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- EMDB-9626: Cryo-EM structure of human Ribonuclease P -

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Basic information

Entry
Database: EMDB / ID: 9626
TitleCryo-EM structure of human Ribonuclease P
Map data
SampleRNase PRibonuclease P
  • nucleic-acidNucleic acid
  • Ribonucleases P/MRP protein subunit POP1
  • (Ribonuclease P protein subunit ...) x 8
  • Ribonuclease P/MRP protein subunit POP5
  • ligand
Function / homologyRibonucleases P/MRP protein subunit Rpp20 / RNAse P, Rpr2/Rpp21 subunit / Rnp2-like domain superfamily / Ribonuclease P/MRP, subunit p29 / RNase P subunit p30 / Ribonuclease P/MRP protein subunit / DNA/RNA-binding protein Alba-like / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Pop1, N-terminal / Ribonuclease P/MRP, subunit p29 superfamily ...Ribonucleases P/MRP protein subunit Rpp20 / RNAse P, Rpr2/Rpp21 subunit / Rnp2-like domain superfamily / Ribonuclease P/MRP, subunit p29 / RNase P subunit p30 / Ribonuclease P/MRP protein subunit / DNA/RNA-binding protein Alba-like / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Pop1, N-terminal / Ribonuclease P/MRP, subunit p29 superfamily / POPLD domain / Ribonuclease P, Rpp40 / Polymerase/histidinol phosphatase-like / Ribonuclease P/MRP protein subunit Pop5 / Ribonuclease P/MRP, p29 subunit / Rof/RNase P-like / 50S ribosomal protein L30e-like / Ribonucleases P/MRP protein subunit Pop1 / Alba-like domain superfamily / RNAse P Rpr2/Rpp21/SNM1 subunit domain / Ribonuclease P 40kDa (Rpp40) subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Domain of unknown function UPF0086 / RNase P subunit p30 / Rpp14/Pop5 family / Alba / tRNA processing in the nucleus / Rpp20 subunit of nuclear RNase MRP and P / Ribonucleases P/MRP protein subunit POP1 / POPLD (NUC188) domain / multimeric ribonuclease P complex / tRNA catabolic process / ribonuclease MRP activity / ribonuclease MRP complex / nucleolar ribonuclease P complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / rRNA processing / fibrillar center / microtubule organizing center / response to drug / nucleolus / RNA binding / extracellular space / nucleoplasm / nucleus / metal ion binding / cytoplasm / Ribonuclease P protein subunit p20 / Ribonuclease P protein subunit p40 / Ribonuclease P protein subunit p14 / Ribonuclease P protein subunit p29 / Ribonuclease P protein subunit p38 / Ribonuclease P protein subunit p30 / Ribonuclease P/MRP protein subunit POP5 / Ribonucleases P/MRP protein subunit POP1 / Ribonuclease P protein subunit p25 / Ribonuclease P protein subunit p21
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 3.92 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 ReportPDB-ID: 6ahr

SummaryFull reportAbout validation report
DateDeposition: Aug 20, 2018 / Header (metadata) release: Dec 5, 2018 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ahr
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9626.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.32 Å/pix.
= 337.92 Å
256 pix
1.32 Å/pix.
= 337.92 Å
256 pix
1.32 Å/pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.02 (by author), 0.03 (movie #1):
Minimum - Maximum-0.09011597 - 0.19876729
Average (Standard dev.)0.00018916799 (0.006135494)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0900.1990.000

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Supplemental data

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Sample components

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Entire RNase P

EntireName: RNase P / Number of components: 13

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Component #1: protein, RNase P

ProteinName: RNase PRibonuclease P / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: nucleic-acid, H1 RNA

Nucleic-acidName: H1 RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUAGGGCGGA GGGAAGCUCA UCAGUGGGGC CACGAGCUGA GUGCGUCCUG UCACUCCACU CCCAUGUCCC UUGGGAAGGU CUGAGACUAG GGCCAGAGGC GGCCCUAACA GGGCUCUCCC UGAGCUUCGG GGAGGUGAGU UCCCAGAGAA CGGGGCUCCG CGCGAGGUCA GACUGGGCAG GAGAUGCCGU GGACCCCGCC CUUCGGGGAG GGGCCCGGCG GAUGCCUCCU UUGCCGGAGC UUGGAACAGA CUCACGGCCA GCGAAGUGAG UUCAAUGGCU GAGGUGAGGU ACCCCGCAGG GGACCUCAUA ACCCAAUUCA GACUACUCUC CUCCGCCCAU U
MassTheoretical: 110.244172 kDa
SourceSpecies: Human (human)

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Component #3: protein, Ribonucleases P/MRP protein subunit POP1

ProteinName: Ribonucleases P/MRP protein subunit POP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 114.896141 kDa
SourceSpecies: Human (human)

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Component #4: protein, Ribonuclease P protein subunit p38

ProteinName: Ribonuclease P protein subunit p38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.891443 kDa
SourceSpecies: Human (human)

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Component #5: protein, Ribonuclease P protein subunit p29

ProteinName: Ribonuclease P protein subunit p29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.474854 kDa
SourceSpecies: Human (human)

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Component #6: protein, Ribonuclease P/MRP protein subunit POP5

ProteinName: Ribonuclease P/MRP protein subunit POP5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.844672 kDa
SourceSpecies: Human (human)

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Component #7: protein, Ribonuclease P protein subunit p25

ProteinName: Ribonuclease P protein subunit p25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.659406 kDa
SourceSpecies: Human (human)

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Component #8: protein, Ribonuclease P protein subunit p20

ProteinName: Ribonuclease P protein subunit p20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.672866 kDa
SourceSpecies: Human (human)

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Component #9: protein, Ribonuclease P protein subunit p14

ProteinName: Ribonuclease P protein subunit p14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.707014 kDa
SourceSpecies: Human (human)

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Component #10: protein, Ribonuclease P protein subunit p30

ProteinName: Ribonuclease P protein subunit p30 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.364277 kDa
SourceSpecies: Human (human)

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Component #11: protein, Ribonuclease P protein subunit p21

ProteinName: Ribonuclease P protein subunit p21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.596068 kDa
SourceSpecies: Human (human)

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Component #12: protein, Ribonuclease P protein subunit p40

ProteinName: Ribonuclease P protein subunit p40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.884844 kDa
SourceSpecies: Human (human)

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Component #13: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5625 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 400198
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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