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- PDB-6lt7: Crystal structure of human RPP20-RPP25 proteins in complex with t... -

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Basic information

Entry
Database: PDB / ID: 6lt7
TitleCrystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncRNA RMRP
Components
  • 50-mer RNA
  • Ribonuclease P protein subunit p20
  • Ribonuclease P protein subunit p25
KeywordsHYDROLASE/RNA / Ribonucleoprotein complex / RNase MRP / RMRP / Cartilage hair hypoplasia / Alba / RNA BINDING PROTEIN / HYDROLASE-RNA complex
Function / homology
Function and homology information


multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing in the nucleus / tRNA processing / centriolar satellite / Major pathway of rRNA processing in the nucleolus and cytosol ...multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing in the nucleus / tRNA processing / centriolar satellite / Major pathway of rRNA processing in the nucleolus and cytosol / rRNA processing / intracellular membrane-bounded organelle / nucleolus / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Ribonucleases P/MRP protein subunit Rpp20/Pop7 / Rpp20 subunit of nuclear RNase MRP and P / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Ribonuclease P protein subunit p20 / Ribonuclease P protein subunit p25
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsHuang, J. / Yin, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570766 China
National Natural Science Foundation of China (NSFC)U1632130 China
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncRNA RMRP.
Authors: Yin, C. / Bai, G. / Zhang, Y. / Huang, J.
History
DepositionJan 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease P protein subunit p20
B: Ribonuclease P protein subunit p25
C: 50-mer RNA
D: Ribonuclease P protein subunit p20
E: Ribonuclease P protein subunit p25
F: 50-mer RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,16812
Polymers104,7966
Non-polymers3726
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16300 Å2
ΔGint-89 kcal/mol
Surface area37020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.168, 144.168, 74.223
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Ribonuclease P protein subunit p20 / RNaseP protein p20 / Ribonucleases P/MRP protein subunit POP7 homolog / hPOP7


Mass: 15853.733 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POP7, RPP20 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75817, ribonuclease P
#2: Protein Ribonuclease P protein subunit p25 / RNase P protein subunit p25


Mass: 20668.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPP25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BUL9, ribonuclease P
#3: RNA chain 50-mer RNA / RMRP_P3


Mass: 15875.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.25 Å3/Da / Density % sol: 71.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 20% of PEG 3350, 0.2 M ammonium tartrate dibasic, pH 6.6

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 47259 / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.062 / Rrim(I) all: 0.198 / Χ2: 2 / Net I/σ(I): 4.1 / Num. measured all: 482821
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.758.10.80323800.8330.2930.8570.51699.7
2.75-2.89.10.76123430.8770.2640.8070.497100
2.8-2.859.70.68123570.9160.2290.7180.514100
2.85-2.9110.10.58723380.9350.1930.6180.517100
2.91-2.9710.30.56523710.9370.1840.5950.542100
2.97-3.0410.20.4723650.9530.1540.4940.557100
3.04-3.129.60.37323740.9670.1270.3940.668100
3.12-3.210.20.31823770.9740.1040.3350.68100
3.2-3.310.90.26723390.9810.0840.280.788100
3.3-3.410.90.23823720.980.0760.250.861100
3.4-3.5210.80.20224080.9840.0640.2130.929100
3.52-3.6610.80.1823360.9870.0580.1891.074100
3.66-3.8310.70.16823380.9880.0540.1771.354100
3.83-4.039.90.15323620.980.0510.1611.737100
4.03-4.2910.20.14323790.9880.0470.1512.046100
4.29-4.62110.14323600.9740.0460.152.628100
4.62-5.0810.90.14123560.9790.0460.1492.71100
5.08-5.8110.30.14223610.9790.0470.1492.795100
5.81-7.3210.40.14323750.9880.0470.153.394100
7.32-5010.20.17923680.920.0630.1914.704100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→35.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.844 / SU ML: 0.178 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.24
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 2250 4.8 %RANDOM
Rwork0.1916 ---
obs0.1938 44933 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 225.81 Å2 / Biso mean: 62.135 Å2 / Biso min: 27.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----3.12 Å2
Refinement stepCycle: final / Resolution: 2.7→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3671 2060 24 271 6026
Biso mean--91.7 58.89 -
Num. residues----578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126039
X-RAY DIFFRACTIONr_bond_other_d0.0020.0184627
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.5128616
X-RAY DIFFRACTIONr_angle_other_deg1.3741.88110803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8945472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.23619.557203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1815613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.921545
X-RAY DIFFRACTIONr_chiral_restr0.0990.2899
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021293
LS refinement shellResolution: 2.703→2.773 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 161 -
Rwork0.346 3335 -
all-3496 -
obs--99.74 %

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