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- PDB-2ww9: Cryo-EM structure of the active yeast Ssh1 complex bound to the y... -

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Basic information

Entry
Database: PDB / ID: 2ww9
TitleCryo-EM structure of the active 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 / homologyProtein translocase SecE domain superfamily / SecY domain superfamily / Ribosomal protein L19, eukaryotic / Protein transport Sec61-beta/Sbh / SecY conserved site / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L4 domain superfamily ...Protein translocase SecE domain superfamily / SecY domain superfamily / Ribosomal protein L19, eukaryotic / Protein transport Sec61-beta/Sbh / SecY conserved site / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L4 domain superfamily / Preprotein translocase subunit SecE / Ribosomal protein L29/L35 superfamily / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Translocon Sec61/SecY, plug domain / Ribosomal protein L22/L17, conserved site / Ribosomal protein L29, conserved site / Protein transport protein SecG/Sec61-beta/Sbh / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L2, domain 2 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L1e signature. / Ribosomal protein L23, N-terminal domain / Ribosomal protein L29 signature. / Ribosomal protein L19e signature. / Ribosomal protein L22 signature. / Ribosomal protein L39e signature. / Ribosomal protein L23 signature. / Ribosomal proteins L26 eukaryotic, L24P archaeal / 60S ribosomal protein L4 C-terminal domain / Plug domain of Sec61p / Sec61beta family / Ribosomal protein L22p/L17e / Ribosomal protein L19e / Ribosomal protein L31e / Ribosomal L39 protein / Ribosomal L29 protein / SecE/Sec61-gamma subunits of protein translocation complex / Ribosomal protein L4/L1 family / KOW motif / SecY translocase / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L19/L19e / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / XBP1(S) activates chaperone genes / SRP-dependent cotranslational protein targeting to membrane / L13a-mediated translational silencing of Ceruloplasmin expression / Ribosomal protein L31e signature. / Ribosomal protein L24 signature. / Protein secE/sec61-gamma signature. / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L31e / Ribosomal protein L39e / Protein secY signature 1. / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L29/L35 / Translation protein SH3-like domain superfamily / Protein translocase SEC61 complex, gamma subunit / Ribosomal protein L24/L26, conserved site / KOW / Protein translocase complex, SecE/Sec61-gamma subunit / Ribosomal protein L4/L1e / SecY/SEC61-alpha family / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L22/L17 / Ssh1 translocon complex / Sec61 translocon complex / posttranslational protein targeting to membrane, translocation / endoplasmic reticulum Sec complex / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation / ARF guanyl-nucleotide exchange factor activity / P-P-bond-hydrolysis-driven protein transmembrane transporter activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / regulation of translational fidelity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein transmembrane transporter activity / ribosomal large subunit biogenesis / SRP-dependent cotranslational protein targeting to membrane / protein transporter activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / mRNA binding / structural constituent of ribosome / translation / structural molecule activity / RNA binding / integral component of membrane
Function and homology information
Specimen sourceSACCHAROMYCES CEREVISIAE (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8.6 Å resolution
AuthorsBecker, 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 Westhof / Reid Gilmore / Elisabet C Mandon / Roland Beckmann
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 22, 2009 / Release: Dec 8, 2009
RevisionDateData content typeGroupProviderType
1.0Dec 8, 2009Structure modelrepositoryInitial release
1.1Jul 20, 2011Structure modelDatabase references / Derived calculations / Other / Refinement description / Structure summary
1.2Oct 28, 2015Structure modelOther
1.3Apr 19, 2017Structure modelOther

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Structure visualization

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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
Polyers261,77615
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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Protein/peptide , 1 types, 1 molecules A

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


Mass: 53350.344 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P38353

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

#2: Protein/peptide PROTEIN TRANSPORT PROTEIN SSS1 / Protein targeting / 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: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P35179
#3: Protein/peptide 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: (natural) SACCHAROMYCES CEREVISIAE (baker'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 / Details: H5_H6_H7 FRAGMENT / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast)
#5: RNA chain 25S RRNA


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


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


Mass: 5700.419 Da / Num. of mol.: 1 / Details: H59 FRAGMENT / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast)

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

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


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


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


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


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


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


Mass: 12980.158 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P0C2H8
#14: Protein/peptide 60S RIBOSOMAL PROTEIN L35 /


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


Mass: 6358.640 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P04650

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: ACTIVE-YEAST 80S-RNC-SSH1 COMPLEX / 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
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
pH: 7.5
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
MicroscopyMicroscope model: 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 / Calibrated magnification: 38000 / Nominal defocus max: 4500 nm / Nominal defocus min: 1200 nm / Cs: 2.26 mm
Specimen holderTemperature: 84 kelvins / Tilt angle min: 0 deg.
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 185

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: DEFOCUS GROUP VOLUMES
SymmetryPoint symmetry: C1
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 8.6 Å / Number of particles: 35800 / Nominal pixel size: 1.2375 / Actual pixel size: 1.2375
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1667.
Symmetry type: POINT
Atomic model buildingDetails: METHOD--MANUAL FOLLOWED BY MDFF REFINEMENT PROTOCOL--SINGLE PARTICLE CRYO EM
Ref protocol: OTHER / Ref space: REAL
Least-squares processHighest resolution: 8.6 Å
Refine hist #LASTHighest resolution: 8.6 Å
Number of atoms included #LASTProtein: 11299 / Nucleic acid: 3002 / Ligand: 0 / Solvent: 0 / Total: 14301

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