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- PDB-9l6y: Crystal structure of the L7Ae derivative protein LS12 in complex ... -

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Basic information

Entry
Database: PDB / ID: 9l6y
TitleCrystal structure of the L7Ae derivative protein LS12 in complex with its co-evolved target CS2 RNA
Components
  • CS2 RNA
  • Large ribosomal subunit protein eL8
KeywordsRNA BINDING PROTEIN / Protein-RNA complex
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, archaea / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsTeramoto, T. / Nakashima, M. / Fukunaga, K. / Yokobayashi, Y. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15701 Japan
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural insights into lab-coevolved RNA-RBP pairs and applications of synthetic riboswitches in cell-free system.
Authors: Fukunaga, K. / Teramoto, T. / Nakashima, M. / Ohtani, T. / Katsuki, R. / Matsuura, T. / Yokobayashi, Y. / Kakuta, Y.
History
DepositionDec 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large ribosomal subunit protein eL8
B: CS2 RNA
C: Large ribosomal subunit protein eL8
D: CS2 RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7129
Polymers47,5114
Non-polymers2005
Water00
1
A: Large ribosomal subunit protein eL8
B: CS2 RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8364
Polymers23,7562
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-24 kcal/mol
Surface area11070 Å2
MethodPISA
2
C: Large ribosomal subunit protein eL8
D: CS2 RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8765
Polymers23,7562
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-25 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.300, 55.280, 83.050
Angle α, β, γ (deg.)90.00, 106.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Large ribosomal subunit protein eL8 / 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13100.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16) (archaea)
Gene: rpl7ae, AF_0764 / Production host: Escherichia coli (E. coli) / References: UniProt: O29494
#2: RNA chain CS2 RNA


Mass: 10655.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 40% PEG300, 100 mM Sodium cacodylate/HCl, pH 6.5, 200 mM Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.12→50 Å / Num. obs: 8762 / % possible obs: 98 % / Redundancy: 4 % / CC1/2: 0.993 / Rrim(I) all: 0.17 / Net I/σ(I): 8.13
Reflection shellResolution: 3.12→3.3 Å / Mean I/σ(I) obs: 1.44 / Num. unique obs: 1433 / CC1/2: 0.615 / Rrim(I) all: 1.128

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BW0

4bw0


Resolution: 3.12→45.42 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2572 877 10.03 %
Rwork0.2199 --
obs0.2237 8745 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.12→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 1372 5 0 3168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.756
X-RAY DIFFRACTIONf_dihedral_angle_d16.4311014
X-RAY DIFFRACTIONf_chiral_restr0.043606
X-RAY DIFFRACTIONf_plane_restr0.004378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.320.35061460.31691321X-RAY DIFFRACTION99
3.32-3.570.34471410.27881303X-RAY DIFFRACTION99
3.57-3.930.31891500.23691314X-RAY DIFFRACTION99
3.93-4.50.2491450.19821296X-RAY DIFFRACTION98
4.5-5.670.21941460.19491318X-RAY DIFFRACTION98
5.67-45.420.21471490.20161316X-RAY DIFFRACTION96

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