[English] 日本語
Yorodumi
- PDB-4i67: Crystal structure of the RRM domain of RNA helicase HERA from T. ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i67
TitleCrystal structure of the RRM domain of RNA helicase HERA from T. thermophilus in complex with GGGC RNA
Components
  • 5'-R(P*GP*GP*GP*(RPC))-3'
  • Heat resistant RNA dependent ATPase
KeywordsHYDROLASE/RNA / unwinding / ATPase / heat resistant / RNA recognition motif / RNA binding / DEAD box protein / HYDROLASE-RNA complex
Function / homology
Function and homology information


nucleic acid binding / hydrolase activity / RNA helicase activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
Alpha-Beta Plaits - #1800 / : / : / RNA helicase Hera, dimerization domain / DEAD box helicase Hera, RNA-binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. ...Alpha-Beta Plaits - #1800 / : / : / RNA helicase Hera, dimerization domain / DEAD box helicase Hera, RNA-binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Heat resistant RNA dependent ATPase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsRudolph, M.G. / Klostermeier, D.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera.
Authors: Steimer, L. / Wurm, J.P. / Linden, M.H. / Rudolph, M.G. / Wohnert, J. / Klostermeier, D.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Nov 26, 2014Group: Structure summary
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat resistant RNA dependent ATPase
B: 5'-R(P*GP*GP*GP*(RPC))-3'


Theoretical massNumber of molelcules
Total (without water)10,9542
Polymers10,9542
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.435, 88.435, 28.943
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Heat resistant RNA dependent ATPase / HERA RNA helicase


Mass: 9578.012 Da / Num. of mol.: 1 / Fragment: RRM domain (UNP residues 431-517)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT_C1895 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72GF3, RNA helicase
#2: RNA chain 5'-R(P*GP*GP*GP*(RPC))-3'


Mass: 1375.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 23S ribosomal RNA fragment
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.06 M sodium malonate, pH 6.0, 0.1 M Tris-HCl, pH 7.5, 0.13 M potassium/sodium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
PH range: 6-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.999971
211
ReflectionResolution: 2.33→44.2 Å / Num. obs: 5963 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.76 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 19.1
Reflection shellResolution: 2.33→2.43 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.868 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDS(VERSION March 15data reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I31

3i31


Resolution: 2.33→38.293 Å / SU ML: 0.34 / σ(F): 1.38 / Phase error: 32.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 260 4.54 %RANDOM
Rwork0.1769 ---
obs0.1794 5726 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.33→38.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms585 94 0 11 690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007698
X-RAY DIFFRACTIONf_angle_d1.064964
X-RAY DIFFRACTIONf_dihedral_angle_d16.066280
X-RAY DIFFRACTIONf_chiral_restr0.062109
X-RAY DIFFRACTIONf_plane_restr0.005110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.93580.37571170.2722702X-RAY DIFFRACTION100
2.9358-38.29860.21361430.1622764X-RAY DIFFRACTION100
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)
19.19490.8722.34579.4716-3.49249.25530.0381-0.50410.16040.0715-0.09330.23530.3014-0.60830.01720.60420.03460.06330.5124-0.07630.460839.368-9.2319-5.4987
23.4657-2.8465-3.69483.04111.07399.4296-0.84671.176-1.025-1.0647-0.5748-0.13181.41050.18631.09481.45340.26670.11080.9635-0.00170.943645.2416-14.5341-15.3797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

+
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