2I39 | pdb_00002i39

Crystal structure of Vaccinia virus N1L protein

• PDB DOI: https://doi.org/10.2210/pdb2I39/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Orthopoxvirus vaccinia
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-17 Released: 2006-11-21 
• Deposition Author(s): Aoyagi, M., Aleshin, A.E., Stec, B., Liddington, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.247 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.201 (DCC) 

Literature

Vaccinia virus N1L protein resembles a B cell lymphoma-2 (Bcl-2) family protein.

Aoyagi, M., Zhai, D., Jin, C., Aleshin, A.E., Stec, B., Reed, J.C., Liddington, R.C.

(2007) Protein Sci 16: 118-124

• PubMed: 17123957 
• DOI: https://doi.org/10.1110/ps.062454707
• Primary Citation Related Structures: 
  2I39


• PubMed Abstract: 
  

  Poxviruses encode immuno-modulatory proteins capable of subverting host defenses. The poxvirus vaccinia expresses a small 14-kDa protein, N1L, that is critical for virulence. We report the crystal structure of N1L, which reveals an unexpected but striking resemblance to host apoptotic regulators of the B cell lymphoma-2 (Bcl-2) family. Although N1L lacks detectable Bcl-2 homology (BH) motifs at the sequence level, we show that N1L binds with high affinity to the BH3 peptides of pro-apoptotic Bcl-2 family proteins in vitro, consistent with a role for N1L in modulating host antiviral defenses.

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Organizational Affiliation: 
• Burnham Institute for Medical Research, La Jolla, CA 92037, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 97.13 kDa 
• Atom Count: 6,177 
• Modeled Residue Count: 710 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein N1	A, B, C, D, E, F	137	Orthopoxvirus vaccinia	Mutation(s): 0  Gene Names: N1L (VACWR028)
UniProt
Find proteins for Q49PX0 (Vaccinia virus (strain LC16m0)) Explore Q49PX0  Go to UniProtKB:  Q49PX0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	G [auth A], H [auth E]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.247 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.201 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.64	α = 90
b = 109.99	β = 110.92
c = 69.58	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): Aoyagi, M., Aleshin, A.E., Stec, B., Liddington, R.C.

Revision History  

• Version 1.0: 2006-11-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations