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- PDB-3wy9: Crystal structure of a complex of the archaeal ribosomal stalk pr... -

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Basic information

Entry
Database: PDB / ID: 3wy9
TitleCrystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha
Components
  • 50S ribosomal protein L12
  • Elongation factor 1-alpha
KeywordsTRANSLATION/RIBOSOMAL PROTEIN / multi-domain / GTPase / aminoacyl-tRNA delivery / GTP / aminoacyl-tRNA / stalk protein / TRANSLATION-RIBOSOMAL PROTEIN complex
Function / homology
Function and homology information


translational elongation / translation elongation factor activity / ribosome / structural constituent of ribosome / ribonucleoprotein complex / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Ribosomal protein L12, archaea / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Translation elongation factor EF1A, eukaryotic/archaeal / 60s Acidic ribosomal protein / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site ...Ribosomal protein L12, archaea / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Translation elongation factor EF1A, eukaryotic/archaeal / 60s Acidic ribosomal protein / Translation elongation factor EFTu/EF1A, C-terminal / 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. / 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 / Large ribosomal subunit protein P1 / Elongation factor 1-alpha
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIto, K. / Honda, T. / Suzuki, T. / Miyoshi, T. / Murakami, R. / Yao, M. / Uchiumi, T.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Molecular insights into the interaction of the ribosomal stalk protein with elongation factor 1 alpha.
Authors: Ito, K. / Honda, T. / Suzuki, T. / Miyoshi, T. / Murakami, R. / Yao, M. / Uchiumi, T.
History
DepositionAug 22, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor 1-alpha
B: Elongation factor 1-alpha
C: 50S ribosomal protein L12
D: 50S ribosomal protein L12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1146
Polymers104,2284
Non-polymers8862
Water2,450136
1
A: Elongation factor 1-alpha
C: 50S ribosomal protein L12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5573
Polymers52,1142
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-12 kcal/mol
Surface area20420 Å2
MethodPISA
2
B: Elongation factor 1-alpha
D: 50S ribosomal protein L12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5573
Polymers52,1142
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-12 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.256, 87.420, 82.461
Angle α, β, γ (deg.)90.00, 92.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Elongation factor 1-alpha / EF-1-alpha / Elongation factor Tu / EF-Tu


Mass: 48426.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: tuf, PH1484, PHCC033 / Production host: Escherichia coli (E. coli) / References: UniProt: O59153
#2: Protein/peptide 50S ribosomal protein L12 / / Acidic ribosomal protein P1 homolog


Mass: 3687.892 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 77-108 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Pyrococcus horikoshii OT3 (archaea) / References: UniProt: O57705
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / 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.: 136 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 200mM NaCl, 100mM phosphate-citrate, pH 4.2, 20% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Mar 2, 2010
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 49622 / % possible obs: 100 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.34 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.97 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.836 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 1.4 / σ(I): 2 / ESU R: 0.28 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23795 2516 5.1 %RANDOM
Rwork0.19425 ---
all0.19648 ---
obs0.19648 47104 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å22.33 Å2
2---1.81 Å2-0 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6912 0 56 136 7104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197116
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9799652
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00324.795292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.022151282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.161534
X-RAY DIFFRACTIONr_chiral_restr0.0970.21108
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215240
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5592.63530
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4383.8884402
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5332.9143585
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.42121.87710620
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 173 -
Rwork0.201 3449 -
obs--99.31 %
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)
10.7277-0.23970.12571.6486-0.56760.75340.0749-0.13520.03570.0914-0.0130.0828-0.0592-0.062-0.06190.0555-0.0381-0.00130.0688-0.00380.017237.0197-1.902916.2458
21.7578-0.1886-0.40320.84050.0460.66820.05690.08750.2972-0.06130.0293-0.0276-0.0802-0.0315-0.08620.0716-0.0352-0.00320.08010.03360.056176.630121.122719.5134
320.4524-6.2039.76343.5786-2.54687.8838-0.1195-0.6177-0.46190.12850.18690.02610.173-0.1163-0.06740.1068-0.05350.01040.0990.04890.072264.5908-0.292325.8372
42.47573.09850.91122.15333.47673.13250.14430.0202-0.3548-0.3687-0.1261-0.55260.25480.0715-0.01820.0588-0.0091-0.00930.14220.03280.065462.1597-4.550615.6179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 427
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION2B5 - 427
4X-RAY DIFFRACTION2B500
5X-RAY DIFFRACTION3C83 - 108
6X-RAY DIFFRACTION4D83 - 108

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