4XRU

Structure of Pnkp1/Rnl/Hen1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex.

Wang, P.Selvadurai, K.Huang, R.H.

(2015) Nat Commun 6: 6876-6876

  • DOI: 10.1038/ncomms7876
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ribotoxins cleave essential RNAs for cell killing, and RNA repair neutralizes the damage inflicted by ribotoxins for cell survival. Here we report a new bacterial RNA repair complex that performs RNA repair linked to immunity. This new RNA repair com ...

    Ribotoxins cleave essential RNAs for cell killing, and RNA repair neutralizes the damage inflicted by ribotoxins for cell survival. Here we report a new bacterial RNA repair complex that performs RNA repair linked to immunity. This new RNA repair complex is a 270-kDa heterohexamer composed of three proteins-Pnkp1, Rnl and Hen1-that are required to repair ribotoxin-cleaved RNA in vitro. The crystal structure of the complex reveals the molecular architecture of the heterohexamer as two rhomboid-shaped ring structures of Pnkp1-Rnl-Hen1 heterotrimer fused at the Pnkp1 dimer interface. The four active sites required for RNA repair are located on the inner rim of each ring. The architecture and the locations of the active sites of the Pnkp1-Rnl-Hen1 heterohexamer suggest an ordered series of repair reactions at the broken RNA ends that confer immunity to recurrent damage.


    Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pnkp1
A, D
312Capnocytophaga gingivalisMutation(s): 0 
Find proteins for C2M8N3 (Capnocytophaga gingivalis)
Go to UniProtKB:  C2M8N3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Rnl
B, E
394Capnocytophaga gingivalisMutation(s): 0 
Find proteins for C2M8N4 (Capnocytophaga gingivalis)
Go to UniProtKB:  C2M8N4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hen1
C, F
436Capnocytophaga gingivalisMutation(s): 0 
Find proteins for C2M7I7 (Capnocytophaga gingivalis)
Go to UniProtKB:  C2M7I7
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, D, E
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
B, C, E, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

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Download CCD File 
C, F
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 108.483α = 90.00
b = 187.245β = 106.04
c = 111.999γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-01-21 
  • Released Date: 2015-04-22 
  • Deposition Author(s): Wang, P.

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Database references