[English] 日本語
Yorodumi
- PDB-1yyw: Crystal structure of RNase III from Aquifex aeolicus complexed wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yyw
TitleCrystal structure of RNase III from Aquifex aeolicus complexed with double stranded RNA at 2.8-Angstrom Resolution
Components
  • 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
  • Ribonuclease III
KeywordsHYDROLASE/RNA / Ribonuclease III / double-stranded RNA / RNA interference / endonucleolytic cleavage / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


ribonuclease III / ribonuclease III activity / tRNA processing / RNA processing / mRNA processing / rRNA processing / double-stranded RNA binding / regulation of gene expression / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 ...Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Ribonuclease 3
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGan, J. / Tropea, J.E. / Austin, B.P. / Court, D.L. / Waugh, D.S. / Ji, X.
CitationJournal: Structure / Year: 2005
Title: Intermediate states of ribonuclease III in complex with double-stranded RNA
Authors: Gan, J. / Tropea, J.E. / Austin, B.P. / Court, D.L. / Waugh, D.S. / Ji, X.
History
DepositionFeb 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
F: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
G: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
H: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
I: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
J: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
K: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
L: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
A: Ribonuclease III
B: Ribonuclease III
C: Ribonuclease III
D: Ribonuclease III


Theoretical massNumber of molelcules
Total (without water)134,72812
Polymers134,72812
Non-polymers00
Water1,69394
1
E: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
F: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
G: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
H: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
A: Ribonuclease III
B: Ribonuclease III


Theoretical massNumber of molelcules
Total (without water)67,3646
Polymers67,3646
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
J: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
K: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
L: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
C: Ribonuclease III
D: Ribonuclease III


Theoretical massNumber of molelcules
Total (without water)67,3646
Polymers67,3646
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.428, 95.906, 166.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: RNA chain
5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'


Mass: 3767.272 Da / Num. of mol.: 8 / Source method: obtained synthetically
#2: Protein
Ribonuclease III / / RNase III


Mass: 26147.381 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rnc / Plasmid: pHPK1409 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: O67082, ribonuclease III
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.57 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, iso-propanol, tri-sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2iso-propanol11
3tri-sodium citrate11
4H2O11
5PEG400012
6iso-propanol12
7tri-sodium citrate12
8H2O12

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Dec 14, 2003 / Details: mirror
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→29.98 Å / Num. all: 31417 / Num. obs: 31417 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1526 / % possible all: 44.8

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1I4S

1i4s


Resolution: 2.8→29.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 141699.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1878 6 %RANDOM
Rwork0.243 ---
all0.246 31417 --
obs0.246 31417 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.5893 Å2 / ksol: 0.277748 e/Å3
Displacement parametersBiso mean: 62.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--4 Å20 Å2
3----3.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.42 Å
Luzzati d res low-30 Å
Luzzati sigma a0.54 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7310 1992 0 94 9396
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it3.731.5
X-RAY DIFFRACTIONc_mcangle_it6.132
X-RAY DIFFRACTIONc_scbond_it5.12
X-RAY DIFFRACTIONc_scangle_it7.432.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 205 6.5 %
Rwork0.388 2935 -
obs--55.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION5TRIS.PARAMTRIS.TOP

+
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