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- PDB-1r5b: Crystal structure analysis of sup35 -

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Basic information

Entry
Database: PDB / ID: 1r5b
TitleCrystal structure analysis of sup35
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 / magnesium ion binding / cytosol
Similarity search - Function
Eukaryotic peptide chain release factor GTP-binding subunit / GTP-eEF1A C-terminal domain-like / : / 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. / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain ...Eukaryotic peptide chain release factor GTP-binding subunit / GTP-eEF1A C-terminal domain-like / : / 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. / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Eukaryotic peptide chain release factor GTP-binding subunit
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 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 10, 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: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)52,1031
Polymers52,1031
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.796, 83.796, 165.937
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, SPCC584.04 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: O74718
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 59.9 %
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 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9787, 0.9724, 0.9791
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 12, 2003
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.97241
30.97911
ReflectionResolution: 2.35→20 Å / Num. all: 28714 / Num. obs: 24790 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.2
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2 / Num. unique all: 2840 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.427 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Hydrogens have been added in the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1284 5.1 %RANDOM
Rwork0.255 ---
obs0.256 23902 99.35 %-
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: 33.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 0 159 3381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213273
X-RAY DIFFRACTIONr_bond_other_d0.0030.023008
X-RAY DIFFRACTIONr_angle_refined_deg1.291.964413
X-RAY DIFFRACTIONr_angle_other_deg0.82637013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7175406
X-RAY DIFFRACTIONr_chiral_restr0.0740.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023601
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02636
X-RAY DIFFRACTIONr_nbd_refined0.2020.2728
X-RAY DIFFRACTIONr_nbd_other0.220.23671
X-RAY DIFFRACTIONr_nbtor_other0.0850.22090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.24
X-RAY DIFFRACTIONr_mcbond_it0.411.52029
X-RAY DIFFRACTIONr_mcangle_it0.78123286
X-RAY DIFFRACTIONr_scbond_it1.14831244
X-RAY DIFFRACTIONr_scangle_it1.9244.51127
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 88
Rwork0.33 1739
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.0396-0.29780.51340.1095-3.32644.2188-0.1486-1.3905-1.20610.4424-0.0957-0.23430.08151.74330.24430.5017-0.2759-0.01960.94040.03380.533922.68116.176163.1833
23.92521.64280.60722.90621.36344.97780.2181-0.51810.07480.2628-0.19150.26850.0741-0.5555-0.02660.0582-0.07380.07510.2156-0.06520.1043-8.74638.513660.3267
39.41522.0757-2.69256.77880.54195.8247-0.11810.1029-1.5487-0.5231-0.1514-0.74650.54020.75980.26950.09130.08010.05480.1155-0.00920.273919.93738.884341.309
43.83462.70332.21426.54795.05110.18470.715-1.3320.59020.8785-0.3518-0.8151-0.97371.4826-0.36320.6089-0.52810.12360.9074-0.1510.418626.724729.170259.1425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA215 - 23620 - 41
2X-RAY DIFFRACTION2AA237 - 46342 - 268
3X-RAY DIFFRACTION3AA464 - 554269 - 359
4X-RAY DIFFRACTION4AA555 - 662360 - 467

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