3DOF

Complex of ARL2 and BART, Crystal Form 2

• PDB DOI: https://doi.org/10.2210/pdb3DOF/pdb

• Classification: SIGNALING PROTEIN/HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-04 Released: 2009-03-03 
• Deposition Author(s): Zhang, T., Li, S., Ding, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.294 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 

Starting Model: experimental

Literature

Crystal structure of the ARL2-GTP-BART complex reveals a novel recognition and binding mode of small GTPase with effector

Zhang, T., Li, S., Zhang, Y., Zhong, C., Lai, Z., Ding, J.

(2009) Structure 17: 602-610

• PubMed: 19368893 
• DOI: https://doi.org/10.1016/j.str.2009.01.014
• Primary Citation of Related Structures:  
  3DOE, 3DOF


• PubMed Abstract: 
  

  ARL2 is a member of the ADP-ribosylation factor family but has unique biochemical features. BART is an effector of ARL2 that is essential for nuclear retention of STAT3 and may also be involved in mitochondria transport and apoptosis. Here we report the crystal structure and biochemical characterization of human ARL2-GTP-BART complex. ARL2-GTP assumes a typical small GTPase fold with a unique N-terminal alpha helix conformation. BART consists of a six alpha helix bundle. The interactions between ARL2 and BART involve two interfaces: a conserved N-terminal LLXIL motif of ARL2 is embedded in a hydrophobic cleft of BART and the switch regions of ARL2 interact with helix alpha3 of BART. Both interfaces are essential for the binding as verified by mutagenesis study. This novel recognition and binding mode is different from that of other small GTPase-effector interactions and provides molecular basis for the high specificity of ARL2 for BART.

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Organizational Affiliation: 

Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 41.5 kDa 
• Atom Count: 2,574 
• Modelled Residue Count: 309 
• Deposited Residue Count: 357 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor-like protein 2	A	192	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P36404 (Homo sapiens) Explore P36404  Go to UniProtKB:  P36404
PHAROS:  P36404 GTEx:  ENSG00000213465

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor-like protein 2-binding protein	B	165	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2Y0 (Homo sapiens) Explore Q9Y2Y0  Go to UniProtKB:  Q9Y2Y0
PHAROS:  Q9Y2Y0 GTEx:  ENSG00000102931

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	C [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.294 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.663	α = 90
b = 45.165	β = 90
c = 175.879	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Zhang, T., Li, S., Ding, J.

Revision History  

• Version 1.0: 2009-03-03
  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