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- PDB-5yt0: Crystal structure of the complex of archaeal ribosomal stalk prot... -

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Basic information

Entry
Database: PDB / ID: 5yt0
TitleCrystal structure of the complex of archaeal ribosomal stalk protein aP1 and archaeal translation initiation factor aIF5B
Components
  • Archaeal ribosomal stalk protein aP1
  • Probable translation initiation factor IF-2
KeywordsTRANSLATION / translation initiation factor / ribosomal stalk protein / complex
Function / homology
Function and homology information


translational elongation / translation initiation factor activity / ribosome / structural constituent of ribosome / ribonucleoprotein complex / GTPase activity / GTP binding
Similarity search - Function
Ribosomal protein L12, archaea / Translation initiation factor aIF-2, archaea / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily ...Ribosomal protein L12, archaea / Translation initiation factor aIF-2, archaea / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / 60s Acidic ribosomal protein / Translation factors / 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. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / 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
GUANOSINE-5'-DIPHOSPHATE / Probable translation initiation factor IF-2 / 50S ribosomal protein L12
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMurakami, R. / Singh, C.R. / Morris, J. / Tang, L. / Harmon, I. / Miyoshi, T. / Ito, K. / Asano, K. / Uchiumi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
the Japan Society for the Promotion of Science15K06964 Japan
CitationJournal: Mol. Cell. Biol. / Year: 2018
Title: The Interaction between the Ribosomal Stalk Proteins and Translation Initiation Factor 5B Promotes Translation Initiation
Authors: Murakami, R. / Singh, C.R. / Morris, J. / Tang, L. / Harmon, I. / Takasu, A. / Miyoshi, T. / Ito, K. / Asano, K. / Uchiumi, T.
History
DepositionNov 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: Probable translation initiation factor IF-2
B: Archaeal ribosomal stalk protein aP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1543
Polymers42,7112
Non-polymers4431
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, pull-down assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-17 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.720, 79.016, 101.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable translation initiation factor IF-2


Mass: 40318.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Strain: K1 / Gene: infB, APE_2374 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y9B3
#2: Protein/peptide Archaeal ribosomal stalk protein aP1


Mass: 2391.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aeropyrum pernix K1 (archaea) / References: UniProt: Q9Y9W9*PLUS
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M citric acid, pH 6.5, 35%(w/v) PEG600

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→42.7 Å / Num. obs: 35221 / % possible obs: 98.3 % / Redundancy: 7 % / Net I/σ(I): 26.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→42.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.729 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21711 1758 5 %RANDOM
Rwork0.17087 ---
obs0.17323 33408 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.277 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.89→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 28 151 2839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192742
X-RAY DIFFRACTIONr_bond_other_d0.0020.022800
X-RAY DIFFRACTIONr_angle_refined_deg2.612.0123714
X-RAY DIFFRACTIONr_angle_other_deg1.27636430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45622.703111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76815493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7891528
X-RAY DIFFRACTIONr_chiral_restr0.1860.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212984
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02572
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3833.4441365
X-RAY DIFFRACTIONr_mcbond_other4.3643.4431364
X-RAY DIFFRACTIONr_mcangle_it5.0915.1341698
X-RAY DIFFRACTIONr_mcangle_other5.15.1351699
X-RAY DIFFRACTIONr_scbond_it7.1034.3881377
X-RAY DIFFRACTIONr_scbond_other7.1014.3871377
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.2936.2072015
X-RAY DIFFRACTIONr_long_range_B_refined11.66229.0513039
X-RAY DIFFRACTIONr_long_range_B_other11.69528.7772984
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 122 -
Rwork0.208 2323 -
obs--94.99 %

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