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- PDB-5e02: Structure of RNA Helicase FRH a Critical Component of the Neurosp... -

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Basic information

Entry
Database: PDB / ID: 500
TitleStructure of RNA Helicase FRH a Critical Component of the Neurospora Crassa Circadian Clock
Components
  • FRQ-interacting RNA helicase
  • RNA (5'-R(*AP*AP*AP*A)-3')
KeywordsHydrolase / RNA BINDING PROTEIN/RNA / circadian clock / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


RNA catabolic process / maturation of 5.8S rRNA / RNA helicase activity / hydrolase activity / RNA binding / ATP binding / nucleus
Similarity search - Function
rRNA-processing arch domain / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain ...rRNA-processing arch domain / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RNA / FRQ-interacting RNA helicase / FRQ-interacting RNA helicase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsConrad, K.S. / Crane, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5F32GM099391-02 United States
CitationJournal: Embo J. / Year: 2016
Title: Structure of the frequency-interacting RNA helicase: a protein interaction hub for the circadian clock.
Authors: Conrad, K.S. / Hurley, J.M. / Widom, J. / Ringelberg, C.S. / Loros, J.J. / Dunlap, J.C. / Crane, B.R.
History
DepositionSep 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRQ-interacting RNA helicase
C: RNA (5'-R(*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,3363
Polymers125,9092
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-10 kcal/mol
Surface area49520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.432, 106.600, 125.298
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FRQ-interacting RNA helicase / Probable ATP dependent RNA helicase


Mass: 124637.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: B9B11.040, frh, NCU03363.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q873J5, UniProt: Q1K502*PLUS
#2: RNA chain RNA (5'-R(*AP*AP*AP*A)-3')


Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: sodium citrate, PEG600 / PH range: 5.5-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.8→106.6 Å / Num. obs: 9816 / % possible obs: 93.7 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.094 / Net I/σ(I): 7.8 / Num. measured all: 32399
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.8-4.013.31.4161.2466714020.5520.88494.1
12.02-106.62.80.0329.98903190.9990.0282.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XGT

4xgt


Resolution: 3.8→81.192 Å / SU ML: 0.63 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 37.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3206 966 9.99 %
Rwork0.2775 8701 -
obs0.2819 9667 91.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 394.36 Å2 / Biso mean: 145.5236 Å2 / Biso min: 83.78 Å2
Refinement stepCycle: final / Resolution: 3.8→81.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7688 85 27 0 7800
Biso mean--184.59 --
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037960
X-RAY DIFFRACTIONf_angle_d0.8910775
X-RAY DIFFRACTIONf_chiral_restr0.0341205
X-RAY DIFFRACTIONf_plane_restr0.0041381
X-RAY DIFFRACTIONf_dihedral_angle_d13.9053052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8003-4.00070.40841310.36961185131690
4.0007-4.25130.35591300.33491169129988
4.2513-4.57960.31091440.30311282142696
4.5796-5.04040.30541400.26881273141394
5.0404-5.76950.38521360.30651232136892
5.7695-7.26830.40291440.30881290143494
7.2683-81.21030.25461410.22231270141188

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