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

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Database: PDB / ID: 2wwb
TitleCRYO-EM STRUCTURE OF THE MAMMALIAN SEC61 COMPLEX BOUND TO THE ACTIVELY TRANSLATING WHEAT GERM 80S RIBOSOME
Components
  • (25S RRNA) x 3
  • (60S RIBOSOMAL PROTEIN ...) x 8
  • (PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ...Protein targeting) x 3
  • 5.8S RRNA5.8S ribosomal RNA
KeywordsRIBOSOME / 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) / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / protein transmembrane transporter activity / regulation of translational fidelity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / phospholipid binding / ribosome binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / mRNA binding / endoplasmic reticulum membrane / endoplasmic reticulum / RNA binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. ...Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L35 / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein uL29A / Protein transport protein Sec61 subunit alpha isoform 1 / Large ribosomal subunit protein uL4B ...RNA / RNA (> 10) / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein uL29A / Protein transport protein Sec61 subunit alpha isoform 1 / Large ribosomal subunit protein uL4B / Protein transport protein Sec61 subunit gamma / Protein transport protein Sec61 subunit beta
Similarity search - Component
Biological speciesCANIS LUPUS FAMILIARIS (dog)
TRITICUM AESTIVUM (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.48 Å
AuthorsBecker, 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.
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 ...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
DepositionOct 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Revision 1.2Apr 19, 2017Group: Other
Revision 2.0Oct 3, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / em_software ...atom_site / em_software / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_software.image_processing_id

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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)258,75715
Polymers258,75715
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ... , 3 types, 3 molecules ABC

#1: Protein PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1 / Protein targeting / SEC61ALPHA / SEC61 ALPHA-1


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
#2: Protein PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA / Protein targeting / SEC61GAMMA


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 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA / Protein targeting / SEC61BETA


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

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RNA chain , 4 types, 4 molecules DEFG

#4: RNA chain 5.8S RRNA / 5.8S ribosomal RNA


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)
#5: RNA chain 25S RRNA


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 25S RRNA


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 25S RRNA


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)

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

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


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
#9: Protein 60S RIBOSOMAL PROTEIN L17-A / Ribosome / 60S RIBOSOMAL PROTEIN L17 / L20A / YL17


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 60S RIBOSOMAL PROTEIN L19 / / L23 / YL14 / RP15L / RP33


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 60S RIBOSOMAL PROTEIN L25 / / YL25 / RP16L / YP42'


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 60S RIBOSOMAL PROTEIN L26-A / Ribosome / 60S RIBOSOMAL PROTEIN L26 / L33 / YL33


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 60S RIBOSOMAL PROTEIN L31-A / Ribosome / 60S RIBOSOMAL PROTEIN L31 / L34 / YL28


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 60S RIBOSOMAL PROTEIN L35 /


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 60S RIBOSOMAL PROTEIN L39 / / L46 / YL40


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

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Details

Sequence detailsSOURCE ORGANISM FOR COORDINATES OF CHAINS D, E, AND F WERE PROVIDED AS SACCHAROMYCES CEREVISIAE ...SOURCE 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 experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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
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
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
SpecimenConc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: 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

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 155
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: DEFOCUS GROUP VOLUMES
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 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 buildingProtocol: FLEXIBLE FIT / Details: METHOD--MANUAL FOLLOWED BY MDFF
RefinementHighest resolution: 6.48 Å
Refinement stepCycle: LAST / Highest resolution: 6.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11394 2919 0 0 14313

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