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- PDB-5yv5: Crystal structure of the complex of archaeal ribosomal stalk prot... -

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Basic information

Entry
Database: PDB / ID: 5yv5
TitleCrystal structure of the complex of archaeal ribosomal stalk protein aP1 and archaeal ribosome recycling factor aABCE1.
Components
  • ATPase RIL
  • Archaeal ribosomal stalk protein aP1
KeywordsTRANSLATION / Ribosome recycling / Ribosomal stalk / Complex
Function / homology
Function and homology information


translational elongation / oxidoreductase activity / ribosome / structural constituent of ribosome / ribonucleoprotein complex / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Ribosomal protein L12, archaea / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S binding domain / 60s Acidic ribosomal protein / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site ...Ribosomal protein L12, archaea / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S binding domain / 60s Acidic ribosomal protein / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATPase RIL / Large ribosomal subunit protein P1
Similarity search - Component
Biological speciesPyrococcus furiosus COM1 (archaea)
Pyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsImai, H. / Abe, T. / Miyoshi, T. / Nishikawa, S. / Ito, K. / Uchiumi, T.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The ribosomal stalk protein is crucial for the action of the conserved ATPase ABCE1
Authors: Imai, H. / Abe, T. / Miyoshi, T. / Nishikawa, S.I. / Ito, K. / Uchiumi, T.
History
DepositionNov 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase RIL
B: Archaeal ribosomal stalk protein aP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2666
Polymers62,3632
Non-polymers9034
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-47 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.011, 64.731, 147.073
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 ATPase RIL


Mass: 60483.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_02505 / Production host: Escherichia coli (E. coli) / References: UniProt: I6V0C7
#2: Protein/peptide Archaeal ribosomal stalk protein aP1


Mass: 1879.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus (archaea) / References: UniProt: Q8TZJ7*PLUS
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15% (w/v) PEG 4000, 10% (v/v) 2-propanol, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→19.98 Å / Num. obs: 31682 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Redundancy: 3.18 % / Net I/σ(I): 21.03
Reflection shellResolution: 2.1→2.22 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YQT

1yqt


Resolution: 2.1→19.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.942 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24376 1714 5.1 %RANDOM
Rwork0.19439 ---
obs0.19695 31682 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.331 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.1→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4199 0 56 292 4547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194332
X-RAY DIFFRACTIONr_bond_other_d0.0010.024140
X-RAY DIFFRACTIONr_angle_refined_deg1.1042.0025860
X-RAY DIFFRACTIONr_angle_other_deg0.71339579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5085529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00523.8200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.515774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3721536
X-RAY DIFFRACTIONr_chiral_restr0.0610.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214772
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02878
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_it1.1572.8532122
X-RAY DIFFRACTIONr_mcbond_other1.1572.8512121
X-RAY DIFFRACTIONr_mcangle_it2.0164.2692649
X-RAY DIFFRACTIONr_mcangle_other2.0154.2712650
X-RAY DIFFRACTIONr_scbond_it1.2763.0142210
X-RAY DIFFRACTIONr_scbond_other1.2763.0142210
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2124.443211
X-RAY DIFFRACTIONr_long_range_B_refined4.1333.2264866
X-RAY DIFFRACTIONr_long_range_B_other4.02333.0514806
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.098→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 89 -
Rwork0.207 1851 -
obs--77.88 %

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