3U6Y

Crystal structure of ALBA2-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb3U6Y/pdb
• NAKB: 3U6Y

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Aeropyrum pernix K1, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-13 Released: 2012-02-22 
• Deposition Author(s): Kumarevel, T., Tanaka, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.244 
• R-Value Observed: 0.244 

Starting Model: experimental

Literature

Crystal structure of archaeal chromatin protein Alba2-double-stranded DNA complex from Aeropyrum pernix K1.

Tanaka, T., Padavattan, S., Kumarevel, T.

(2012) J Biol Chem 287: 10394-10402

• PubMed: 22334696 
• DOI: https://doi.org/10.1074/jbc.M112.343210
• Primary Citation of Related Structures:  
  3U6Y


• PubMed Abstract: 
  

  All thermophilic and hyperthermophilic archaea encode homologs of dimeric Alba (Sac10b) proteins that bind cooperatively at high density to DNA. Here, we report the 2.0 Å resolution crystal structure of an Alba2 (Ape10b2)-dsDNA complex from Aeropyrum pernix K1. A rectangular tube-like structure encompassing duplex DNA reveals the positively charged residues in the monomer-monomer interface of each dimer packing on either side of the bound dsDNA in successive minor grooves. The extended hairpin loop connecting strands β3 and β4 undergoes significant conformational changes upon DNA binding to accommodate the other Alba2 dimer during oligomerization. Mutational analysis of key interacting residues confirmed the specificity of Alba2-dsDNA interactions.

---

Organizational Affiliation: 

RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.

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: 25.89 kDa 
• Atom Count: 1,933 
• Modelled Residue Count: 208 
• Deposited Residue Count: 214 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA/RNA-binding protein Alba 2	A, B [auth C]	102	Aeropyrum pernix K1	Mutation(s): 0  Gene Names: albA2, APE_1823
UniProt
Find proteins for Q9YAX2 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YAX2  Go to UniProtKB:  Q9YAX2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*C)-3')	C [auth D]	5	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*CP*CP*G)-3')	D [auth E]	5	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.244 
• R-Value Observed: 0.244 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.556	α = 90
b = 74.29	β = 90
c = 88.198	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-22 
Deposition Author(s): Kumarevel, T., Tanaka, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Database references, Source and taxonomy
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary