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- PDB-1dt9: THE CRYSTAL STRUCTURE OF HUMAN EUKARYOTIC RELEASE FACTOR ERF1-MEC... -

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Basic information

Entry
Database: PDB / ID: 1dt9
TitleTHE CRYSTAL STRUCTURE OF HUMAN EUKARYOTIC RELEASE FACTOR ERF1-MECHANISM OF STOP CODON RECOGNITION AND PEPTIDYL-TRNA HYDROLYSIS
ComponentsPROTEIN (EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1)
KeywordsTRANSLATION / erf1 / trna mimicry / protein sythesis / stop codon recognition / peptidyl-trna hydrolysis
Function / homology
Function and homology information


translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Protein hydroxylation / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / ribosome binding / RNA binding / 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 / eRF1 domain 1/Pelota-like / eRF1 domain 3 ...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 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / 50S ribosomal protein L30e-like / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic peptide chain release factor subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsFrolova, L.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis.
Authors: Song, H. / Mugnier, P. / Das, A.K. / Webb, H.M. / Evans, D.R. / Tuite, M.F. / Hemmings, B.A. / Barford, D.
#1: Journal: RNA / Year: 1999
Title: Mutations in the Highly Conserved GGQ Motif of Class 1 Polypeptide Release Factors Abolish Ability of Human eRF1 to Trigger Peptidyl-tRNA Hydrolysis.
Authors: Frolova, L.Y. / Tsivkovskii, R.Y. / Sivolobova, G.F. / Oparina, N.Y. / Serpinsky, O.I. / Blinov, V.M. / Tatkov, S.I. / Kisselev, L.L.
#2: Journal: Nature / Year: 1994
Title: A Highly Conserved Eukaryotic Protein Family Possesing Properties of Polypeptide Chain Release Factor
Authors: Frolova, L. / Le Goff, X. / Rasmussen, H.H. / Cheperegin, S. / Drugeon, G. / Kress, M. / Arman, I. / Haenni, A.L. / Celis, J.E. / Philippe, M. / Justesen, J. / Kisselev, L.
History
DepositionJan 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1)


Theoretical massNumber of molelcules
Total (without water)49,0931
Polymers49,0931
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.080, 77.080, 194.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1) / ERF1


Mass: 49092.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62495
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes, PEG4000, Glycerol, NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: protein was mixed with equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2100 mMHEPES1reservoir
314-22 %(w/v)PEG40001reservoir
415 %(v/v)glycerol1reservoir
5200 mM1reservoirNaCl

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 82505 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.406 / Num. unique all: 16712 / % possible all: 98
Reflection
*PLUS
Num. obs: 16712 / Num. measured all: 82505
Reflection shell
*PLUS
% possible obs: 98 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.7→20 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.314 997 -
Rwork0.246 --
obs-14553 97 %
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 0 110 3241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_d2

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