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- PDB-9uh7: large lobe of human Ribonuclease MRP -

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Basic information

Entry
Database: PDB / ID: 9uh7
Titlelarge lobe of human Ribonuclease MRP
Components
  • (Ribonuclease P protein subunit ...) x 6
  • Nucleolus and neural progenitor protein
  • RNA (270-MER)
  • Ribonuclease P/MRP protein subunit POP5
  • Ribonucleases P/MRP protein subunit POP1
  • UPF0711 protein C18orf21
KeywordsRNA BINDING PROTEIN/RNA / RNase MRP / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease P RNA binding / ribonuclease MRP complex / ribonuclease P complex / tRNA decay / ribonuclease P activity / tRNA processing in the nucleus / tRNA 5'-leader removal / tRNA processing ...multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease P RNA binding / ribonuclease MRP complex / ribonuclease P complex / tRNA decay / ribonuclease P activity / tRNA processing in the nucleus / tRNA 5'-leader removal / tRNA processing / negative regulation of neuron differentiation / positive regulation of Notch signaling pathway / RNA 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 / rRNA processing / nucleolus / : / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nucleolus and neural progenitor protein-like, N-terminal domain / Protein of unknown function DUF4674 / : / Nucleolus and neural progenitor protein, N-terminal / Ribonuclease MRP subunit P24-like / Ribonuclease P protein subunit Rpp40 / Ribonuclease P 40kDa (Rpp40) subunit / : / Ribonuclease P/MRP protein subunit Pop5 / Pop1, N-terminal ...Nucleolus and neural progenitor protein-like, N-terminal domain / Protein of unknown function DUF4674 / : / Nucleolus and neural progenitor protein, N-terminal / Ribonuclease MRP subunit P24-like / Ribonuclease P protein subunit Rpp40 / Ribonuclease P 40kDa (Rpp40) subunit / : / Ribonuclease P/MRP protein subunit Pop5 / Pop1, N-terminal / POPLD domain / 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/MRP subunit Rpp29 / RNase P subunit p30 / 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
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 p30 / Ribonuclease MRP protein subunit p24 / Ribonuclease MRP subunit P64 ...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 p30 / Ribonuclease MRP protein subunit p24 / Ribonuclease MRP subunit P64 / Ribonuclease P/MRP protein subunit POP5 / Ribonucleases P/MRP protein subunit POP1 / Ribonuclease P protein subunit p25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsZhou, B. / Lan, P. / Wu, J. / Lei, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural insights into the evolution of RNase P and RNase MRP ribonucleoprotein complexes
Authors: Zhou, B. / Lan, P. / Wu, J. / Lei, M.
History
DepositionApr 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (270-MER)
B: Ribonucleases P/MRP protein subunit POP1
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: UPF0711 protein C18orf21
L: Ribonuclease P protein subunit p40
M: Nucleolus and neural progenitor protein


Theoretical massNumber of molelcules
Total (without water)485,97712
Polymers485,97712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (270-MER)


Mass: 86578.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Protein , 4 types, 4 molecules BEKM

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


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


Mass: 18844.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q969H6
#9: Protein UPF0711 protein C18orf21 / HBV X-transactivated gene 13 protein / HBV XAg-transactivated protein 13


Mass: 24876.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q32NC0
#11: Protein Nucleolus and neural progenitor protein


Mass: 64653.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6NW34

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Ribonuclease P protein subunit ... , 6 types, 7 molecules DFGHIJL

#3: Protein Ribonuclease P protein subunit p29 / hPOP4


Mass: 25474.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95707
#5: 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 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BUL9
#6: 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 / Source: (natural) Homo sapiens (human) / References: UniProt: O75817
#7: Protein Ribonuclease P protein subunit p14


Mass: 13707.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95059
#8: 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 / Source: (natural) Homo sapiens (human) / References: UniProt: P78346
#10: 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 / Source: (natural) Homo sapiens (human) / References: UniProt: O75818

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Details

Has protein modificationN

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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

ComponentName: hsMRP / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.2_5419model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 777423 / Symmetry type: POINT
RefinementHighest resolution: 2.84 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325188
ELECTRON MICROSCOPYf_angle_d0.65535064
ELECTRON MICROSCOPYf_dihedral_angle_d17.5195813
ELECTRON MICROSCOPYf_chiral_restr0.0394160
ELECTRON MICROSCOPYf_plane_restr0.0043692

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