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- PDB-4cxg: Regulation of the mammalian elongation cycle by 40S subunit rolli... -

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Basic information

Entry
Database: PDB / ID: 4cxg
TitleRegulation of the mammalian elongation cycle by 40S subunit rolling: a eukaryotic-specific ribosome rearrangement
Components
  • 18S RRNA - H44
  • 18S RRNA - H5-H14
  • 18S RRNA - H8
  • 28S RRNA - H89
  • 28S RRNA - H95
  • 40S RIBOSOMAL PROTEIN US12
  • ELONGATION FACTOR 1A
  • MESSENGER RNA
  • TRANSFER RNA
KeywordsTRANSLATION / MAMMALIAN 80S RIBOSOME / ELONGATION CYCLE / TRNA SELECTION / EUKARYOTIC TERNARY COMPLEX
Function / homology
Function and homology information


Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency ...Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / rough endoplasmic reticulum / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation elongation factor activity / stress granule assembly / small-subunit processome / cytosolic ribosome / maintenance of translational fidelity / ribosomal small subunit biogenesis / Regulation of expression of SLITs and ROBOs / cytosolic small ribosomal subunit / cytoplasmic translation / SARS-CoV-2 modulates host translation machinery / ribosome / structural constituent of ribosome / translation / GTPase activity / synapse / GTP binding / nucleolus / endoplasmic reticulum / RNA binding / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EF1A, eukaryotic/archaeal / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S23, eukaryotic/archaeal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain ...Translation elongation factor EF1A, eukaryotic/archaeal / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S23, eukaryotic/archaeal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Small GTP-binding protein domain / Ribosomal protein S12 signature. / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHENYLALANINE / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS12 / Elongation factor 1-alpha
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
ESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsBudkevich, T.V. / Giesebrecht, J. / Behrmann, E. / Loerke, J. / Ramrath, D.J.F. / Mielke, T. / Ismer, J. / Hildebrand, P. / Tung, C.-S. / Nierhaus, K.H. ...Budkevich, T.V. / Giesebrecht, J. / Behrmann, E. / Loerke, J. / Ramrath, D.J.F. / Mielke, T. / Ismer, J. / Hildebrand, P. / Tung, C.-S. / Nierhaus, K.H. / Sanbonmatsu, K.Y. / Spahn, C.M.T.
CitationJournal: Cell / Year: 2014
Title: Regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement.
Authors: Tatyana V Budkevich / Jan Giesebrecht / Elmar Behrmann / Justus Loerke / David J F Ramrath / Thorsten Mielke / Jochen Ismer / Peter W Hildebrand / Chang-Shung Tung / Knud H Nierhaus / ...Authors: Tatyana V Budkevich / Jan Giesebrecht / Elmar Behrmann / Justus Loerke / David J F Ramrath / Thorsten Mielke / Jochen Ismer / Peter W Hildebrand / Chang-Shung Tung / Knud H Nierhaus / Karissa Y Sanbonmatsu / Christian M T Spahn /
Abstract: The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution ...The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80S ribosome in the posttranslocational state and in complex with the eukaryotic eEF1A⋅Val-tRNA⋅GMPPNP ternary complex, revealing significant differences in the elongation mechanism between bacteria and mammals. Surprisingly, and in contrast to bacterial ribosomes, a rotation of the small subunit around its long axis and orthogonal to the well-known intersubunit rotation distinguishes the posttranslocational state from the classical pretranslocational state ribosome. We term this motion "subunit rolling." Correspondingly, a mammalian decoding complex visualized in substates before and after codon recognition reveals structural distinctions from the bacterial system. These findings suggest how codon recognition leads to GTPase activation in the mammalian system and demonstrate that in mammalia subunit rolling occurs during tRNA selection.
History
DepositionApr 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 2.0Aug 23, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / em_3d_fitting ...atom_site / em_3d_fitting / em_software / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id
Revision 3.0Jun 26, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_seq_map_depositor_info / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
1: 18S RRNA - H44
2: 28S RRNA - H89
A: ELONGATION FACTOR 1A
X: 40S RIBOSOMAL PROTEIN US12
Y: TRANSFER RNA
a: 18S RRNA - H5-H14
b: 18S RRNA - H8
c: 28S RRNA - H95
x: MESSENGER RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,57910
Polymers184,4149
Non-polymers1651
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

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RNA chain , 7 types, 7 molecules 12Yabcx

#1: RNA chain 18S RRNA - H44


Mass: 43635.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#2: RNA chain 28S RRNA - H89


Mass: 15974.376 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#5: RNA chain TRANSFER RNA /


Mass: 24686.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#6: RNA chain 18S RRNA - H5-H14


Mass: 15424.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#7: RNA chain 18S RRNA - H8


Mass: 5445.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#8: RNA chain 28S RRNA - H95


Mass: 6140.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#9: RNA chain MESSENGER RNA /


Mass: 8527.686 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: FOR MODELING MRNA (CHAIN 1, PDB ID CODE 3I8G) WAS USED
Source: (synth.) ESCHERICHIA COLI (E. coli)

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Protein , 2 types, 2 molecules AX

#3: Protein ELONGATION FACTOR 1A / EF-1-ALPHA / ELONGATION FACTOR TU / EF-TU / ELONGATION FACTOR 1A


Mass: 48734.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: Q9YAV0*PLUS
#4: Protein 40S RIBOSOMAL PROTEIN US12 / / 40S RIBOSOMAL PROTEIN S23


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62266*PLUS

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Non-polymers , 1 types, 1 molecules

#10: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2

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Details

Sequence detailsAUTHORS HAVE USED SEQUENCE FOR MODEL BUILDING, WITH FOLLOWING PDB-GENBANK OR UNIPROT RESIDUE ...AUTHORS HAVE USED SEQUENCE FOR MODEL BUILDING, WITH FOLLOWING PDB-GENBANK OR UNIPROT RESIDUE MAPPING: CHAIN A 1- 437 UNP Q9YAV0 1- 437 CHAIN X 1- 143 UNP P62266 1- 143 CHAIN Y 1- 76 GB X00655 1- 76 CHAIN 1 1701-1835 GB X03205 1701-1835 CHAIN 2 4359-4408 GB M11167 4359-4408 CHAIN a 458- 505 GB X03205 458- 505 CHAIN b 151- 167 GB X03205 151- 167 CHAIN c 4553-4571 GB M11167 4553-4571

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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: INITIAL CODON SAMPLING STATE OF 80S MAMMALIAN RIBOSOME
Type: RIBOSOME
Buffer solutionName: 20 MM HEPES-KOH, 5 MM MGCL2, 100 MM NH4CL, 6 MM MERCAPROETHANOL, 0.8 MM SPERMIDINE, 0.6 MM SPERMINE
pH: 7.5
Details: 20 MM HEPES-KOH, 5 MM MGCL2, 100 MM NH4CL, 6 MM MERCAPROETHANOL, 0.8 MM SPERMIDINE, 0.6 MM SPERMINE
SpecimenConc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN ETHANE, HUMIDITY 80, INSTRUMENT - FEI VITROBOT MARK II, METHOD - BLOT FOR 2 SEC BEFORE PLUNGING

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Sep 22, 2008 / Details: MINIMAL DOSE SYSTEM
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: 65520 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 230

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2UCSF Chimeramodel fitting
3SPARX3D reconstruction
4SPIDER3D reconstruction
CTF correctionDetails: DEFOCUS GROUP
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MULTI-REFERENCE TEMPLATE MATCHING / Resolution: 8.7 Å / Num. of particles: 79705 / Nominal pixel size: 1.26 Å / Actual pixel size: 1.26 Å
Magnification calibration: CROSS- -CORRELATION WITH KNOWN STRUCTURE
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2623. (DEPOSITION ID: 12411).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY
RefinementHighest resolution: 8.7 Å
Refinement stepCycle: LAST / Highest resolution: 8.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4318 7940 11 0 12269

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