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- PDB-6ji2: Crystal structure of archaeal ribosomal protein aP1, aPelota, and... -

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Basic information

Entry
Database: PDB / ID: 6ji2
TitleCrystal structure of archaeal ribosomal protein aP1, aPelota, and GTP-bound aEF1A complex
Components
  • Archaeal ribosomal stalk protein aP1
  • Elongation factor 1-alpha
  • Protein pelota homolog
KeywordsTRANSLATION / translation elongation ribosomal stalk
Function / homology
Function and homology information


RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / ribosome disassembly / protein-synthesizing GTPase / nonfunctional rRNA decay / translational elongation / translation elongation factor activity / endonuclease activity / Hydrolases; Acting on ester bonds ...RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / ribosome disassembly / protein-synthesizing GTPase / nonfunctional rRNA decay / translational elongation / translation elongation factor activity / endonuclease activity / Hydrolases; Acting on ester bonds / structural constituent of ribosome / ribosome / ribonucleoprotein complex / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L12, archaea / Translation release factor pelota, archaea / Pelota, domain A / eRF1 domain 2 / Translation release factor pelota / Pelota/DOM34, N-terminal domain / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Translation elongation factor EF1A, eukaryotic/archaeal / eRF1 domain 1/Pelota-like ...Ribosomal protein L12, archaea / Translation release factor pelota, archaea / Pelota, domain A / eRF1 domain 2 / Translation release factor pelota / Pelota/DOM34, N-terminal domain / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Translation elongation factor EF1A, eukaryotic/archaeal / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / : / GTP-eEF1A C-terminal domain-like / : / Ribosomal protein L30/S12 / Elongation factor Tu C-terminal domain / 60s Acidic ribosomal protein / 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. / 60s Ribosomal Protein L30; Chain: A; / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / 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. / 50S ribosomal protein L30e-like / SH3 type barrels. / Nucleotidyltransferase; domain 5 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Large ribosomal subunit protein P1 / Elongation factor 1-alpha / Protein pelota homolog
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMaruyama, K. / Imai, H. / Kawamura, M. / Ishino, S. / Ishino, Y. / Ito, K. / Uchiumi, T.
CitationJournal: Sci Rep / Year: 2019
Title: Switch of the interactions between the ribosomal stalk and EF1A in the GTP- and GDP-bound conformations.
Authors: Maruyama, K. / Imai, H. / Kawamura, M. / Ishino, S. / Ishino, Y. / Ito, K. / Uchiumi, T.
History
DepositionFeb 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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: Protein pelota homolog
E: Elongation factor 1-alpha
F: Protein pelota homolog
X: Archaeal ribosomal stalk protein aP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,28211
Polymers184,1415
Non-polymers1,1416
Water1,76598
1
A: Elongation factor 1-alpha
B: Protein pelota homolog
X: Archaeal ribosomal stalk protein aP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5796
Polymers93,0083
Non-polymers5703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-40 kcal/mol
Surface area32930 Å2
MethodPISA
2
E: Elongation factor 1-alpha
F: Protein pelota homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7045
Polymers91,1332
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-37 kcal/mol
Surface area33050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.447, 73.405, 108.142
Angle α, β, γ (deg.)98.64, 93.80, 100.44
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules AEBF

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


Mass: 49662.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Strain: K1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YAV0
#2: Protein Protein pelota homolog


Mass: 41470.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Strain: K1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9YAZ5, Hydrolases; Acting on ester bonds

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Protein/peptide , 1 types, 1 molecules X

#3: Protein/peptide Archaeal ribosomal stalk protein aP1


Mass: 1875.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aeropyrum pernix K1 (archaea) / References: UniProt: Q9Y9W9*PLUS

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Non-polymers , 4 types, 104 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl, pH 8.0, 200 mM Li2SO4, 16% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→106.42 Å / Num. obs: 41897 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.4
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.564

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXM

3wxm


Resolution: 3→106.42 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.873 / SU B: 21.804 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27922 2154 5.1 %RANDOM
Rwork0.1991 ---
obs0.20311 39737 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.131 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å23.03 Å2-3.36 Å2
2--2.3 Å21.71 Å2
3----1.61 Å2
Refinement stepCycle: 1 / Resolution: 3→106.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12375 0 68 98 12541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01912664
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212647
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.98217127
X-RAY DIFFRACTIONr_angle_other_deg0.926329071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44451582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2422.788538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75152293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.10315132
X-RAY DIFFRACTIONr_chiral_restr0.0710.21947
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02114020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022748
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_it2.8068.0616343
X-RAY DIFFRACTIONr_mcbond_other2.8068.0616342
X-RAY DIFFRACTIONr_mcangle_it4.63612.0877920
X-RAY DIFFRACTIONr_mcangle_other4.63612.0877921
X-RAY DIFFRACTIONr_scbond_it2.5948.4376321
X-RAY DIFFRACTIONr_scbond_other2.5948.4376321
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.45612.5139207
X-RAY DIFFRACTIONr_long_range_B_refined7.3562.7813480
X-RAY DIFFRACTIONr_long_range_B_other7.34862.79113470
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.002→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 170 -
Rwork0.313 2851 -
obs--95.48 %

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