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

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Entry
Database: PDB / ID: 2ww9
TitleCryo-EM structure of the active yeast Ssh1 complex bound to the yeast 80S ribosome
DescriptorSEC SIXTY-ONE PROTEIN HOMOLOG
(PROTEIN TRANSPORT PROTEIN ...) x 2
(60S RIBOSOMAL PROTEIN ...) x 8
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
Specimen sourceSaccharomyces cerevisiae / yeast / BAKER'S YEAST / サッカロミセス・セレビシエ /
MethodElectron microscopy (8.6 Å resolution / Particle / Single particle)
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.
CitationScience, 2009, 326, 1369-1373

Science, 2009, 326, 1369-1373 StrPapers
Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome.
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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Polypeptide(L) , 1 types, 1 molecules A

#1: Polypeptide(L)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 / References: UniProt: P38353

Cellular component

Molecular function

Biological process

  • SRP-dependent cotranslational protein targeting to membrane (GO: 0006614)

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

#2: Polypeptide(L)PROTEIN TRANSPORT PROTEIN SSS1 / 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 / References: UniProt: P35179

Cellular component

Molecular function

  • P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO: 0015450)
  • protein transporter activity (GO: 0008565)
  • structural molecule activity (GO: 0005198)

Biological process

  • posttranslational protein targeting to membrane, translocation (GO: 0031204)
  • SRP-dependent cotranslational protein targeting to membrane, translocation (GO: 0006616)
#3: Polypeptide(L)PROTEIN TRANSPORT PROTEIN SEB2 / 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 / References: UniProt: P52871

Cellular component

Molecular function

  • ARF guanyl-nucleotide exchange factor activity (GO: 0005086)

Biological process

  • posttranslational protein targeting to membrane, translocation (GO: 0031204)
  • SRP-dependent cotranslational protein targeting to membrane (GO: 0006614)
  • SRP-dependent cotranslational protein targeting to membrane, translocation (GO: 0006616)

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RNA chain , 4 types, 4 molecules DEFG

#4: RNA chain25S RRNA


Mass: 20302.104 Da / Num. of mol.: 1 / Details: H5_H6_H7 FRAGMENT / Source: (natural) SACCHAROMYCES CEREVISIAE
#5: RNA chain25S RRNA


Mass: 11089.751 Da / Num. of mol.: 1 / Details: H24 FRAGMENT / Source: (natural) SACCHAROMYCES CEREVISIAE
#6: RNA chain25S RRNA


Mass: 8052.861 Da / Num. of mol.: 1 / Details: H50 FRAGMENT / Source: (natural) SACCHAROMYCES CEREVISIAE
#7: RNA chain25S RRNA


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

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

#8: Polypeptide(L)60S RIBOSOMAL PROTEIN L4-B / 60S RIBOSOMAL PROTEIN L4 / L2 / YL2 / RP2


Mass: 39129.102 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE / References: UniProt: P49626

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)60S RIBOSOMAL PROTEIN L17-A / 60S RIBOSOMAL PROTEIN L17 / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE / References: UniProt: P05740

Cellular component

Molecular function

Biological process

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000448)
  • cytoplasmic translation (GO: 0002181)
#10: Polypeptide(L)60S RIBOSOMAL PROTEIN L19 / L23 / YL14 / RP15L / RP33


Mass: 21762.316 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE / References: UniProt: P05735

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)60S RIBOSOMAL PROTEIN L25 / YL25 / RP16L / YP42'


Mass: 15787.612 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE / References: UniProt: P04456

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)60S RIBOSOMAL PROTEIN L26-A / 60S RIBOSOMAL PROTEIN L26 / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE / References: UniProt: P05743

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)60S RIBOSOMAL PROTEIN L31-A / 60S RIBOSOMAL PROTEIN L31 / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE / References: UniProt: P0C2H8

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)60S RIBOSOMAL PROTEIN L35


Mass: 13942.640 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE / References: UniProt: P39741

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)60S RIBOSOMAL PROTEIN L39 / L46 / YL40


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

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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 FIELD / 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: 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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