[English] 日本語
Yorodumi
- PDB-6ahv: Crystal structure of human RPP40 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ahv
TitleCrystal structure of human RPP40
ComponentsRibonuclease P protein subunit p40
KeywordsHYDROLASE / RNase P
Function / homology
Function and homology information


multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing in the nucleus / 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) / nucleoplasm / nucleus
Similarity search - Function
Ribonuclease P protein subunit Rpp40 / Ribonuclease P 40kDa (Rpp40) subunit
Similarity search - Domain/homology
Ribonuclease P protein subunit p40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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 1.1Mar 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonuclease P protein subunit p40


Theoretical massNumber of molelcules
Total (without water)41,8851
Polymers41,8851
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17490 Å2
2
A: Ribonuclease P protein subunit p40

A: Ribonuclease P protein subunit p40


Theoretical massNumber of molelcules
Total (without water)83,7702
Polymers83,7702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3350 Å2
ΔGint-11 kcal/mol
Surface area31640 Å2
MethodPISA
Unit cell
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-MC2221
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-412-

HOH

-
Components

#1: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPP40, RNASEP1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75818, ribonuclease P
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 63 % / Mosaicity: 0.39 °
Crystal growTemperature: 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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Date: Dec 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 17458 / % possible obs: 99.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 40.72 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.045 / Rrim(I) all: 0.103 / Χ2: 0.88 / Net I/σ(I): 7 / Num. measured all: 95185
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.695.60.69617100.7450.3230.770.67499.9
2.69-2.85.70.51317230.8440.2380.5680.70499.8
2.8-2.935.60.417300.8710.1860.4430.80899.9
2.93-3.085.30.27617330.9280.1310.3070.927100
3.08-3.285.30.19517300.9570.0940.2171.0199.7
3.28-3.535.60.14817390.9610.0720.1661.15799.8
3.53-3.885.50.11617450.9770.0560.131.17199.8
3.88-4.455.20.08617600.9840.0430.0961.0499.5
4.45-5.65.50.0717550.9910.0340.0790.80798.9
5.6-505.10.04618330.9960.0230.0520.50498

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-2000data collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→43.434 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2531 877 5.15 %
Rwork0.2179 16156 -
obs0.2198 17033 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.1 Å2 / Biso mean: 49.6534 Å2 / Biso min: 14.6 Å2
Refinement stepCycle: final / Resolution: 2.6→43.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 0 26 2832
Biso mean---38.93 -
Num. residues----345
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_d13.381055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.76290.33831470.29522365251287
2.7629-2.97620.36861290.27772709283899
2.9762-3.27560.28981370.259327452882100
3.2756-3.74930.2591570.220727422899100
3.7493-4.72280.24841450.18392768291399
4.7228-43.43970.18751620.18992827298998
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1948-0.1163-0.07040.2956-0.11230.168-0.0835-0.16990.05130.23610.17710.0832-0.0457-0.01220.21150.23760.02560.11780.22810.21640.19938.98820.14812.043
20.07680.06150.00060.0507-0.00240.0145-0.02070.00790.02920.0062-0.01730.00630.0021-0.005-0.01060.12920.01460.03480.17310.07070.134214.93522.1929.274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 12:356 )A12 - 356
2X-RAY DIFFRACTION2( CHAIN A AND RESID 401:426 )A401 - 426

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more