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- PDB-6ahv: Crystal structure of human RPP40 -

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Basic information

Entry
Database: PDB / ID: 6ahv
TitleCrystal structure of human RPP40
ComponentsRibonuclease P protein subunit p40
KeywordsHYDROLASE / RNase P
Function / homologyRibonuclease P, Rpp40 / Ribonuclease P 40kDa (Rpp40) subunit / tRNA processing in the nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / nucleolar ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA processing / nucleoplasm / nucleus / Ribonuclease P protein subunit p40
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 2.6 Å resolution
AuthorsWu, J. / Niu, S. / Tan, M. / Lan, P. / Lei, M.
CitationJournal: Cell / Year: 2018
Title: Cryo-EM Structure of the Human Ribonuclease P Holoenzyme.
Authors: Jian Wu / Shuangshuang Niu / Ming Tan / Chenhui Huang / Mingyue Li / Yang Song / Qianmin Wang / Juan Chen / Shaohua Shi / Pengfei Lan / Ming Lei
Abstract: Ribonuclease (RNase) P is a ubiquitous ribozyme that cleaves the 5' leader from precursor tRNAs. Here, we report cryo-electron microscopy structures of the human nuclear RNase P alone and in ...Ribonuclease (RNase) P is a ubiquitous ribozyme that cleaves the 5' leader from precursor tRNAs. Here, we report cryo-electron microscopy structures of the human nuclear RNase P alone and in complex with tRNA. Human RNase P is a large ribonucleoprotein complex that contains 10 protein components and one catalytic RNA. The protein components form an interlocked clamp that stabilizes the RNA in a conformation optimal for substrate binding. Human RNase P recognizes the tRNA using a double-anchor mechanism through both protein-RNA and RNA-RNA interactions. Structural comparison of the apo and tRNA-bound human RNase P reveals that binding of tRNA induces a local conformational change in the catalytic center, transforming the ribozyme into an active state. Our results also provide an evolutionary model depicting how auxiliary RNA elements in bacterial RNase P, essential for substrate binding, and catalysis, were replaced by the much more complex and multifunctional protein components in higher organisms.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 20, 2018 / Release: Dec 5, 2018

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease P protein subunit p40


Theoretical massNumber of molelcules
Total (without water)41,8851
Polyers41,8851
Non-polymers00
Water46826
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)17490
2
A: Ribonuclease P protein subunit p40

A: Ribonuclease P protein subunit p40


Theoretical massNumber of molelcules
Total (without water)83,7702
Polyers83,7702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area (Å2)3350
ΔGint (kcal/M)-11
Surface area (Å2)31640
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)73.398, 129.892, 116.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC 2 2 21

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Components

#1: Protein/peptide Ribonuclease P protein subunit p40 / / RNaseP protein p40 / RNase P subunit 1


Mass: 41884.844 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: RPP40, RNASEP1 / Plasmid name: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75818, ribonuclease P
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Formula: H2O / Water

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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: 3.32 / Density percent sol: 63 % / Mosaicity: 0.39 deg.
Crystal growTemp: 277 K / Method: evaporation / pH: 7
Details: 5% v/v TacsimateTM pH 7.0, 100mM Hepes pH 7.0, 10% w/v polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SSRF BEAMLINE BL18U1 / Synchrotron site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Collection date: Dec 31, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 40.72 Å2 / D resolution high: 2.6 Å / D resolution low: 5 Å / Number obs: 17458 / Rmerge I obs: 0.093 / Rpim I all: 0.045 / Rrim I all: 0.103 / Chi squared: 0.88 / NetI over sigmaI: 7 / Number measured all: 95185 / Redundancy: 5.5 % / Percent possible obs: 99.5
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber unique obsCC halfRpim I allRrim I allChi squaredRedundancyPercent possible all
0.6962.6002.69017100.7450.3230.7700.6745.60099.900
0.5132.6902.80017230.8440.2380.5680.7045.70099.800
0.4002.8002.93017300.8710.1860.4430.8085.60099.900
0.2762.9303.08017330.9280.1310.3070.9275.300100.000
0.1953.0803.28017300.9570.0940.2171.0105.30099.700
0.1483.2803.53017390.9610.0720.1661.1575.60099.800
0.1163.5303.88017450.9770.0560.1301.1715.50099.800
0.0863.8804.45017600.9840.0430.0961.0405.20099.500
0.0704.4505.60017550.9910.0340.0790.8075.50098.900
0.0465.60050.00018330.9960.0230.0520.5045.10098.000

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-2000data collection
PHENIXphasing
RefineMethod to determine structure: SAD / Overall SU ML: 0.41 / Cross valid method: THROUGHOUT / Sigma F: 1.36 / Overall phase error: 27.39 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 160.1 Å2 / B iso mean: 49.6534 Å2 / B iso min: 14.6 Å2
Least-squares processR factor R free: 0.2531 / R factor R work: 0.2179 / R factor obs: 0.2198 / Highest resolution: 2.6 Å / Lowest resolution: 43.434 Å / Number reflection R free: 877 / Number reflection R work: 16156 / Number reflection obs: 17033 / Percent reflection R free: 5.15 / Percent reflection obs: 97.05
Refine hist #finalHighest resolution: 2.6 Å / Lowest resolution: 43.434 Å / B iso mean solvent: 38.93 / Number residues total: 345
Number of atoms included #finalProtein: 2806 / Nucleic acid: 0 / Ligand: 0 / Solvent: 26 / Total: 2832
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022884
X-RAY DIFFRACTIONf_angle_d0.6043911
X-RAY DIFFRACTIONf_chiral_restr0.024425
X-RAY DIFFRACTIONf_plane_restr0.003496
X-RAY DIFFRACTIONf_dihedral_angle_d13.3801055
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 6

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
2.60000.33830.29522.76291472365251287.0000
2.76290.36860.27772.97621292709283899.0000
2.97620.28980.25933.275613727452882100.0000
3.27560.25900.22073.749315727422899100.0000
3.74930.24840.18394.72281452768291399.0000
4.72280.18750.189943.43971622827298998.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.1948-0.1163-0.07040.2956-0.11230.1680-0.0835-0.16990.05130.23610.17710.0832-0.0457-0.01220.21150.23760.02560.11780.22810.21640.19938.98820.14812.043
20.07680.06150.00060.0507-0.00240.0145-0.02070.00790.02920.0062-0.01730.00630.0021-0.0050-0.01060.12920.01460.03480.17310.07070.134214.93522.1929.274
Refine TLS group

Beg auth asym ID: A / End auth asym ID: A / Refine ID: X-RAY DIFFRACTION

IDBeg auth seq IDEnd auth seq IDRefine TLS IDSelection details
1123561( CHAIN A AND RESID 12:356 )
24014262( CHAIN A AND RESID 401:426 )

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