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- PDB-3p26: Crystal structure of S. cerevisiae Hbs1 protein (apo-form), a tra... -

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Basic information

Entry
Database: PDB / ID: 3p26
TitleCrystal structure of S. cerevisiae Hbs1 protein (apo-form), a translational GTPase involved in RNA quality control pathways and interacting with Dom34/Pelota
ComponentsElongation factor 1 alpha-like protein
KeywordsSIGNALING PROTEIN / GTP/GDP binding domain / beta-barrel / translational GTPase / Dom34 / Structural Genomics / Paris-Sud Yeast Structural Genomics / YSG
Function / homology
Function and homology information


Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / mRNA decay by 3' to 5' exoribonuclease / nonfunctional rRNA decay / ribosome disassembly / positive regulation of translational initiation / translation elongation factor activity / rescue of stalled ribosome / positive regulation of translation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / mRNA decay by 3' to 5' exoribonuclease / nonfunctional rRNA decay / ribosome disassembly / positive regulation of translational initiation / translation elongation factor activity / rescue of stalled ribosome / positive regulation of translation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / GTPase activity / GTP binding / cytosol / cytoplasm
Similarity search - Function
HBS1-like protein, N-terminal / HBS1 N-terminus / 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. ...HBS1-like protein, N-terminal / HBS1 N-terminus / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Elongation factor 1 alpha-like protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-SAD / Resolution: 2.5 Å
Authorsvan den Elzen, A. / Henri, J. / Lazar, N. / Gas, M.E. / Durand, D. / Lacroute, F. / Nicaise, M. / van Tilbeurgh, H. / Sraphin, B. / Graille, M. / Paris-Sud Yeast Structural Genomics (YSG)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Dissection of Dom34-Hbs1 reveals independent functions in two RNA quality control pathways.
Authors: van den Elzen, A.M. / Henri, J. / Lazar, N. / Gas, M.E. / Durand, D. / Lacroute, F. / Nicaise, M. / van Tilbeurgh, H. / Seraphin, B. / Graille, M.
History
DepositionOct 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 14, 2012Group: Structure summary
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor 1 alpha-like protein
B: Elongation factor 1 alpha-like protein


Theoretical massNumber of molelcules
Total (without water)108,7492
Polymers108,7492
Non-polymers00
Water4,954275
1
A: Elongation factor 1 alpha-like protein


Theoretical massNumber of molelcules
Total (without water)54,3751
Polymers54,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Elongation factor 1 alpha-like protein


Theoretical massNumber of molelcules
Total (without water)54,3751
Polymers54,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.631, 110.631, 188.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Elongation factor 1 alpha-like protein


Mass: 54374.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HBS1, YKR084C, YKR404 / Production host: Escherichia coli (E. coli) / References: UniProt: P32769
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 100mM Tris-HCl, 12% PEG 6000, 150mM NaCl, pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2009
RadiationMonochromator: Channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→34.087 Å / Num. all: 41110 / Num. obs: 39338 / % possible obs: 95.69 % / Observed criterion σ(F): 50 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.54 Å / % possible all: 95.69

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: Se-SAD / Resolution: 2.5→34.087 Å / SU ML: 0.37 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1973 5.02 %RANDOM
Rwork0.2165 ---
obs0.2193 39338 95.69 %-
all-41110 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.324 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1626 Å20 Å20 Å2
2---1.1626 Å2-0 Å2
3---2.3252 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6886 0 0 275 7161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067016
X-RAY DIFFRACTIONf_angle_d1.029477
X-RAY DIFFRACTIONf_dihedral_angle_d17.7752605
X-RAY DIFFRACTIONf_chiral_restr0.0691083
X-RAY DIFFRACTIONf_plane_restr0.0041213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56360.33391440.26582605X-RAY DIFFRACTION95
2.5636-2.63290.33141430.25772636X-RAY DIFFRACTION96
2.6329-2.71030.32051460.2452603X-RAY DIFFRACTION96
2.7103-2.79780.31061350.23832663X-RAY DIFFRACTION96
2.7978-2.89770.36341300.23052661X-RAY DIFFRACTION97
2.8977-3.01370.29821280.23532689X-RAY DIFFRACTION97
3.0137-3.15070.29261330.23292662X-RAY DIFFRACTION96
3.1507-3.31670.25591300.2182671X-RAY DIFFRACTION97
3.3167-3.52430.27011580.21312661X-RAY DIFFRACTION96
3.5243-3.79610.2551450.19382657X-RAY DIFFRACTION95
3.7961-4.17750.25321410.19392665X-RAY DIFFRACTION95
4.1775-4.78060.20731270.1662703X-RAY DIFFRACTION95
4.7806-6.01770.24261620.20462696X-RAY DIFFRACTION95
6.0177-34.08970.26271510.22382793X-RAY DIFFRACTION92

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