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- PDB-1wsu: C-terminal domain of elongation factor selB complexed with SECIS RNA -

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Basic information

Entry
Database: PDB / ID: 1wsu
TitleC-terminal domain of elongation factor selB complexed with SECIS RNA
Components
  • 5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*U*GP*GP*CP*AP*AP*CP*GP*CP*C)-3'
  • Selenocysteine-specific elongation factor
KeywordsTRANSLATION/RNA / winged-helix / TRANSLATION-RNA COMPLEX
Function / homology
Function and homology information


selenocysteine incorporation / translation elongation factor activity / GTPase activity / GTP binding / RNA binding / cytosol
Similarity search - Function
Translation elongation factor SelB, winged helix, type 1 / Elongation factor SelB, winged helix / Translation elongation factor SelB, winged helix, type 2 / Elongation factor SelB, winged helix / Translation elongation factor SelB, winged helix, type 3 / Elongation factor SelB, winged helix / Translation elongation factor, selenocysteine-specific / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 ...Translation elongation factor SelB, winged helix, type 1 / Elongation factor SelB, winged helix / Translation elongation factor SelB, winged helix, type 2 / Elongation factor SelB, winged helix / Translation elongation factor SelB, winged helix, type 3 / Elongation factor SelB, winged helix / Translation elongation factor, selenocysteine-specific / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Small GTP-binding protein domain / Arc Repressor Mutant, subunit A / Translation protein, beta-barrel domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Selenocysteine-specific elongation factor
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYoshizawa, S. / Rasubala, L. / Ose, T. / Kohda, D. / Fourmy, D. / Maenaka, K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structural basis for mRNA recognition by elongation factor SelB
Authors: Yoshizawa, S. / Rasubala, L. / Ose, T. / Kohda, D. / Fourmy, D. / Maenaka, K.
History
DepositionNov 11, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
E: 5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*U*GP*GP*CP*AP*AP*CP*GP*CP*C)-3'
F: 5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*U*GP*GP*CP*AP*AP*CP*GP*CP*C)-3'
G: 5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*U*GP*GP*CP*AP*AP*CP*GP*CP*C)-3'
A: Selenocysteine-specific elongation factor
B: Selenocysteine-specific elongation factor
C: Selenocysteine-specific elongation factor
D: Selenocysteine-specific elongation factor


Theoretical massNumber of molelcules
Total (without water)79,1287
Polymers79,1287
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.865, 169.814, 71.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain 5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*U*GP*GP*CP*AP*AP*CP*GP*CP*C)-3' / SECIS RNA


Mass: 7386.424 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: selenocystein incorporated sequence of RNA. The first 3 and last 3 residues are cloning artifacts.
#2: Protein
Selenocysteine-specific elongation factor / SelB translation factor


Mass: 14242.195 Da / Num. of mol.: 4 / Fragment: SECIS binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Gene: selB / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q46455
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.2 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: tri-sodium citrate dihydrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1tri-sodium citrate dihydrate11
2HEPES11
3HOH11
4tri-sodium citrate dihydrate12
5HEPES12
6HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 3, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 45105 / Num. obs: 41948 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 43.4202 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4435 / % possible all: 74.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LVA

1lva


Resolution: 2.3→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 4099 -RANDOM
Rwork0.2244 ---
all-44691 --
obs-41657 93.2 %-
Displacement parametersBiso mean: 69.1656 Å2
Baniso -1Baniso -2Baniso -3
1-13.831 Å20 Å20 Å2
2---13.211 Å20 Å2
3----0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 1375 0 273 5484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006128
X-RAY DIFFRACTIONc_angle_deg1.15214
X-RAY DIFFRACTIONc_dihedral_angle_d18.76078
X-RAY DIFFRACTIONc_improper_angle_d1.10447
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.324 316 -
Rwork0.291 --
obs--0.733 %

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