1AV6

VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M7G CAPPED RNA HEXAMER AND S-ADENOSYLHOMOCYSTEINE

• PDB DOI: https://doi.org/10.2210/pdb1AV6/pdb
• NAKB: 1AV6

• Classification: TRANSFERASE/RNA
• Organism(s): Vaccinia virus WR
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1997-09-26 Released: 1998-02-25 
• Deposition Author(s): Hodel, A.E., Gershon, P.D., Quiocho, F.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.215 
• R-Value Observed: 0.215 

Starting Model: experimental

Literature

Structural basis for sequence-nonspecific recognition of 5'-capped mRNA by a cap-modifying enzyme.

Hodel, A.E., Gershon, P.D., Quiocho, F.A.

(1998) Mol Cell 1: 443-447

• PubMed: 9660928 
• DOI: https://doi.org/10.1016/s1097-2765(00)80044-1
• Primary Citation of Related Structures:  
  1AV6


• PubMed Abstract: 
  

  Sequence-nonspecific binding of RNA, recognition of a 7-methylguanosine 5' mRNA cap, and methylation of a nucleic acid backbone are three crucial and ubiquitous events in eukaryotic nucleic acid processing and function. These three events occur concurrently in the modification of vaccinia transcripts by the methyltransferase VP39. We report the crystal structure of a ternary complex comprising VP39, coenzyme product S-adenosylhomocysteine, and a 5' m7 G-capped, single-stranded RNA hexamer. This structure reveals a novel and general mechanism for sequence-non-specific recognition of the mRNA transcript in which the protein interacts solely with the sugar-phosphate backbone of a short, single-stranded RNA helix. This report represents the first direct and detailed view of a protein complexed with single-stranded RNA or 5'-capped mRNA.

---

Organizational Affiliation: 

Howard Hughes Medical Institute, Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.44 kDa 
• Atom Count: 2,575 
• Modelled Residue Count: 295 
• Deposited Residue Count: 301 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase	B [auth A]	295	Vaccinia virus WR	Mutation(s): 0  Gene Names: PAPS, VACWR095, F9 EC: 2.1.1.57
UniProt
Find proteins for P07617 (Vaccinia virus (strain Western Reserve)) Explore P07617  Go to UniProtKB:  P07617

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*AP*AP*AP*AP*A)-3')	A [auth B]	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGT	C [auth B]	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE C11 H20 N5 O14 P3 BUJQMJUTTBGELS-KQYNXXCUSA-N
SAH	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.215 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.8	α = 90
b = 64.6	β = 90
c = 99.5	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
SMART	data reduction
SAINT	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-02-25 
Deposition Author(s): Hodel, A.E., Gershon, P.D., Quiocho, F.A.

Revision History  

• Version 1.0: 1998-02-25
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-02-26
  Changes: Data collection, Derived calculations
• Version 1.4: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description