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- PDB-1zav: Ribosomal Protein L10-L12(NTD) Complex, Space Group P21 -

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Basic information

Entry
Database: PDB / ID: 1zav
TitleRibosomal Protein L10-L12(NTD) Complex, Space Group P21
Components
  • 50S ribosomal protein L10
  • 50S ribosomal protein L7/L12Ribosome
KeywordsSTRUCTURAL PROTEIN / ribosome structure and function / L10-L12 complex structure / L10E structure / L7/12 ribosomal stalk / thiostrepton loop of 23S rRNA / translation factor recruitment / GTPase stimulation / mechanism of translation / rapid kinetics
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / mRNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #290 / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ribosomal protein L10, eubacterial, conserved site ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #290 / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Helix non-globular / Special / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL10 / Large ribosomal subunit protein bL12
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDiaconu, M. / Kothe, U. / Schluenzen, F. / Fischer, N. / Harms, J.M. / Tonevitski, A.G. / Stark, H. / Rodnina, M.V. / Wahl, M.C.
CitationJournal: Cell / Year: 2005
Title: Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation.
Authors: Mihaela Diaconu / Ute Kothe / Frank Schlünzen / Niels Fischer / Jörg M Harms / Alexander G Tonevitsky / Holger Stark / Marina V Rodnina / Markus C Wahl /
Abstract: The L7/12 stalk of the large subunit of bacterial ribosomes encompasses protein L10 and multiple copies of L7/12. We present crystal structures of Thermotoga maritima L10 in complex with three L7/12 ...The L7/12 stalk of the large subunit of bacterial ribosomes encompasses protein L10 and multiple copies of L7/12. We present crystal structures of Thermotoga maritima L10 in complex with three L7/12 N-terminal-domain dimers, refine the structure of an archaeal L10E N-terminal domain on the 50S subunit, and identify these elements in cryo-electron-microscopic reconstructions of Escherichia coli ribosomes. The mobile C-terminal helix alpha8 of L10 carries three L7/12 dimers in T. maritima and two in E. coli, in concordance with the different length of helix alpha8 of L10 in these organisms. The stalk is organized into three elements (stalk base, L10 helix alpha8-L7/12 N-terminal-domain complex, and L7/12 C-terminal domains) linked by flexible connections. Highly mobile L7/12 C-terminal domains promote recruitment of translation factors to the ribosome and stimulate GTP hydrolysis by the ribosome bound factors through stabilization of their active GTPase conformation.
History
DepositionApr 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L10
U: 50S ribosomal protein L7/L12
V: 50S ribosomal protein L7/L12
W: 50S ribosomal protein L7/L12
X: 50S ribosomal protein L7/L12
Y: 50S ribosomal protein L7/L12
Z: 50S ribosomal protein L7/L12


Theoretical massNumber of molelcules
Total (without water)40,8977
Polymers40,8977
Non-polymers00
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-121 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.438, 60.375, 83.372
Angle α, β, γ (deg.)90.00, 91.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 50S ribosomal protein L10 /


Mass: 20436.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rplJ / Plasmid: pETM-ZZ / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P29394
#2: Protein/peptide
50S ribosomal protein L7/L12 / Ribosome


Mass: 3409.979 Da / Num. of mol.: 6 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rplL / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P29396
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.7 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Na acetate, ethylene glycol, PEG 1000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 19, 2004
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 34160 / Num. obs: 34091 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 99.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 1700 Random
Rwork0.226 --
obs0.239 34059 -
all-34160 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 0 413 3247
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.17

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