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- PDB-2wwb: CRYO-EM STRUCTURE OF THE MAMMALIAN SEC61 COMPLEX BOUND TO THE ACT... -

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Entry
Database: PDB / ID: 2wwb
TitleCRYO-EM STRUCTURE OF THE MAMMALIAN SEC61 COMPLEX BOUND TO THE ACTIVELY TRANSLATING WHEAT GERM 80S RIBOSOME
DescriptorPROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1
PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA
PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA
(60S ribosomal protein ...) x 8
KeywordsRIBOSOME / PROTEIN EXIT TUNNEL / COTRANSLATIONAL PROTEIN TRANSLOCATION / PROTEIN CONDUCTING CHANNEL / SIGNAL SEQUENCE
Specimen sourceCanis lupus familiaris / mammal / DOG /
Triticum aestivum / plant / BREAD WHEAT / コムギ /
MethodElectron microscopy (6.48 A resolution / Single particle / Vitreous ice (cryo EM))
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

DateDeposition: Oct 22, 2009 / Release: Dec 8, 2009 / Last modification: Jul 20, 2011

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Assembly

Deposited unit
A: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1
B: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA
C: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA
D: 5.8S 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)258,76015
Polyers258,76015
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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Polypeptide(L) , 11 types, 11 molecules ABCHIJKLMNO

#1: Polypeptide(L)PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1 / SEC61ALPHA / SEC61 ALPHA-1


Mass: 52279.926 Da / Num. of mol.: 1 / Source: (natural) CANIS LUPUS FAMILIARIS / References: UniProt: P38377

Cellular component

  • endoplasmic reticulum membrane (GO: 0005789)
  • integral component of endoplasmic reticulum membrane (GO: 0030176)

Biological process

#2: Polypeptide(L)PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA / SEC61GAMMA


Mass: 7752.390 Da / Num. of mol.: 1 / Source: (natural) CANIS LUPUS FAMILIARIS / References: UniProt: P60058

Cellular component

  • endoplasmic reticulum membrane (GO: 0005789)
  • integral component of endoplasmic reticulum membrane (GO: 0030176)

Molecular function

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

Biological process

#3: Polypeptide(L)PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA / SEC61BETA


Mass: 9987.522 Da / Num. of mol.: 1 / Source: (natural) CANIS LUPUS FAMILIARIS / References: UniProt: P60467

Cellular component

Molecular function

  • P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO: 0015450)
  • poly(A) RNA binding (GO: 0044822)

Biological process

  • ER-associated ubiquitin-dependent protein catabolic process (GO: 0030433)
  • protein import into nucleus, translocation (GO: 0000060)
  • retrograde protein transport, ER to cytosol (GO: 0030970)
#8: Polypeptide(L)60S RIBOSOMAL PROTEIN L4-B / 60S RIBOSOMAL PROTEIN L4 / L2 / YL2 / RP2


Mass: 39129.492 Da / Num. of mol.: 1 / Source: (natural) TRITICUM AESTIVUM

Cellular component

Molecular function

Biological process

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


Mass: 20589.709 Da / Num. of mol.: 1 / Source: (natural) TRITICUM AESTIVUM

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: 21762.518 Da / Num. of mol.: 1 / Source: (natural) TRITICUM AESTIVUM
#11: Polypeptide(L)60S RIBOSOMAL PROTEIN L25 / YL25 / RP16L / YP42'


Mass: 15787.753 Da / Num. of mol.: 1 / Source: (natural) TRITICUM AESTIVUM

Cellular component

Molecular function

Biological process

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


Mass: 14265.917 Da / Num. of mol.: 1 / Source: (natural) TRITICUM AESTIVUM

Cellular component

Molecular function

Biological process

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


Mass: 12980.284 Da / Num. of mol.: 1 / Source: (natural) TRITICUM AESTIVUM

Cellular component

Molecular function

Biological process

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


Mass: 13942.775 Da / Num. of mol.: 1 / Source: (natural) TRITICUM AESTIVUM

Cellular component

Molecular function

Biological process

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


Mass: 6358.690 Da / Num. of mol.: 1 / Source: (natural) TRITICUM AESTIVUM

Cellular component

Molecular function

Biological process

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RNA chain , 4 types, 4 molecules DEFG

#4: RNA chain5.8S RRNA


Mass: 20302.246 Da / Num. of mol.: 1 / Details: H5_H6_H7 FRAGMENT / Source: (natural) TRITICUM AESTIVUM
#5: RNA chain25S RRNA


Mass: 11089.833 Da / Num. of mol.: 1 / Details: H24 FRAGMENT / Source: (natural) TRITICUM AESTIVUM
#6: RNA chain25S RRNA


Mass: 8052.915 Da / Num. of mol.: 1 / Details: H50 FRAGMENT / Source: (natural) TRITICUM AESTIVUM
#7: RNA chain25S RRNA


Mass: 4477.753 Da / Num. of mol.: 1 / Details: H59 FRAGMENT / Source: (natural) TRITICUM AESTIVUM

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Details

Sequence detailsSOURCE ORGANISM FOR COORDINATES OF CHAINS D, E, AND F WERE PROVIDED AS SACCHAROMYCES CEREVISIAE WITH EXTERNAL DATABASE REFERENCE GB U53879. SOURCE ORGANISM FOR COORDINATES OF CHAIN G WERE PROVIDED AS ORYZA SATIVA WITH NO EXTERNAL DATABASE REFERENCE PROVIDED. SOURCE ORGANISM FOR COORDINATES OF CHAIN H WERE PROVIDED AS SACCHAROMYCES CEREVISIAE WITH EXTERNAL DATABASE REFERENCE PDB P49626. SOURCE ORGANISM FOR COORDINATES OF CHAIN I WERE PROVIDED AS SACCHAROMYCES CEREVISIAE WITH EXTERNAL DATABASE REFERENCE PDB P05740. SOURCE ORGANISM FOR COORDINATES OF CHAIN J WERE PROVIDED AS SACCHAROMYCES CEREVISIAE WITH EXTERNAL DATABASE REFERENCE PDB P05735. SOURCE ORGANISM FOR COORDINATES OF CHAIN K WERE PROVIDED AS SACCHAROMYCES CEREVISIAE WITH EXTERNAL DATABASE REFERENCE PDB P04456. SOURCE ORGANISM FOR COORDINATES OF CHAIN L WERE PROVIDED AS SACCHAROMYCES CEREVISIAE WITH EXTERNAL DATABASE REFERENCE PDB P05743. SOURCE ORGANISM FOR COORDINATES OF CHAIN M WERE PROVIDED AS SACCHAROMYCES CEREVISIAE WITH EXTERNAL DATABASE REFERENCE PDB P0C2H8. SOURCE ORGANISM FOR COORDINATES OF CHAIN N WERE PROVIDED AS SACCHAROMYCES CEREVISIAE WITH EXTERNAL DATABASE REFERENCE PDB P39741. SOURCE ORGANISM FOR COORDINATES OF CHAIN O WERE PROVIDED AS SACCHAROMYCES CEREVISIAE WITH EXTERNAL DATABASE REFERENCE PDB P04650.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: 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.
Aggregation state: PARTICLE
Buffer solutionName: 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
Sample preparationpH: 7.5 / Sample conc.: 0.02 mg/ml
Specimen supportDetails: OTHER
VitrificationDetails: CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 10 SECONDS BEFORE PLUNGING, USE 2 LAYERS OF FILTER PAPER

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Electron microscopy imaging

MicroscopyMicroscope model: OTHER
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderTemperature: 84 K / Tilt angle max: 0 deg.
CameraType: KODAK SO163
EM image scansNumber digital images: 155
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: SPIDER / Number of particles: 221445
EM single particle entitySymmetry type: MIXED SYMMETRY
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 6.48 A / Nominal pixel size: 1.2375 A/pix / Actual pixel size: 1.2375 A/pix / CTF correction method: DEFOCUS GROUP VOLUMES
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1652.
Atomic model buildingMethod: MANUAL FOLLOWED BY MDFF
Least-squares processHighest resolution: 6.48 A
Refine hist #LASTHighest resolution: 6.48 A
Number of atoms included #LASTProtein: 11394 / Nucleic acid: 2919 / Ligand: 0 / Solvent: 0 / Total: 14313

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