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- PDB-2wwa: Cryo-EM structure of idle yeast Ssh1 complex bound to the yeast 8... -
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Basic information
Entry | Database: PDB / ID: 2wwa | |||||||||
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Title | Cryo-EM structure of idle yeast Ssh1 complex bound to the yeast 80S ribosome | |||||||||
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![]() | RIBOSOME / 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 | ![]() 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 / SRP-dependent cotranslational protein targeting to membrane / signal sequence binding / 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 / SRP-dependent cotranslational protein targeting to membrane / signal sequence binding / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / protein transmembrane transporter activity / regulation of translational fidelity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / guanyl-nucleotide exchange factor activity / ribosomal large subunit biogenesis / ribosome binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / mRNA binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / RNA binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.9 Å | |||||||||
![]() | Becker, 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. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 341.2 KB | Display | ![]() |
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PDB format | ![]() | 250.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1669MC ![]() 1651C ![]() 1652C ![]() 1667C ![]() 1668C ![]() 2ww9C ![]() 2wwbC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53350.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-PROTEIN TRANSPORT PROTEIN ... , 2 types, 2 molecules BC
#2: Protein | Mass: 8958.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein | Mass: 9505.979 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-87 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain , 4 types, 4 molecules DEFG
#4: RNA chain | Mass: 20302.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: H5_H6_H7 FRAGMENT / Source: (natural) ![]() ![]() |
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#5: RNA chain | Mass: 11089.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: H24 FRAGMENT / Source: (natural) ![]() ![]() |
#6: RNA chain | Mass: 8052.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: H50 FRAGMENT / Source: (natural) ![]() ![]() |
#7: RNA chain | Mass: 5700.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: H59 FRAGMENT / Source: (natural) ![]() ![]() |
-60S RIBOSOMAL PROTEIN ... , 8 types, 8 molecules HIJKLMNO
#8: Protein | Mass: 39129.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#9: Protein | Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: AN IDLE YEAST SSH1 COMPLEX BOUND TO A YEAST 80S RIBOSOME Type: RIBOSOME |
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Buffer solution | Name: 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 |
Specimen | Conc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 38000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1200 nm / Cs: 2.26 mm |
Specimen holder | Temperature: 84 K / Tilt angle min: 0 ° |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 185 |
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Processing
EM software | Name: SPIDER / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: DEFOCUS GROUP VOLUMES | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: 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 building | Protocol: OTHER / Space: REAL Details: METHOD--MANUAL FOLLOWED BY MDFF REFINEMENT PROTOCOL--SINGLE PARTICLE CRYO EM | ||||||||||||
Refinement | Highest resolution: 8.9 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.9 Å
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