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- PDB-1r5o: crystal structure analysis of sup35 complexed with GMPPNP -

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Basic information

Entry
Database: PDB / ID: 1r5o
Titlecrystal structure analysis of sup35 complexed with GMPPNP
ComponentsEukaryotic peptide chain release factor GTP-binding subunit
KeywordsTRANSLATION / TRANSLATION TERMINATION / PEPTIDE RELEASE / GTPASE
Function / homology
Function and homology information


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) / cytoplasmic translational termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / GTPase activity ...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) / cytoplasmic translational termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / GTPase activity / GTP binding / cytosol
Similarity search - Function
Eukaryotic peptide chain release factor GTP-binding subunit / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. ...Eukaryotic peptide chain release factor GTP-binding subunit / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Eukaryotic peptide chain release factor GTP-binding subunit
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKong, C. / Song, H.
CitationJournal: Mol.Cell / Year: 2004
Title: Crystal structure and functional analysis of the eukaryotic class II release factor eRF3 from S. pombe
Authors: Kong, C. / Ito, K. / Walsh, M.A. / Wada, M. / Liu, Y. / Kumar, S. / Barford, D. / Nakamura, Y. / Song, H.
History
DepositionOct 11, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6252
Polymers52,1031
Non-polymers5221
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.524, 82.524, 168.076
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 Eukaryotic peptide chain release factor GTP-binding subunit / ERF2 / Translation release factor 3 / ERF3 / ERF-3


Mass: 52103.195 Da / Num. of mol.: 1 / Fragment: residues 196-662
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: sup35 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21-star / References: UniProt: O74718
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.09 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, Ethylene Glycol, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9724 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 10, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 11985 / Num. obs: 11894 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 5.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 0.7 / Num. unique all: 1134 / Rsym value: 0.14 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R5B

1r5b


Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.813 / SU B: 23.886 / SU ML: 0.423 / Cross valid method: THROUGHOUT / ESU R Free: 0.621 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31959 452 4.6 %RANDOM
Rwork0.26597 ---
obs0.26836 9417 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.353 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2--1.33 Å20 Å2
3----2.65 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 32 56 3310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213307
X-RAY DIFFRACTIONr_bond_other_d0.0020.023017
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9734467
X-RAY DIFFRACTIONr_angle_other_deg0.83137036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6475406
X-RAY DIFFRACTIONr_chiral_restr0.0730.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023613
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02636
X-RAY DIFFRACTIONr_nbd_refined0.2330.2945
X-RAY DIFFRACTIONr_nbd_other0.2460.23969
X-RAY DIFFRACTIONr_nbtor_other0.0850.21980
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.24
X-RAY DIFFRACTIONr_mcbond_it1.081.52029
X-RAY DIFFRACTIONr_mcangle_it2.00123286
X-RAY DIFFRACTIONr_scbond_it1.41131278
X-RAY DIFFRACTIONr_scangle_it2.5544.51181
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.44 36
Rwork0.284 650

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