3LNQ | pdb_00003lnq

Structure of Aristaless homeodomain in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb3LNQ/pdb
• NAKB: 3LNQ

• Classification: Gene Regulation/DNA
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-02 Released: 2010-04-28 
• Deposition Author(s): Takamura, Y., Miyazono, K., Nagata, K., Saigo, K., Kojima, T., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.251 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless

Miyazono, K., Zhi, Y., Takamura, Y., Nagata, K., Saigo, K., Kojima, T., Tanokura, M.

(2010) EMBO J 29: 1613-1623

• PubMed: 20389279 
• DOI: https://doi.org/10.1038/emboj.2010.53
• Primary Citation Related Structures: 
  3A01, 3A02, 3A03, 3LNQ


• PubMed Abstract: 
  

  To achieve accurate gene regulation, some homeodomain proteins bind cooperatively to DNA to increase those site specificities. We report a ternary complex structure containing two homeodomain proteins, aristaless (Al) and clawless (Cll), bound to DNA. Our results show that the extended conserved sequences of the Cll homeodomain are indispensable to cooperative DNA binding. In the Al-Cll-DNA complex structure, the residues in the extended regions are used not only for the intermolecular contacts between the two homeodomain proteins but also for the sequence-recognition mechanism of DNA by direct interactions. The residues in the extended N-terminal arm lie within the minor groove of DNA to form direct interactions with bases, whereas the extended conserved region of the C-terminus of the homeodomain interacts with Al to stabilize and localize the third alpha helix of the Cll homeodomain. This structure suggests a novel mode for the cooperativity of homeodomain proteins.

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Organizational Affiliation: 
• Department of Applied Biological Chemistry, University of Tokyo, Bunkyo-ku, Tokyo, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.86 kDa 
• Atom Count: 1,113 
• Modeled Residue Count: 86 
• Deposited Residue Count: 86 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein aristaless	A	58	Drosophila melanogaster	Mutation(s): 0  Gene Names: al, CG3935
UniProt
Find proteins for Q06453 (Drosophila melanogaster) Explore Q06453  Go to UniProtKB:  Q06453

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*GP*TP*TP*TP*AP*AP*TP*TP*AP*GP*GP*G)-3'	B	14	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*CP*TP*AP*AP*TP*TP*AP*AP*AP*CP*CP*C)-3'	C	14	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.251 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.35	α = 90
b = 42.35	β = 90
c = 162.73	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-28 
Deposition Author(s): Takamura, Y., Miyazono, K., Nagata, K., Saigo, K., Kojima, T., Tanokura, M.

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description