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- PDB-9l6x: Crystal structure of the L7Ae derivative protein LS4 in complex w... -

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Basic information

Entry
Database: PDB / ID: 9l6x
TitleCrystal structure of the L7Ae derivative protein LS4 in complex with its co-evolved target CS1 RNA
Components
  • CS1 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: 1.89 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: CS1 RNA
C: Large ribosomal subunit protein eL8
D: CS1 RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9847
Polymers49,9114
Non-polymers733
Water3,999222
1
A: Large ribosomal subunit protein eL8
B: CS1 RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0285
Polymers24,9552
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-32 kcal/mol
Surface area11480 Å2
MethodPISA
2
C: Large ribosomal subunit protein eL8
D: CS1 RNA


Theoretical massNumber of molelcules
Total (without water)24,9552
Polymers24,9552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-16 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.870, 91.880, 61.210
Angle α, β, γ (deg.)90.00, 106.11, 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: 13208.235 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 CS1 RNA


Mass: 11747.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4% Tacsimate, pH 4.0, 12% PEG 3,350

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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: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 34786 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rrim(I) all: 0.115 / Net I/σ(I): 11.35
Reflection shellResolution: 1.89→1.99 Å / Num. unique obs: 5390 / CC1/2: 0.539 / Rrim(I) all: 1.785

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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: 1.89→45.94 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 1992 5.74 %
Rwork0.1986 --
obs0.2009 34734 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 1558 3 222 3551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.172
X-RAY DIFFRACTIONf_dihedral_angle_d13.0351106
X-RAY DIFFRACTIONf_chiral_restr0.069637
X-RAY DIFFRACTIONf_plane_restr0.009385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.35381420.32862358X-RAY DIFFRACTION100
1.94-1.990.31381440.30732318X-RAY DIFFRACTION100
1.99-2.050.33191360.27862348X-RAY DIFFRACTION100
2.05-2.110.31711390.25952301X-RAY DIFFRACTION100
2.11-2.190.28191430.252343X-RAY DIFFRACTION100
2.19-2.280.27821370.2392327X-RAY DIFFRACTION100
2.28-2.380.28771520.23082305X-RAY DIFFRACTION100
2.38-2.510.28331380.23122342X-RAY DIFFRACTION100
2.51-2.660.30011440.22932342X-RAY DIFFRACTION100
2.66-2.870.29791410.22582344X-RAY DIFFRACTION100
2.87-3.160.24711450.21242346X-RAY DIFFRACTION100
3.16-3.610.24911420.17912332X-RAY DIFFRACTION100
3.62-4.550.18151430.15922355X-RAY DIFFRACTION100
4.55-45.940.16451460.14412381X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 31.8298 Å / Origin y: -17.602 Å / Origin z: 16.8212 Å
111213212223313233
T0.1554 Å20.002 Å20.0306 Å2-0.1797 Å2-0.0325 Å2--0.1579 Å2
L0.5335 °2-0.5208 °20.2903 °2-1.47 °2-0.6213 °2--0.69 °2
S-0.0282 Å °0.0167 Å °-0.014 Å °0.0453 Å °0.0093 Å °-0.0827 Å °-0.0146 Å °0.0331 Å °0.0112 Å °
Refinement TLS groupSelection details: all

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