5DY9

Y68T Hfq from Methanococcus jannaschii in complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of RNA-binding properties of the archaeal Hfq-like protein from Methanococcus jannaschii.

Nikulin, A.Mikhailina, A.Lekontseva, N.Balobanov, V.Nikonova, E.Tishchenko, S.

(2017) J. Biomol. Struct. Dyn. 35: 1615-1628

  • DOI: 10.1080/07391102.2016.1189849
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Sm and Sm-like proteins are widely distributed among bacteria, archaea and eukarya. They participate in many processes related to RNA-processing and regulation of gene expression. While the function of the bacterial Lsm protein Hfq and eukaryotic ...

    The Sm and Sm-like proteins are widely distributed among bacteria, archaea and eukarya. They participate in many processes related to RNA-processing and regulation of gene expression. While the function of the bacterial Lsm protein Hfq and eukaryotic Sm/Lsm proteins is rather well studied, the role of Lsm proteins in Archaea is investigated poorly. In this work, the RNA-binding ability of an archaeal Hfq-like protein from Methanococcus jannaschii has been studied by X-ray crystallography, anisotropy fluorescence and surface plasmon resonance. It has been found that MjaHfq preserves the proximal RNA-binding site that usually recognizes uridine-rich sequences. Distal adenine-binding and lateral RNA-binding sites show considerable structural changes as compared to bacterial Hfq. MjaHfq did not bind mononucleotides at these sites and would not recognize single-stranded RNA as its bacterial homologues. Nevertheless, MjaHfq possesses affinity to poly(A) RNA that seems to bind at the unstructured positive-charged N-terminal tail of the protein.


    Organizational Affiliation

    a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hfq-like protein
A, B, C, D, E, F, G, H, I, J, K, L
71Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 1 
Find proteins for Q58830 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58830
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
F, K
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
C, E, F, J
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
E, H, I, K
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

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Download CCD File 
A, E, G
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
G, H, I
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
E, J, L
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.636α = 90.00
b = 67.635β = 90.95
c = 91.165γ = 90.00
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
PHENIXrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Scientific FoundationRussian Federation14-14-00496

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references
  • Version 1.2: 2017-05-24
    Type: Database references