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- PDB-5new: RNA-RNA base stacking in the crystal structure of an Hfq6:RNA dimer -

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Basic information

Entry
Database: PDB / ID: 5new
TitleRNA-RNA base stacking in the crystal structure of an Hfq6:RNA dimer
Components
  • RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*UP*U)-3')
  • RNA-binding protein Hfq
KeywordsRNA / Hfq sRNA RNA-RNA interaction base stacking
Function / homology
Function and homology information


regulation of translation, ncRNA-mediated / regulation of RNA stability / regulation of DNA-templated transcription / RNA binding / cytosol
Similarity search - Function
RNA-binding protein Hfq / Hfq protein / SH3 type barrels. - #100 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA / RNA-binding protein Hfq
Similarity search - Component
Biological speciesEscherichia coli S88 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.511 Å
AuthorsSchulz, E.C. / Barabas, O.
CitationJournal: Sci Rep / Year: 2017
Title: Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq.
Authors: Schulz, E.C. / Seiler, M. / Zuliani, C. / Voigt, F. / Rybin, V. / Pogenberg, V. / Mucke, N. / Wilmanns, M. / Gibson, T.J. / Barabas, O.
History
DepositionMar 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: RNA-binding protein Hfq
B: RNA-binding protein Hfq
H: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3379
Polymers24,8564
Non-polymers4805
Water79344
1
A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
H: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*U)-3')
hetero molecules

A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
H: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*U)-3')
hetero molecules

A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
H: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,01027
Polymers74,56912
Non-polymers1,44115
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area20800 Å2
ΔGint-293 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.880, 66.880, 227.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein RNA-binding protein Hfq


Mass: 11179.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli S88 (bacteria) / Gene: hfq, ECS88_4758 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7MKX6
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')


Mass: 1930.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: RNA chain RNA (5'-R(P*UP*U)-3')


Mass: 567.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M phosphate-citrate buffer pH 4.2, 27% PEG 1000, and 0.2 M LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979681 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979681 Å / Relative weight: 1
ReflectionResolution: 2.51→40.6 Å / Num. obs: 6816 / % possible obs: 96.8 % / Redundancy: 4.6 % / Net I/σ(I): 15.03

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.511→40.6 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.65
RfactorNum. reflection% reflection
Rfree0.2522 341 5 %
Rwork0.1964 --
obs0.1993 6816 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 44.329 Å2 / ksol: 0.392 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.6352 Å20 Å20 Å2
2---10.6352 Å20 Å2
3---21.2704 Å2
Refinement stepCycle: LAST / Resolution: 2.511→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 172 25 44 1261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091252
X-RAY DIFFRACTIONf_angle_d1.0951733
X-RAY DIFFRACTIONf_dihedral_angle_d14.53483
X-RAY DIFFRACTIONf_chiral_restr0.067210
X-RAY DIFFRACTIONf_plane_restr0.006187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5105-3.16280.2921630.22333088X-RAY DIFFRACTION94
3.1628-40.60630.23631780.18633387X-RAY DIFFRACTION99

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