4J6W

Crystal structure of HFQ from Pseudomonas aeruginosa in complex with CTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Hfq binds ribonucleotides in three different RNA-binding sites.

Murina, V.Lekontseva, N.Nikulin, A.

(2013) Acta Crystallogr.,Sect.D 69: 1504-1513

  • DOI: 10.1107/S090744491301010X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Hfq protein forms a doughnut-shaped homohexamer that possesses RNA-binding activity. There are two distinct RNA-binding surfaces located on the proximal and the distal sides of the hexamer. The proximal side is involved in the binding of mRNA and ...

    The Hfq protein forms a doughnut-shaped homohexamer that possesses RNA-binding activity. There are two distinct RNA-binding surfaces located on the proximal and the distal sides of the hexamer. The proximal side is involved in the binding of mRNA and small noncoding RNAs (sRNAs), while the distal side has an affinity for A-rich RNA sequences. In this work, the ability of various ribonucleotides to form complexes with Hfq from Pseudomonas aeruginosa has been tested using X-ray crystallography. ATP and ADPNP have been located in the distal R-site, which is a site for poly(A) RNA binding. UTP has been found in the so-called lateral RNA-binding site at the proximal surface. CTP has been found in both the distal R-site and the proximal U-binding site. GTP did not form a complex with Hfq under the conditions tested. The results have demonstrated the power of the crystallographic method for locating ribonucleotides and predicting single-stranded RNA-binding sites on the protein surface.


    Organizational Affiliation

    Institute of Protein Research, RAS, Institutskaya 4, Pushchino 142290, Moscow Region, Russian Federation.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein hfq
A, B, C, D, E, F
82Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: hfq
Find proteins for Q9HUM0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HUM0
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
C
Query on C

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A, C, D, E
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CDP
Query on CDP

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F
CYTIDINE-5'-DIPHOSPHATE
C9 H15 N3 O11 P2
ZWIADYZPOWUWEW-XVFCMESISA-N
 Ligand Interaction
P6G
Query on P6G

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D
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
CTP
Query on CTP

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A, B, C, D, E, F
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.280α = 90.00
b = 74.550β = 90.00
c = 109.610γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PROCESSdata reduction
MAR345dtbdata collection
PHENIXrefinement
PHENIXmodel building
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references