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- PDB-4crn: Cryo-EM of a pretermination complex with eRF1 and eRF3 -

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Basic information

Entry
Database: PDB / ID: 4crn
TitleCryo-EM of a pretermination complex with eRF1 and eRF3
DescriptorERF3 IN RIBOSOME BOUND ERF1-ERF3-GDPNP COMPLEX
ERF1 IN RIBOSOME-BOUND ERF1-ERF3-GDPNP COMPLEX
KeywordsTRANSLATION / TERMINATION / CRYO-EM
Specimen sourceSaccharomyces cerevisiae / yeast / BAKER'S YEAST / サッカロミセス・セレビシエ /
MethodElectron microscopy (9.1 Å resolution / Particle / Single particle)
AuthorsPreis, A. / Heuer, A. / Barrio-Garcia, C. / Hauser, A. / Eyler, D. / Berninghausen, O. / Green, R. / Becker, T. / Beckmann, R.
CitationCell Rep, 2014, 8, 59-65

Cell Rep, 2014, 8, 59-65 Yorodumi Papers
Cryoelectron microscopic structures of eukaryotic translation termination complexes containing eRF1-eRF3 or eRF1-ABCE1.
Anne Preis / Andre Heuer / Clara Barrio-Garcia / Andreas Hauser / Daniel E Eyler / Otto Berninghausen / Rachel Green / Thomas Becker / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 28, 2014 / Release: Jul 23, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 23, 2014Structure modelrepositoryInitial release
1.1May 11, 2016Structure modelStructure summary
1.2Aug 23, 2017Structure modelData collectionem_image_scans / em_software_em_software.image_processing_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Assembly

Deposited unit
P: ERF3 IN RIBOSOME BOUND ERF1-ERF3-GDPNP COMPLEX
X: ERF1 IN RIBOSOME-BOUND ERF1-ERF3-GDPNP COMPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3963
Polyers96,8732
Non-polymers5221
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Polypeptide(L)ERF3 IN RIBOSOME BOUND ERF1-ERF3-GDPNP COMPLEX


Mass: 47840.965 Da / Num. of mol.: 1
Details: FOR CHAIN P (ERF3) THE FIRST 254 AMINO ACIDS ARE MISSING.
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
References: UniProt: P05453

Cellular component

Molecular function

Biological process

  • cytoplasmic translational termination (GO: 0002184)
  • nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO: 0000288)
  • translational termination (GO: 0006415)
#2: Polypeptide(L)ERF1 IN RIBOSOME-BOUND ERF1-ERF3-GDPNP COMPLEX


Mass: 49032.375 Da / Num. of mol.: 1
Details: FOR CHAIN X THE LAST 25 AMINO ACIDS (416-440) ARE MISSING
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
References: UniProt: P12385

Cellular component

Molecular function

  • translation release factor activity (GO: 0003747)
  • translation release factor activity, codon specific (GO: 0016149)

Biological process

#3: ChemicalChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp (GMPPNP, energy-carrying molecule analogue) *YM


Mass: 522.196 Da / Num. of mol.: 1 / Formula: C10H17N6O13P3
Sequence detailsTHE FIRST 254 AMINO ACIDS FOR THE N-TERMINAL DOMAIN ARE MISSING IN THE MODEL THE LAST AMINO ACIDS (RESIDUES 416-440) ARE MISSING IN THE MODEL

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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: CMV-STALLED WHEAT GERM 80S-RNC BOUND TO ERF1 AND ABCE1-ADPNP
Type: RIBOSOME
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE, VITROBOT MARK 4

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Feb 20, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 147136 / Nominal defocus max: 3500 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm
Image recordingElectron dose: 0.02 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)

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Processing

EM software
IDNameCategoryImage processing ID
1CootMODEL FITTING
2UCSF ChimeraMODEL FITTING
3STARFISHPARTICLE SELECTION1
4SPIDERRECONSTRUCTION1
SymmetryPoint symmetry: C1
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 9.1 Å / Number of particles: 39309
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2597 (DEPOSITION ID: 12368).
Symmetry type: POINT
Least-squares processHighest resolution: 9.1 Å
Refine hist #LASTHighest resolution: 9.1 Å
Number of atoms included #LASTProtein: 6661 / Nucleic acid: 0 / Ligand: 32 / Solvent: 0 / Total: 6693

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