1AV6

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

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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


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

  • 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.


Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferaseB [auth A]295Vaccinia virus WRMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07617
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*AP*AP*AP*AP*A)-3')A [auth B]6N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGT
Query on MGT
Download Ideal Coordinates CCD File 
C [auth B]7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
C11 H20 N5 O14 P3
BUJQMJUTTBGELS-KQYNXXCUSA-N
SAH
Query on SAH
Download Ideal Coordinates CCD File 
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 = 61.8α = 90
b = 64.6β = 90
c = 99.5γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
SMARTdata reduction
SAINTdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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