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P35179
#3: Protein PROTEIN TRANSPORT PROTEIN SEB2 / Protein targeting / SBH2P / SSH1 COMPLEX SUBUNIT SEB2 / SSH1 COMPLEX SUBUNIT BETA


Mass: 9505.979 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-87 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P52871

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RNA chain , 4 types, 4 molecules DEFG

#4: RNA chain 25S RRNA


Mass: 20302.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: H5_H6_H7 FRAGMENT / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#5: RNA chain 25S RRNA


Mass: 11089.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: H24 FRAGMENT / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#6: RNA chain 25S RRNA


Mass: 8052.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: H50 FRAGMENT / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#7: RNA chain 25S RRNA


Mass: 5700.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: H59 FRAGMENT / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)

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60S RIBOSOMAL PROTEIN ... , 8 types, 8 molecules HIJKLMNO

#8: Protein 60S RIBOSOMAL PROTEIN L4-B / Ribosome / 60S RIBOSOMAL PROTEIN L4 / L2 / YL2 / RP2


Mass: 39129.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P49626
#9: Protein 60S RIBOSOMAL PROTEIN L17-A / Ribosome / 60S RIBOSOMAL PROTEIN L17 / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05740
#10: Protein 60S RIBOSOMAL PROTEIN L19 / / L23 / YL14 / RP15L / RP33


Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05735, UniProt: P0CX82*PLUS
#11: Protein 60S RIBOSOMAL PROTEIN L25 / / YL25 / RP16L / YP42'


Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04456
#12: Protein 60S RIBOSOMAL PROTEIN L26-A / Ribosome / 60S RIBOSOMAL PROTEIN L26 / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05743
#13: Protein 60S RIBOSOMAL PROTEIN L31-A / Ribosome / 60S RIBOSOMAL PROTEIN L31 / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0C2H8
#14: Protein 60S RIBOSOMAL PROTEIN L35 /


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39741, UniProt: P0CX84*PLUS
#15: Protein 60S RIBOSOMAL PROTEIN L39 / / L46 / YL40


Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04650

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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: AN IDLE YEAST SSH1 COMPLEX BOUND TO A YEAST 80S RIBOSOME
Type: RIBOSOME
Buffer solutionName: 20 MM HEPES/KOH, PH 7.5 100 MM KOAC, 10 MM MG(OAC)2, 1.5 MM DTT, 0.1 % (W/V) DIGITONIN
pH: 7.5
Details: 20 MM HEPES/KOH, PH 7.5 100 MM KOAC, 10 MM MG(OAC)2, 1.5 MM DTT, 0.1 % (W/V) DIGITONIN
SpecimenConc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: CRYOGEN - ETHANE, HUMIDITY - 95, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 10 SECONDS BEFORE PLUNGING, USE 2 LAYER OF FILTER PAPER,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Calibrated magnification: 38000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1200 nm / Cs: 2.26 mm
Specimen holderTemperature: 84 K / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 185

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: DEFOCUS GROUP VOLUMES
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 8.9 Å / Num. of particles: 20400 / Nominal pixel size: 1.2375 Å / Actual pixel size: 1.2375 Å
Details: SUBDATASET RESULTED FROM SORTING AS DESCRIBED IN THE PAPER. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1669.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: METHOD--MANUAL FOLLOWED BY MDFF REFINEMENT PROTOCOL--SINGLE PARTICLE CRYO EM
RefinementHighest resolution: 8.9 Å
Refinement stepCycle: LAST / Highest resolution: 8.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11299 3002 0 0 14301

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