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Yorodumi- PDB-2wwb: CRYO-EM STRUCTURE OF THE MAMMALIAN SEC61 COMPLEX BOUND TO THE ACT... -
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-Basic information
Entry | Database: PDB / ID: 2wwb | |||||||||
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Title | CRYO-EM STRUCTURE OF THE MAMMALIAN SEC61 COMPLEX BOUND TO THE ACTIVELY TRANSLATING WHEAT GERM 80S RIBOSOME | |||||||||
Components |
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Keywords | RIBOSOME / PROTEIN EXIT TUNNEL / COTRANSLATIONAL PROTEIN TRANSLOCATION / PROTEIN CONDUCTING CHANNEL / SIGNAL SEQUENCE | |||||||||
Function / homology | Function and homology information Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / pronephric nephron development / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / pronephric nephron development / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / post-translational protein targeting to membrane, translocation / 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 / phospholipid binding / ribosome binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / mRNA binding / endoplasmic reticulum membrane / endoplasmic reticulum / RNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | CANIS LUPUS FAMILIARIS (dog) TRITICUM AESTIVUM (bread wheat) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.48 Å | |||||||||
Authors | 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. | |||||||||
Citation | Journal: 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 |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 2wwb.cif.gz | 343.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wwb.ent.gz | 251.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wwb_validation.pdf.gz | 898.7 KB | Display | wwPDB validaton report |
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Full document | 2wwb_full_validation.pdf.gz | 984 KB | Display | |
Data in XML | 2wwb_validation.xml.gz | 52.8 KB | Display | |
Data in CIF | 2wwb_validation.cif.gz | 80.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2wwb ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2wwb | HTTPS FTP |
-Related structure data
Related structure data | 1652MC 1651C 1667C 1668C 1669C 2ww9C 2wwaC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 52279.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / Organ: PANCREAS / References: UniProt: P38377 |
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#2: Protein | Mass: 7752.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / Organ: PANCREAS / References: UniProt: P60058 |
#3: Protein | Mass: 9987.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / Organ: PANCREAS / References: UniProt: P60467 |
-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: COORDINATE SOURCE ORIGINALLY FROM SACCHAROMYCES CEREVISIAE Source: (natural) TRITICUM AESTIVUM (bread wheat) |
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#5: RNA chain | Mass: 11089.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COORDINATE SOURCE ORIGINALLY FROM SACCHAROMYCES CEREVISIAE Source: (natural) TRITICUM AESTIVUM (bread wheat) |
#6: RNA chain | Mass: 8052.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COORDINATE SOURCE ORIGINALLY FROM SACCHAROMYCES CEREVISIAE Source: (natural) TRITICUM AESTIVUM (bread wheat) |
#7: RNA chain | Mass: 4477.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COORDINATE SOURCE ORIGINALLY FROM ORYZA SATIVA / Source: (natural) TRITICUM AESTIVUM (bread wheat) |
-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 Details: COORDINATE SOURCE ORIGINALLY FROM SACCHAROMYCES CEREVISIAE Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P49626*PLUS |
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#9: Protein | Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COORDINATE SOURCE ORIGINALLY FROM SACCHAROMYCES CEREVISIAE Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P05740*PLUS |
#10: Protein | Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COORDINATE SOURCE ORIGINALLY FROM SACCHAROMYCES CEREVISIAE Source: (natural) TRITICUM AESTIVUM (bread wheat) |
#11: Protein | Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COORDINATE SOURCE ORIGINALLY FROM SACCHAROMYCES CEREVISIAE Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P04456*PLUS |
#12: Protein | Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COORDINATE SOURCE ORIGINALLY FROM SACCHAROMYCES CEREVISIAE Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P05743*PLUS |
#13: Protein | Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COORDINATE SOURCE ORIGINALLY FROM SACCHAROMYCES CEREVISIAE Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P0C2H8*PLUS |
#14: Protein | Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COORDINATE SOURCE ORIGINALLY FROM SACCHAROMYCES CEREVISIAE Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P0CX84*PLUS |
#15: Protein | Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COORDINATE SOURCE ORIGINALLY FROM SACCHAROMYCES CEREVISIAE Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P04650*PLUS |
-Details
Sequence details | SOURCE ORGANISM FOR COORDINATES OF CHAINS D, E, AND F WERE PROVIDED AS SACCHAROMYCES CEREVISIAE ...SOURCE ORGANISM FOR COORDINATE |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ACTIVELY TRANSLATING WHEAT GERM (O. SATIVA) 80S RIBOSOME PROGRAMMED WITH A NASCENT POLYPEPTIDE CHAIN CONTAINING A P- SITE TRNA AND THE TYPE I SIGNAL ANCHOR SEQUENCE OF DPAP-B ( ...Name: ACTIVELY TRANSLATING WHEAT GERM (O. SATIVA) 80S RIBOSOME PROGRAMMED WITH A NASCENT POLYPEPTIDE CHAIN CONTAINING A P- SITE TRNA AND THE TYPE I SIGNAL ANCHOR SEQUENCE OF DPAP-B ( DIPEPTIDYLAMINOPEPTIDASE B) BOUND TO THE MAMMALIAN (CANIS FAMILIARIS) SEC61 COMPLEX. Type: RIBOSOME |
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Buffer solution | Name: 30 MM HEPES/KOH, PH 7.5 180 MM KOAC, 10 MM MG(OAC)2, 1 MM DTT, 3.5 % (W/V) GLYCEROL 0.3 % (W/V) DIGITONIN pH: 7.5 Details: 30 MM HEPES/KOH, PH 7.5 180 MM KOAC, 10 MM MG(OAC)2, 1 MM DTT, 3.5 % (W/V) GLYCEROL 0.3 % (W/V) DIGITONIN |
Specimen | Conc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: OTHER |
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 LAYERS OF FILTER PAPER |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 38000 X / Nominal defocus max: 4700 nm / Nominal defocus min: 1250 nm / Cs: 2.26 mm |
Specimen holder | Temperature: 84 K / Tilt angle max: 0 ° |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 155 |
Radiation wavelength | Relative weight: 1 |
-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: 6.48 Å / Num. of particles: 221445 / Nominal pixel size: 1.2375 Å / Actual pixel size: 1.2375 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1652. Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Details: METHOD--MANUAL FOLLOWED BY MDFF | ||||||||||||
Refinement | Highest resolution: 6.48 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6.48 Å
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