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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
  • tRNA
KeywordsHYDROLASE/RNA / Ribonuclease P / RNA-protein complex / 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 complex / tRNA decay / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing in the nucleus / tRNA processing ...multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / tRNA decay / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing in the nucleus / tRNA processing / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / centriolar satellite / fibrillar center / rRNA processing / response to xenobiotic stimulus / intracellular membrane-bounded organelle / nucleolus / extracellular space / RNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Ribonuclease P protein subunit Rpp38 / Ribonuclease P protein subunit Rpp40 / Ribonuclease P 40kDa (Rpp40) subunit / Ribonuclease P, Pop5 subunit / : / Pop1, N-terminal / POPLD domain / Ribonuclease P/MRP protein subunit Pop5 / Ribonucleases P/MRP protein subunit Pop1 / : ...Ribonuclease P protein subunit Rpp38 / Ribonuclease P protein subunit Rpp40 / Ribonuclease P 40kDa (Rpp40) subunit / Ribonuclease P, Pop5 subunit / : / Pop1, N-terminal / POPLD domain / Ribonuclease P/MRP protein subunit Pop5 / Ribonucleases P/MRP protein subunit Pop1 / : / Ribonucleases P/MRP protein subunit POP1, N-terminal / POPLD (NUC188) domain / POP1 C-terminal domain / Ribonucleases P/MRP protein subunit Rpp20/Pop7 / Rpp20 subunit of nuclear RNase MRP and P / RNase P subunit Pop5/Rpp14/Rnp2-like / RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily / Rpp14/Pop5 family / RNase P subunit p30 / Ribonuclease P subunit, Rpr2/Snm1/Rpp21 / Ribonuclease P/MRP subunit Rpp29 / RNase P subunit p30 / RNAse P Rpr2/Rpp21/SNM1 subunit domain / Ribonuclease P protein subunit Rpp29/RNP1 / Ribonuclease P/MRP subunit Rpp29 superfamily / Ribonuclease P/MRP, subunit p29 / A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins. / Rof/RNase P-like / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / 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 ...: / : / RNA / RNA (> 10) / RNA (> 100) / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
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.
History
DepositionAug 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Polymers492,76913
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area65880 Å2
ΔGint-428 kcal/mol
Surface area173340 Å2

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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 method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: GenBank: 31969
#12: RNA chain tRNA


Mass: 23168.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: in vitro transcription / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGlms / Production host: Homo sapiens (human) / References: GenBank: 3217024

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Protein , 2 types, 2 molecules BE

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


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


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

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

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


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


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


Mass: 20659.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BUL9, ribonuclease P
#7: Protein 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 method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: O75817, ribonuclease P
#8: Protein Ribonuclease P protein subunit p14


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


Mass: 29364.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P78346, ribonuclease P
#10: Protein 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 method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H633, ribonuclease P
#11: Protein Ribonuclease P protein subunit p40 / RNaseP protein p40 / RNase P subunit 1


Mass: 41884.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / 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 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1RNase P with tRNACOMPLEX#1-#120MULTIPLE SOURCES
2RNase PCOMPLEX#1-#111NATURAL
3RNACOMPLEX#121RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
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 / Num. of particles: 287700 / Symmetry type: POINT

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