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- PDB-6cwx: Crystal structure of human ribonuclease P/MRP proteins Rpp20/Rpp25 -

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Basic information

Entry
Database: PDB / ID: 6cwx
TitleCrystal structure of human ribonuclease P/MRP proteins Rpp20/Rpp25
Components
  • Ribonuclease P protein subunit p20
  • Ribonuclease P protein subunit p25
KeywordsHYDROLASE / endonuclease / ribonuclease P / ribonuclease P complex / ribonuclease MRP / ribonuclease MRP complex / tRNA processing / rRNA processing / nucleic acid binding / RNA binding / protein binding / protein heterodimer / heterodimer / dimer / nucleus / nucleolus
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 / Major pathway of rRNA processing in the nucleolus and cytosol / centriolar satellite ...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 / Major pathway of rRNA processing in the nucleolus and cytosol / centriolar satellite / 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
FORMIC ACID / Ribonuclease P protein subunit p20 / Ribonuclease P protein subunit p25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.25 Å
AuthorsChan, C.W. / Kiesel, B.R. / Mondragon, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM058443 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)4T32 GM008152 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32 GM008382 United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Crystal Structure of Human Rpp20/Rpp25 Reveals Quaternary Level Adaptation of the Alba Scaffold as Structural Basis for Single-stranded RNA Binding.
Authors: Chan, C.W. / Kiesel, B.R. / Mondragon, A.
History
DepositionMar 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease P protein subunit p20
B: Ribonuclease P protein subunit p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2356
Polymers36,9512
Non-polymers2844
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-42 kcal/mol
Surface area13770 Å2
MethodPISA
2
A: Ribonuclease P protein subunit p20
B: Ribonuclease P protein subunit p25
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)893,645144
Polymers886,82548
Non-polymers6,82096
Water86548
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation6_676z+1,-x+2,-y+11
crystal symmetry operation7_674-z+1,-x+2,y-11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_564y,z+1,x-11
crystal symmetry operation10_766-y+2,z+1,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_764-y+2,-z+1,x-11
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_775-y+2,-x+2,-z1
crystal symmetry operation15_575y,-x+2,z1
crystal symmetry operation16_755-y+2,x,z1
crystal symmetry operation17_566x,z+1,-y+11
crystal symmetry operation18_764-x+2,z+1,y-11
crystal symmetry operation19_766-x+2,-z+1,-y+11
crystal symmetry operation20_564x,-z+1,y-11
crystal symmetry operation21_656z+1,y,-x+11
crystal symmetry operation22_674z+1,-y+2,x-11
crystal symmetry operation23_654-z+1,y,x-11
crystal symmetry operation24_676-z+1,-y+2,-x+11
Buried area121590 Å2
ΔGint-1370 kcal/mol
Surface area262750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.190, 182.190, 182.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432

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Components

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


Mass: 16020.300 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POP7, RPP20 / Plasmid: pHTT7K / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O75817, ribonuclease P
#2: Protein Ribonuclease P protein subunit p25 / RNase P protein subunit p25


Mass: 20930.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPP25 / Plasmid: pHTT7K / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9BUL9, ribonuclease P
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.42 Å3/Da / Density % sol: 63.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM potassium formate, pH 7.5, 300 mM magnesium sulfate, 4.5% PEG 300, 4.5% PEG 400, 4.5% PEG 1000, 4.5% PEG 4000, and 4.5% PEG 8000
PH range: 7.0 - 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→48.69 Å / Num. obs: 24742 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.028 / Rrim(I) all: 0.087 / Net I/σ(I): 16.4
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2265 / CC1/2: 0.924 / Rpim(I) all: 0.165 / Rrim(I) all: 0.523 / % possible all: 100

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
iMOSFLM7.2.1data reduction
Aimless0.5.29data scaling
autoSHARP3.10.1phasing
BUCCANEER1.5model building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 2.25→48.69 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.799 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1211 4.9 %RANDOM
Rwork0.2134 ---
obs0.2143 23502 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.26 Å2 / Biso mean: 54.096 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.25→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 16 100 1862
Biso mean--71.43 43.65 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191785
X-RAY DIFFRACTIONr_bond_other_d0.0010.021732
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9922405
X-RAY DIFFRACTIONr_angle_other_deg0.86634001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4775221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77922.43274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03215304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9251520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211934
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02350
LS refinement shellResolution: 2.251→2.309 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 76 -
Rwork0.272 1720 -
all-1796 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3461-0.7537-0.32812.82340.53620.4970.09310.06060.2128-0.23190.078-0.202-0.06650.1548-0.17110.1584-0.03080.04710.14320.00960.1093240.4611164.022636.1985
20.5458-0.3401-0.03181.82890.53010.99740.05220.09160.1079-0.12860.020.5029-0.1010.0764-0.07230.14160.01410.00830.02470.03020.2952220.9172164.510239.6873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 140
2X-RAY DIFFRACTION2B22 - 157

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