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

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 6ahv
TitleCrystal structure of human RPP40
ComponentsRibonuclease P protein subunit p40
KeywordsHYDROLASE / RNase P
Function / homologyRibonuclease P, Rpp40 / Ribonuclease P 40kDa (Rpp40) subunit / tRNA processing in the nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / nucleolar ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA processing / nucleoplasm / nucleus / Ribonuclease P protein subunit p40
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 2.6 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

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: Ribonuclease P protein subunit p40

Theoretical massNumber of molelcules
Total (without water)41,8851

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)17490
A: Ribonuclease P protein subunit p40

A: Ribonuclease P protein subunit p40

Theoretical massNumber of molelcules
Total (without water)83,7702
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area (Å2)3350
ΔGint (kcal/M)-11
Surface area (Å2)31640
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-MC 2 2 21


#1: Protein/peptide Ribonuclease P protein subunit p40 / / RNaseP protein p40 / RNase P subunit 1

Mass: 41884.844 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: RPP40, RNASEP1 / Plasmid name: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75818, ribonuclease P
#2: Water ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 26 / Formula: H2O / Water

Experimental details


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

Sample preparation

CrystalDensity Matthews: 3.32 / Density percent sol: 63 % / Mosaicity: 0.39 deg.
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Type: SSRF BEAMLINE BL18U1 / Synchrotron site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Collection date: Dec 31, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 40.72 Å2 / D resolution high: 2.6 Å / D resolution low: 5 Å / Number obs: 17458 / Rmerge I obs: 0.093 / Rpim I all: 0.045 / Rrim I all: 0.103 / Chi squared: 0.88 / NetI over sigmaI: 7 / Number measured all: 95185 / Redundancy: 5.5 % / Percent possible obs: 99.5
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber unique obsCC halfRpim I allRrim I allChi squaredRedundancyPercent possible all


HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data collection
RefineMethod to determine structure: SAD / Overall SU ML: 0.41 / Cross valid method: THROUGHOUT / Sigma F: 1.36 / Overall phase error: 27.39 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 160.1 Å2 / B iso mean: 49.6534 Å2 / B iso min: 14.6 Å2
Least-squares processR factor R free: 0.2531 / R factor R work: 0.2179 / R factor obs: 0.2198 / Highest resolution: 2.6 Å / Lowest resolution: 43.434 Å / Number reflection R free: 877 / Number reflection R work: 16156 / Number reflection obs: 17033 / Percent reflection R free: 5.15 / Percent reflection obs: 97.05
Refine hist #finalHighest resolution: 2.6 Å / Lowest resolution: 43.434 Å / B iso mean solvent: 38.93 / Number residues total: 345
Number of atoms included #finalProtein: 2806 / Nucleic acid: 0 / Ligand: 0 / Solvent: 26 / Total: 2832
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_d13.3801055
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 6

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
Refine TLS group

Beg auth asym ID: A / End auth asym ID: A / Refine ID: X-RAY DIFFRACTION

IDBeg auth seq IDEnd auth seq IDRefine TLS IDSelection details
1123561( CHAIN A AND RESID 12:356 )
24014262( CHAIN A AND RESID 401:426 )

About Yorodumi


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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more


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.

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