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- PDB-2ply: Structure of the mRNA binding fragment of elongation factor SelB ... -

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Basic information

Entry
Database: PDB / ID: 2ply
TitleStructure of the mRNA binding fragment of elongation factor SelB in complex with SECIS RNA.
Components
  • RNA (5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP*C)-3')
  • Selenocysteine-specific elongation factor
Keywordstranslation/RNA / protein-rna / complex / rna / winged helix / selb / SECIS / 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
Arc Repressor Mutant, subunit A - #2770 / 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 / Selenocysteine-specific elongation factor, beta-barrel domain / Translation elongation factor SelB, winged helix, type 3 / Elongation factor SelB, winged helix / Translation elongation factor, selenocysteine-specific / : ...Arc Repressor Mutant, subunit A - #2770 / 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 / Selenocysteine-specific elongation factor, beta-barrel domain / 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: 2.6 Å
AuthorsSoler, N. / Fourmy, D. / Yoshizawa, S.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB.
Authors: Soler, N. / Fourmy, D. / Yoshizawa, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and preliminary X-ray analysis of the mRNA-binding domain of elongation factor SelB from Escherichia coli in complex with RNA
Authors: Soler, N. / Fourmy, D. / Yoshizawa, S.
History
DepositionApr 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: RNA (5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP*C)-3')
E: RNA (5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP*C)-3')
A: Selenocysteine-specific elongation factor
B: Selenocysteine-specific elongation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,91428
Polymers74,2564
Non-polymers65824
Water1,964109
1
C: RNA (5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP*C)-3')
A: Selenocysteine-specific elongation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,58118
Polymers37,1282
Non-polymers45316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: RNA (5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP*C)-3')
B: Selenocysteine-specific elongation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,33410
Polymers37,1282
Non-polymers2068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.640, 120.838, 50.865
Angle α, β, γ (deg.)90.00, 100.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain / Protein , 2 types, 4 molecules CEAB

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


Mass: 7386.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: In vitro transcription
#2: Protein Selenocysteine-specific elongation factor / SelB translation factor


Mass: 29741.746 Da / Num. of mol.: 2 / Mutation: S535W, F536V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Gene: selB / Production host: Escherichia coli (E. coli) / References: UniProt: Q46455

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Non-polymers , 5 types, 133 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG4000, 0.1M Na-Acetate pH 4.6, 0.2M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2Na-Acetate11
3Ammonium sulfate11
4PEG400012
5Na-Acetate12
6Ammonium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2003
RadiationMonochromator: 2mirrors: N2 cooled + sagittaly bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.6→95.563 Å / Num. all: 27498 / Num. obs: 28977 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.517 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.6 Å17.56 Å
Translation2.6 Å17.56 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
Xnemodata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WSU,1LVA

1wsu

1lva


Resolution: 2.6→95.35 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.84 / SU B: 9.5 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28691 1474 5.1 %RANDOM
Rwork0.22677 ---
obs0.22978 27498 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.325 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.92 Å2
2--0.06 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 976 24 109 4422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224680
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2372.2246574
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27622.471170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.16915561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.11537
X-RAY DIFFRACTIONr_chiral_restr0.2260.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023257
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.22109
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.23098
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3050.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2720.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8941.52232
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70623519
X-RAY DIFFRACTIONr_scbond_it2.63332730
X-RAY DIFFRACTIONr_scangle_it4.0414.53055
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.519 116 -
Rwork0.369 2034 -
obs--100 %

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