6VR4

Virion-packaged DNA-dependent RNA polymerase of crAss-like phage phi14:2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and function of virion RNA polymerase of a crAss-like phage.

Drobysheva, A.V.Panafidina, S.A.Kolesnik, M.V.Klimuk, E.I.Minakhin, L.Yakunina, M.V.Borukhov, S.Nilsson, E.Holmfeldt, K.Yutin, N.Makarova, K.S.Koonin, E.V.Severinov, K.V.Leiman, P.G.Sokolova, M.L.

(2020) Nature 589: 306-309

  • DOI: 10.1038/s41586-020-2921-5
  • Primary Citation of Related Structures:  
    6VR4

  • PubMed Abstract: 
  • CrAss-like phages are a recently described expansive group of viruses that includes the most abundant virus in the human gut 1-3 . The genomes of all crAss-like phages encode a large virion-packaged protein 2,4 that contains a DFDxD sequence motif, which forms the catalytic site in cellular multisubunit RNA polymerases (RNAPs) 5 ...

    CrAss-like phages are a recently described expansive group of viruses that includes the most abundant virus in the human gut 1-3 . The genomes of all crAss-like phages encode a large virion-packaged protein 2,4 that contains a DFDxD sequence motif, which forms the catalytic site in cellular multisubunit RNA polymerases (RNAPs) 5 . Here, using Cellulophaga baltica crAss-like phage phi14:2 as a model system, we show that this protein is a DNA-dependent RNAP that is translocated into the host cell along with the phage DNA and transcribes early phage genes. We determined the crystal structure of this 2,180-residue enzyme in a self-inhibited state, which probably occurs before virion packaging. This conformation is attained with the help of a cleft-blocking domain that interacts with the active site and occupies the cavity in which the RNA-DNA hybrid binds. Structurally, phi14:2 RNAP is most similar to eukaryotic RNAPs that are involved in RNA interference 6,7 , although most of the phi14:2 RNAP structure (nearly 1,600 residues) maps to a new region of the protein fold space. Considering this structural similarity, we propose that eukaryal RNA interference polymerases have their origins in phage, which parallels the emergence of the mitochondrial transcription apparatus 8 .


    Organizational Affiliation

    Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia. maria.sokolova@skolkovotech.ru.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-dependent RNA polymeraseA, B2194Cellulophaga phage phi14:2Mutation(s): 0 
Gene Names: Phi14:2_gp077
UniProt
Find proteins for S0A2C3 (Cellulophaga phage phi14:2)
Explore S0A2C3 
Go to UniProtKB:  S0A2C3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS0A2C3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
AA [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth B],
CA [auth B],
N [auth A],
O [auth A],
P [auth A],
BA [auth B],
CA [auth B],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 266.441α = 90
b = 297.181β = 90
c = 92.015γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2020-12-09
    Changes: Database references
  • Version 1.3: 2021-01-20
    Changes: Database references