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- PDB-9h45: Crystal Structure of Hfq V22A -

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Basic information

Entry
Database: PDB / ID: 9h45
TitleCrystal Structure of Hfq V22A
Components
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*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 (> 10) / RNA-binding protein Hfq
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsMcQuail, J. / Krepl, M. / Katsuya-Gaviria, K. / Tabib-Salazar, A. / Burchell, L. / Bischler, T. / Grafenhan, T. / Brear, P. / Sponer, J. / Luisi, B.
Funding support1items
OrganizationGrant numberCountry
Other government
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
DepositionOct 17, 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

Downloads & links

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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
Q: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)72,7897
Polymers72,7897
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-66 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.250, 67.150, 84.580
Angle α, β, γ (deg.)90.00, 104.64, 90.00
Int Tables number5
Space group name H-MC121

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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.: 6
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*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 5880.748 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 15 %v/v PEGSH 0.15 M NH4 Acet 0.1 M Na3 Cit

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.08→57.66 Å / Num. obs: 37712 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.968 / Rmerge(I) obs: 0.509 / Rpim(I) all: 0.209 / Rrim(I) all: 0.551 / Net I/σ(I): 3.3 / Num. measured all: 258949
Reflection shellResolution: 2.08→2.12 Å / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 2.025 / Num. measured all: 12714 / Num. unique obs: 1912 / CC1/2: 0.246 / Rpim(I) all: 0.841 / Rrim(I) all: 2.196 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→56.24 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3233 1879 4.99 %
Rwork0.274 --
obs0.2764 37680 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→56.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 396 0 282 3703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.679
X-RAY DIFFRACTIONf_dihedral_angle_d8.285653
X-RAY DIFFRACTIONf_chiral_restr0.047621
X-RAY DIFFRACTIONf_plane_restr0.007592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.140.40081580.3422742X-RAY DIFFRACTION100
2.14-2.20.32261590.32252705X-RAY DIFFRACTION99
2.2-2.270.3711440.3282737X-RAY DIFFRACTION100
2.27-2.350.37411370.31362795X-RAY DIFFRACTION100
2.35-2.450.39491550.31522754X-RAY DIFFRACTION100
2.45-2.560.37081570.3272739X-RAY DIFFRACTION100
2.56-2.690.40261490.33542778X-RAY DIFFRACTION100
2.69-2.860.35561370.2882762X-RAY DIFFRACTION100
2.86-3.080.30271390.29422790X-RAY DIFFRACTION100
3.08-3.390.30861480.24352768X-RAY DIFFRACTION100
3.39-3.880.25481330.23092797X-RAY DIFFRACTION100
3.88-4.890.24471250.19852805X-RAY DIFFRACTION100
4.89-56.240.32691380.26212629X-RAY DIFFRACTION91

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