6VR4

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

• PDB DOI:  https://doi.org/10.2210/pdb6VR4/pdb

• Classification: VIRAL PROTEIN, TRANSFERASE, TRANSCRIPTION
• Organism(s): Cellulophaga phage phi14:2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-02-06 Released: 2020-07-29 
• Deposition Author(s): Leiman, P.G., Sokolova, M.L.

---

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 

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

• PubMed: 33208949 
• DOI: https://doi.org/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 . 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. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 503.24 kDa 
• Atom Count: 34,715 
• Modelled Residue Count: 4,332 
• Deposited Residue Count: 4,388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-dependent RNA polymerase	A, B	2,194	Cellulophaga phage phi14:2	Mutation(s): 0  Gene Names: Phi14:2_gp077
UniProt
Find proteins for S0A2C3 (Cellulophaga phage phi14:2) Explore S0A2C3  Go to UniProtKB:  S0A2C3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	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
NA	BA [auth B], CA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 266.441	α = 90
b = 297.181	β = 90
c = 92.015	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Leiman, P.G., Sokolova, M.L.

Revision History  

• 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