4XRP

Structure of the Pnkp1/Rnl/Hen1 RNA repair complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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:  
    4XRP, 4XRU

  • 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 complex is a 270-kDa heterohexamer composed of three proteins-Pnkp1, Rnl and Hen1-that are required to repair ribotoxin-cleaved RNA in vitro ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pnkp1A, D312Capnocytophaga gingivalis ATCC 33624Mutation(s): 0 
Gene Names: CAPGI0001_2485
UniProt
Find proteins for C2M8N3 (Capnocytophaga gingivalis)
Explore C2M8N3 
Go to UniProtKB:  C2M8N3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC2M8N3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RnlB, E394Capnocytophaga gingivalis ATCC 33624Mutation(s): 0 
Gene Names: CAPGI0001_2487
UniProt
Find proteins for C2M8N4 (Capnocytophaga gingivalis)
Explore C2M8N4 
Go to UniProtKB:  C2M8N4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC2M8N4
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Hen1C, F436Capnocytophaga gingivalis ATCC 33624Mutation(s): 0 
Gene Names: CAPGI0001_1566
UniProt
Find proteins for C2M7I7 (Capnocytophaga gingivalis)
Explore C2M7I7 
Go to UniProtKB:  C2M7I7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC2M7I7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
M [auth B],
O [auth C],
U [auth E],
I [auth A],
J [auth A],
M [auth B],
O [auth C],
U [auth E],
V [auth E],
W [auth F],
X [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
G [auth A],
S [auth D]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
N [auth B],
P [auth C],
Q [auth C],
R [auth C],
Y [auth F]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
L [auth B],
T [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.16α = 90
b = 179.201β = 103.7
c = 114.333γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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