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- PDB-5a8l: Human eRF1 and the hCMV nascent peptide in the translation termin... -

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Basic information

Entry
Database: PDB / ID: 5a8l
TitleHuman eRF1 and the hCMV nascent peptide in the translation termination complex
Components
  • (60S RIBOSOMAL PROTEIN ...) x 3
  • 28S RIBOSOMAL RNA
  • EUKARYOTIC RELEASE FACTOR ERF1
  • HUMAN 18S RIBOSOMAL RNA
  • MRNA
  • NASCENT CHAIN
  • P-SITE TRNA
KeywordsTRANSLATION / HUMAN / 80S / RIBOSOME / ERF1
Function / homology
Function and homology information


translation termination factor activity / translation release factor complex / cytoplasmic translational termination / regulation of translational termination / translation release factor activity, codon specific / protein methylation / translation release factor activity / sequence-specific mRNA binding / peptidyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...translation termination factor activity / translation release factor complex / cytoplasmic translational termination / regulation of translational termination / translation release factor activity, codon specific / protein methylation / translation release factor activity / sequence-specific mRNA binding / peptidyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / 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 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / rough endoplasmic reticulum / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / ribosome binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / postsynaptic density / nuclear body / structural constituent of ribosome / translation / ribonucleoprotein complex / focal adhesion / nucleolus / endoplasmic reticulum / RNA binding / extracellular exosome / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / eRF1 domain 2 / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily ...Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / eRF1 domain 2 / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / 50S ribosomal protein L30e-like / Nucleotidyltransferase; domain 5 / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L22/L17 / Ribosomal protein L22p/L17e / Ribosomal protein L22/L17 superfamily / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL4 / Eukaryotic peptide chain release factor subunit 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMatheisl, S. / Berninghausen, O. / Becker, T. / Beckmann, R.
CitationJournal: Nucleic Acids Res / Year: 2015
Title: Structure of a human translation termination complex.
Authors: Sarah Matheisl / Otto Berninghausen / Thomas Becker / Roland Beckmann /
Abstract: In contrast to bacteria that have two release factors, RF1 and RF2, eukaryotes only possess one unrelated release factor eRF1, which recognizes all three stop codons of the mRNA and hydrolyses the ...In contrast to bacteria that have two release factors, RF1 and RF2, eukaryotes only possess one unrelated release factor eRF1, which recognizes all three stop codons of the mRNA and hydrolyses the peptidyl-tRNA bond. While the molecular basis for bacterial termination has been elucidated, high-resolution structures of eukaryotic termination complexes have been lacking. Here we present a 3.8 Å structure of a human translation termination complex with eRF1 decoding a UAA(A) stop codon. The complex was formed using the human cytomegalovirus (hCMV) stalling peptide, which perturbs the peptidyltransferase center (PTC) to silence the hydrolysis activity of eRF1. Moreover, unlike sense codons or bacterial stop codons, the UAA stop codon adopts a U-turn-like conformation within a pocket formed by eRF1 and the ribosome. Inducing the U-turn conformation for stop codon recognition rationalizes how decoding by eRF1 includes monitoring geometry in order to discriminate against sense codons.
History
DepositionJul 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 2.0Aug 23, 2017Group: Atomic model / Data collection / Derived calculations
Category: atom_site / em_software / 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.fitting_id / _em_software.image_processing_id
Revision 2.1May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure viewerMolecule:
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Assembly

Deposited unit
A: 28S RIBOSOMAL RNA
B: HUMAN 18S RIBOSOMAL RNA
D: 60S RIBOSOMAL PROTEIN L17
G: 60S RIBOSOMAL PROTEIN L12
H: 60S RIBOSOMAL PROTEIN L4
P: P-SITE TRNA
Q: EUKARYOTIC RELEASE FACTOR ERF1
R: MRNA
Z: NASCENT CHAIN


Theoretical massNumber of molelcules
Total (without water)2,375,3209
Polymers2,375,3209
Non-polymers00
Water00
1


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

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Components

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RNA chain , 4 types, 4 molecules ABPR

#1: RNA chain 28S RIBOSOMAL RNA


Mass: 1625941.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HELA S3 / Source: (natural) HOMO SAPIENS (human) / References: GenBank: 337381
#2: RNA chain HUMAN 18S RIBOSOMAL RNA


Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HELA S3 / Source: (natural) HOMO SAPIENS (human) / References: GenBank: 36162
#6: RNA chain P-SITE TRNA


Mass: 5771.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HELA S3 / Source: (natural) HOMO SAPIENS (human)
#8: RNA chain MRNA


Mass: 2823.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HELA S3 / Source: (natural) HOMO SAPIENS (human)

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60S RIBOSOMAL PROTEIN ... , 3 types, 3 molecules DGH

#3: Protein 60S RIBOSOMAL PROTEIN L17 / 60S RIBOSOMAL PROTEIN L23 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HELA S3 / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P18621
#4: Protein 60S RIBOSOMAL PROTEIN L12


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HELA S3 / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P30050
#5: Protein 60S RIBOSOMAL PROTEIN L4 / 60S RIBOSOMAL PROTEIN L1


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HELA S3 / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P36578

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Protein / Protein/peptide , 2 types, 2 molecules QZ

#7: Protein EUKARYOTIC RELEASE FACTOR ERF1


Mass: 48476.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HELA S3 / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P62495
#9: Protein/peptide NASCENT CHAIN


Mass: 2435.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HELA S3 / Source: (natural) HOMO SAPIENS (human)

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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: CMV STALLED HUMAN 80S RIBOSOME BOUND TO THE TRANSLATION TERMINATION FACTOR ERF1
Type: RIBOSOME
Buffer solutionName: 20 MM HEPES, 100 MM KOAC, 2.5 MM MG(OAC)2, 0. 25 MM SPERMIDINE, 2 MM DTT, 0.06 U/UL RNASIN ( AMBION), 1/625 EDTA-FREE COMPLETE PROTEASE INHIBITOR (ROCHE)
pH: 7.5
Details: 20 MM HEPES, 100 MM KOAC, 2.5 MM MG(OAC)2, 0. 25 MM SPERMIDINE, 2 MM DTT, 0.06 U/UL RNASIN ( AMBION), 1/625 EDTA-FREE COMPLETE PROTEASE INHIBITOR (ROCHE)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT MARK IV,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Mar 11, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingFilm or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 3

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2UCSF Chimeramodel fitting
3SPIDER3D reconstruction
CTF correctionDetails: DEFOCUS GROUPS
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Num. of particles: 33165 / Actual pixel size: 1.062 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3099. (DEPOSITION ID: 13610).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEXIBLE
Atomic model buildingPDB-ID: 3E1Y

3e1y


Accession code: 3E1Y / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.8 Å
Refinement stepCycle: LAST / Highest resolution: 3.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 7396 0 0 12264

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