[English] 日本語
Yorodumi
- PDB-3iab: Crystal structure of RNase P /RNase MRP proteins Pop6, Pop7 in a ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iab
TitleCrystal structure of RNase P /RNase MRP proteins Pop6, Pop7 in a complex with the P3 domain of RNase MRP RNA
Components
  • P3 domain of the RNA component of RNase MRP
  • Ribonucleases P/MRP protein subunit POP6
  • Ribonucleases P/MRP protein subunit POP7
KeywordsHYDROLASE/RNA / RNase P / RNase MRP / Ribonuclease P / Ribonuclease MRP / Pop6 / Pop6p / Pop7 / Pop7p / P3 / NME1 / yeast / tRNA / pre-tRNA / rRNA / Ribozyme / PROTEIN-RNA COMPLEX / ALBA / heterodimer / Coiled coil / Hydrolase / Nucleus / rRNA processing / tRNA processing / Phosphoprotein / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P / ribonuclease P activity / rRNA primary transcript binding / tRNA 5'-leader removal / telomerase holoenzyme complex / tRNA processing ...nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P / ribonuclease P activity / rRNA primary transcript binding / tRNA 5'-leader removal / telomerase holoenzyme complex / tRNA processing / maturation of 5.8S rRNA / rRNA processing / RNA binding / nucleus / cytosol
Similarity search - Function
Ribonuclease P/MRP subunit Pop7, fungi / Ribonucleases P/MRP protein subunit Rpp20/Pop7 / Rpp20 subunit of nuclear RNase MRP and P / Alba-like domain / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Ribonucleases P/MRP protein subunit POP7 / Ribonucleases P/MRP protein subunit POP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsPerederina, A. / Esakova, O.A. / Quan, C. / Khanova, E. / Krasilnikov, A.S.
CitationJournal: Embo J. / Year: 2010
Title: Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain
Authors: Perederina, A. / Esakova, O. / Quan, C. / Khanova, E. / Krasilnikov, A.S.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonucleases P/MRP protein subunit POP6
B: Ribonucleases P/MRP protein subunit POP7
R: P3 domain of the RNA component of RNase MRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4516
Polymers49,2543
Non-polymers1963
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-107 kcal/mol
Surface area19030 Å2
MethodPISA
2
A: Ribonucleases P/MRP protein subunit POP6
B: Ribonucleases P/MRP protein subunit POP7
R: P3 domain of the RNA component of RNase MRP
hetero molecules

A: Ribonucleases P/MRP protein subunit POP6
B: Ribonucleases P/MRP protein subunit POP7
R: P3 domain of the RNA component of RNase MRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,90112
Polymers98,5096
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+3/21
Buried area17150 Å2
ΔGint-283 kcal/mol
Surface area35380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.514, 126.514, 76.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11B-141-

ZN

-
Components

#1: Protein Ribonucleases P/MRP protein subunit POP6 / RNA-processing protein POP6 / RNases P/MRP 18.2 kDa subunit


Mass: 18440.576 Da / Num. of mol.: 1 / Fragment: Pop6 / Mutation: L141M
Source method: isolated from a genetically manipulated source
Details: Co-expression with Pop7
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POP6, YGR030C / Plasmid: 762 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P53218, ribonuclease P
#2: Protein Ribonucleases P/MRP protein subunit POP7 / RNA-processing protein POP7 / RNases P/MRP 15.8 kDa subunit


Mass: 15984.972 Da / Num. of mol.: 1 / Fragment: Pop7 / Mutation: none
Source method: isolated from a genetically manipulated source
Details: Co-expression with Pop6
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POP7, RPP2, YBR1219, YBR167C / Plasmid: 762 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P38291, ribonuclease P
#3: RNA chain P3 domain of the RNA component of RNase MRP


Mass: 14828.875 Da / Num. of mol.: 1 / Fragment: P3 domain
Mutation: circular permutation; A49C, A50C, U59G, U60G (yeast sequence numbering). See important note regarging nucleotide numbering in the model.
Source method: obtained synthetically
Details: In vitro transcription; circular permutation of naturally occurring sequence.
References: ribonuclease P
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE MODEL INCLUDES NUCLEOTIDES 29-50 AND 59-79 OF THE ORIGINAL YEAST P3 DOMAIN. THE CRYSTALLIZED ...THE MODEL INCLUDES NUCLEOTIDES 29-50 AND 59-79 OF THE ORIGINAL YEAST P3 DOMAIN. THE CRYSTALLIZED CONSTRUCT CONTAINS A GAAA LINKER CONNECTING G78 AND C29 (YEAST NUMBERING). IN THE MODEL, THE NUMBERING OF NUCLEOTIDES 59 TO 78 MATCHES THAT IN YEAST; THE MODEL NUCLEOTIDES 79-82 ARE THE LINKER; THE NUMBERING OF NUCLEOTIDES 83-104 IS SHIFTED RELATIVE TO THAT IN YEAST BY 54 (YEAST NUCLEOTIDE 29 IS CALLED 83 IN THE MODEL, ETC).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 2M Ammonium Sulfate, 200 mM Potassium Chloride, 2% PEG 400, 5% D-trehalose, 2 mM Zinc Chloride, 5 mM Magnesium Chloride, 100 mM HEPES-Na, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 17601 / Num. obs: 16350 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 82.1 Å2 / Rmerge(I) obs: 0.057
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2 / Num. unique all: 934 / % possible all: 93.3

-
Processing

Software
NameClassification
HKL-2000data collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: none

Resolution: 2.7→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residues 1-3, 122-128 in Pop6 (chain A) and residues 1-13, 105-124 in Pop7 (chain B) are disordered
RfactorNum. reflection% reflectionSelection details
Rfree0.265 821 -RANDOM
Rwork0.25 ---
all0.25 17659 --
obs0.25 16346 92.6 %-
Displacement parametersBiso mean: 89.9 Å2
Baniso -1Baniso -2Baniso -3
1--10.219 Å20 Å20 Å2
2---10.219 Å20 Å2
3---20.437 Å2
Refine analyzeLuzzati coordinate error obs: 0.68 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 985 3 50 3087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.054
X-RAY DIFFRACTIONc_angle_deg1.14
LS refinement shellResolution: 2.7→2.774 Å
RfactorNum. reflection% reflection
Rfree0.333 44 -
Rwork0.355 --
obs-970 92.7 %

+
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://pdbjlc1.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