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- PDB-4i67: Crystal structure of the RRM domain of RNA helicase HERA from T. ... -

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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 / RNA helicase activity / hydrolase activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
Alpha-Beta Plaits - #1800 / : / RNA helicase Hera, dimerization 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 / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain ...Alpha-Beta Plaits - #1800 / : / RNA helicase Hera, dimerization 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 / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 2.98 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

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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

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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'

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