1V39 | pdb_00001v39

DC26 MUTANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE AND M7G(5')PPPG

• PDB DOI: https://doi.org/10.2210/pdb1V39/pdb

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


• Deposited: 1996-12-16 Released: 1997-09-17 
• Deposition Author(s): Hodel, A.E., Gershon, P.D., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 
  0.223 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Specific protein recognition of an mRNA cap through its alkylated base.

Hodel, A.E., Gershon, P.D., Shi, X., Wang, S.M., Quiocho, F.A.

(1997) Nat Struct Biol 4: 350-354

• PubMed: 9145102 
• DOI: https://doi.org/10.1038/nsb0597-350
• Primary Citation Related Structures: 
  1P39, 1V39, 1VP3, 1VP9, 2VP3


• PubMed Abstract: 
  

  The specific binding of N7-methylguanine cap analogues to the RNA methyltransferase VP39 was observed through X-ray crystallography, providing a prototypical structure for a complex between a protein and an mRNA 5' cap.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.98 kDa 
• Atom Count: 2,662 
• Modeled Residue Count: 291 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP39	A	322	Vaccinia virus WR	Mutation(s): 0  EC: 2.7.7.19 (PDB Primary Data), 2.1.1.57 (UniProt)
UniProt
Find proteins for P07617 (Vaccinia virus (strain Western Reserve)) Explore P07617  Go to UniProtKB:  P07617

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M7G	C [auth A]	7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE C11 H18 N5 O11 P2 SBASPRRECYVBRF-KQYNXXCUSA-O
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work:  0.223 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.6	α = 90
b = 67.3	β = 117.3
c = 79.6	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-09-17 
Deposition Author(s): Hodel, A.E., Gershon, P.D., Quiocho, F.A.

Revision History  

• Version 1.0: 1997-09-17
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 2.0: 2023-08-09
  Changes: Atomic model, Database references, Derived calculations, Other, Refinement description
• Version 3.0: 2024-03-06
  Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary