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- PDB-5sze: Crystal structure of Aquifex aeolicus Hfq-RNA complex at 1.5A -

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Basic information

Entry
Database: PDB / ID: 5sze
TitleCrystal structure of Aquifex aeolicus Hfq-RNA complex at 1.5A
Components
  • RNA (5'-R(P*UP*UP*U)-3')
  • RNA-binding protein Hfq
KeywordsRNA-binding protein/RNA / Hfq / Aquifex / RNA-binding / RNA-binding protein-RNA complex
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
DI(HYDROXYETHYL)ETHER / RNA / RNA-binding protein Hfq
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsStanek, K. / Patterson, J. / Randolph, P.S. / Mura, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-135095 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode.
Authors: Stanek, K.A. / Patterson-West, J. / Randolph, P.S. / Mura, C.
History
DepositionAug 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,5144
Polymers11,2902
Non-polymers2242
Water64936
1
A: RNA-binding protein Hfq
C: RNA (5'-R(P*UP*UP*U)-3')
hetero molecules

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

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

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

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

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


Theoretical massNumber of molelcules
Total (without water)69,08624
Polymers67,74012
Non-polymers1,34612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
2
A: RNA-binding protein Hfq
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)58,33418
Polymers56,9886
Non-polymers1,34612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area14650 Å2
ΔGint-25 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.190, 66.190, 34.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-211-

HOH

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Components

#1: Protein RNA-binding protein Hfq


Mass: 9497.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: hfq, aq_108, aq_108B / Production host: Escherichia coli (E. coli) / References: UniProt: O66512
#2: RNA chain RNA (5'-R(P*UP*UP*U)-3')


Mass: 1792.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.92 Å3/Da / Density % sol: 35.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: sodium cacodylate, PEG 8000, MPD, guanidinium

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9195 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 1.5→34.21 Å / Num. obs: 13177 / % possible obs: 94.9 % / Redundancy: 3.5 % / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
PHENIX(1.10-2155_1309: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U1S

1u1s


Resolution: 1.5→34.21 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.86
RfactorNum. reflection% reflection
Rfree0.172 662 5.03 %
Rwork0.1441 --
obs0.1457 13171 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms590 43 15 36 684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005668
X-RAY DIFFRACTIONf_angle_d0.754904
X-RAY DIFFRACTIONf_dihedral_angle_d12.301401
X-RAY DIFFRACTIONf_chiral_restr0.05107
X-RAY DIFFRACTIONf_plane_restr0.004104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5003-1.61620.20951260.13432466X-RAY DIFFRACTION94
1.6162-1.77880.19711410.12192460X-RAY DIFFRACTION95
1.7788-2.03620.15491570.11982474X-RAY DIFFRACTION95
2.0362-2.56520.16851210.14092569X-RAY DIFFRACTION97
2.5652-34.21890.17061170.15812540X-RAY DIFFRACTION94

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