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- PDB-9gu5: Crystal Structure of Hfq V22A -

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Basic information

Entry
Database: PDB / ID: 9gu5
TitleCrystal Structure of Hfq V22A
Components
  • RNA (5'-R(P*AP*AP*AP*A)-3')
  • RNA-binding protein Hfq
KeywordsHYDROLASE / RNA-chaperone
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / bacterial nucleoid / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / RNA folding chaperone / tRNA processing / tRNA binding / regulation of DNA-templated transcription ...sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / bacterial nucleoid / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / RNA folding chaperone / tRNA processing / tRNA binding / regulation of DNA-templated transcription / DNA binding / RNA binding / ATP binding / cytosol
Similarity search - Function
RNA-binding protein Hfq / Hfq protein / : / Sm domain profile. / LSM domain superfamily
Similarity search - Domain/homology
RNA / RNA-binding protein Hfq
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
RNA interference vector pBSK-Gus (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMcQuail, J. / Krepl, M. / Katsuya-Gaviria, K. / Tabib-Salazar, A. / Burchell, L. / Bischler, T. / Grafenhan, T. / Brear, P. / Luisi, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Transcriptome-scale analysis uncovers conserved residues in the hydrophobic core of the bacterial RNA chaperone Hfq required for small regulatory RNA stability.
Authors: McQuail, J. / Krepl, M. / Katsuya-Gaviria, K. / Tabib-Salazar, A. / Burchell, L. / Bischler, T. / Grafenhan, T. / Brear, P. / Sponer, J. / Luisi, B.F. / Wigneshweraraj, S.
History
DepositionSep 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq
D: RNA-binding protein Hfq
E: RNA-binding protein Hfq
F: RNA-binding protein Hfq
G: RNA-binding protein Hfq
H: RNA-binding protein Hfq
I: RNA-binding protein Hfq
J: RNA-binding protein Hfq
K: RNA-binding protein Hfq
L: RNA-binding protein Hfq
M: RNA (5'-R(P*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,11214
Polymers135,08713
Non-polymers241
Water66737
1
A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq
D: RNA-binding protein Hfq
E: RNA-binding protein Hfq
F: RNA-binding protein Hfq
M: RNA (5'-R(P*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)68,1807
Polymers68,1807
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: RNA-binding protein Hfq
H: RNA-binding protein Hfq
I: RNA-binding protein Hfq
J: RNA-binding protein Hfq
K: RNA-binding protein Hfq
L: RNA-binding protein Hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9327
Polymers66,9086
Non-polymers241
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.182, 69.212, 73.193
Angle α, β, γ (deg.)63.54, 89.30, 60.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
RNA-binding protein Hfq / HF-1 / Host factor-I protein / HF-I


Mass: 11151.301 Da / Num. of mol.: 12 / Mutation: V22A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hfq, b4172, JW4130 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A6X3
#2: RNA chain RNA (5'-R(P*AP*AP*AP*A)-3')


Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) RNA interference vector pBSK-Gus (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22.5 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acet, 0.1 M BIS-TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9737 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 2.64→63.07 Å / Num. obs: 29610 / % possible obs: 98.8 % / Redundancy: 3.6 % / CC1/2: 0.759 / Rmerge(I) obs: 0.231 / Net I/σ(I): 6
Reflection shellResolution: 2.64→2.68 Å / Rmerge(I) obs: 2.319 / Num. unique obs: 1471 / CC1/2: 0.336 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→57.69 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 44.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3871 2043 4.63 %
Rwork0.2737 --
obs0.2785 22210 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→57.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6130 88 1 37 6256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02
X-RAY DIFFRACTIONf_angle_d1.979
X-RAY DIFFRACTIONf_dihedral_angle_d9.622882
X-RAY DIFFRACTIONf_chiral_restr0.0811037
X-RAY DIFFRACTIONf_plane_restr0.0191080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.43681260.40642719X-RAY DIFFRACTION97
2.97-3.040.45921890.41112791X-RAY DIFFRACTION98
3.04-3.120.43641750.35112745X-RAY DIFFRACTION98
3.12-3.220.45961560.33112742X-RAY DIFFRACTION98
3.22-3.320.38811840.31872840X-RAY DIFFRACTION98
3.32-3.440.44831140.3152809X-RAY DIFFRACTION98
3.44-3.580.38021380.30232768X-RAY DIFFRACTION99
3.58-3.740.40031360.27142845X-RAY DIFFRACTION99
3.74-3.940.42711400.27242766X-RAY DIFFRACTION99
3.94-4.180.4288920.27682869X-RAY DIFFRACTION98
4.18-4.50.38951280.21512789X-RAY DIFFRACTION98
4.51-4.960.34451060.2042944X-RAY DIFFRACTION99
4.96-5.670.3397840.25432846X-RAY DIFFRACTION99
5.68-7.140.30471450.27812786X-RAY DIFFRACTION99
7.15-57.690.35111300.24452837X-RAY DIFFRACTION98

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