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- PDB-6ahu: Cryo-EM structure of human Ribonuclease P with mature tRNA -

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Basic information

Entry
Database: PDB / ID: 6ahu
TitleCryo-EM structure of human Ribonuclease P with mature tRNA
Components
  • (Ribonuclease P protein subunit ...) x 8
  • H1 RNA
  • Ribonuclease P/MRP protein subunit POP5
  • Ribonucleases P/MRP protein subunit POP1
  • tRNATransfer RNA
KeywordsHYDROLASE/RNA / Ribonuclease P / RNA-protein complex / HYDROLASE-RNA complex
Function / homologyPolymerase/histidinol phosphatase-like / 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 ...Polymerase/histidinol phosphatase-like / 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 / Ribonucleases P/MRP protein subunit Rpp20 / 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 / gb:31969: / gb:3217024:
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.66 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

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Assembly

Deposited unit
A: H1 RNA
B: Ribonucleases P/MRP protein subunit POP1
C: Ribonuclease P protein subunit p38
D: Ribonuclease P protein subunit p29
E: Ribonuclease P/MRP protein subunit POP5
F: Ribonuclease P protein subunit p25
G: Ribonuclease P protein subunit p20
H: Ribonuclease P protein subunit p14
I: Ribonuclease P protein subunit p30
J: Ribonuclease P protein subunit p30
K: Ribonuclease P protein subunit p21
L: Ribonuclease P protein subunit p40
T: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,83414
Polyers492,76913
Non-polymers651
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)65880
ΔGint (kcal/M)-428
Surface area (Å2)173340

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Components

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RNA chain , 2 types, 2 molecules AT

#1: RNA chain H1 RNA


Mass: 110244.172 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Details: cell / References: GenBank: 31969
#12: RNA chain tRNA / Transfer RNA


Mass: 23168.760 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Details: in vitro transcription / Plasmid name: pGlms / Production host: Homo sapiens (human) / References: GenBank: 3217024

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Protein/peptide , 2 types, 2 molecules BE

#2: Protein/peptide Ribonucleases P/MRP protein subunit POP1 / hPOP1


Mass: 114896.141 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Details: cell / References: UniProt: Q99575, ribonuclease P
#5: Protein/peptide Ribonuclease P/MRP protein subunit POP5 / hPop5


Mass: 18844.672 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Details: cell / References: UniProt: Q969H6, ribonuclease P

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Ribonuclease P protein subunit ... , 8 types, 9 molecules CDFGHIJKL

#3: Protein/peptide Ribonuclease P protein subunit p38 / / RNaseP protein p38


Mass: 31891.443 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Details: cell / References: UniProt: P78345, ribonuclease P
#4: Protein/peptide Ribonuclease P protein subunit p29 / / hPOP4


Mass: 25474.854 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Details: cell / References: UniProt: O95707, ribonuclease P
#6: Protein/peptide Ribonuclease P protein subunit p25 / / RNase P protein subunit p25


Mass: 20659.406 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Details: cell / References: UniProt: Q9BUL9, ribonuclease P
#7: Protein/peptide Ribonuclease P protein subunit p20 / / RNaseP protein p20 / Ribonucleases P/MRP protein subunit POP7 homolog / hPOP7


Mass: 15672.866 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Details: cell / References: UniProt: O75817, ribonuclease P
#8: Protein/peptide Ribonuclease P protein subunit p14 /


Mass: 13707.014 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Details: cell / References: UniProt: O95059, ribonuclease P
#9: Protein/peptide Ribonuclease P protein subunit p30 / / RNaseP protein p30 / RNase P subunit 2


Mass: 29364.277 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / Details: cell / References: UniProt: P78346, ribonuclease P
#10: Protein/peptide Ribonuclease P protein subunit p21 / / RNaseP protein p21 / Ribonuclease P/MRP 21 kDa subunit / Ribonucleoprotein V


Mass: 17596.068 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Details: cell / References: UniProt: Q9H633, ribonuclease P
#11: Protein/peptide Ribonuclease P protein subunit p40 / / RNaseP protein p40 / RNase P subunit 1


Mass: 41884.844 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Details: cell / References: UniProt: O75818, ribonuclease P

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Non-polymers , 1 types, 1 molecules

#13: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1RNase P with tRNACOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 120MULTIPLE SOURCES
2RNase PCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 111NATURAL
3RNACOMPLEX121RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens (human)
239606Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: pGlms
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.5625 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 287700 / Symmetry type: POINT

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