Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

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

Macromolecule Content

• Total Structure Weight: 44.87 kDa 
• Atom Count: 3232 
• Modelled Residue Count: 383 
• Deposited Residue Count: 405 
• Unique protein chains: 1

3G5B

The structure of UNC5b cytoplasmic domain

• PDB DOI: 10.2210/pdb3G5B/pdb

• Classification: APOPTOSIS
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2009-02-04 Released: 2009-04-07 
• Deposition Author(s): Wang, R., Wei, Z., Zhang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Autoinhibition of UNC5b revealed by the cytoplasmic domain structure of the receptor

Wang, R., Wei, Z., Jin, H., Wu, H., Yu, C., Wen, W., Chan, L.-N., Wen, Z., Zhang, M.

(2009) Mol Cell 33: 692-703

• PubMed: 19328064 
• DOI: 10.1016/j.molcel.2009.02.016
• Primary Citation of Related Structures:  
  3G5B


• PubMed Abstract: 
  

The cytoplasmic domains of UNC5 are responsible for its netrin-mediated signaling events in axonal migrations, blood vessel patterning, and apoptosis, although the molecular mechanisms governing these processes are unknown. To provide a foundation for the elucidation of the UNC5-mediated signaling mechanism, we determined the crystal structure of the cytoplasmic portion of UNC5b. We found that it contains three distinctly folded domains, namely ZU5, UPA, and death domain (DD). These three domains form a structural supramodule, with ZU5 binding to both UPA and DD, thereby locking the ZU5-UPA-DD supramodule in a closed conformation and suppressing its biological activities. Release of the closed conformation of the ZU5-UPA-DD supramodule leads to the activation of the receptor in the promotion of apoptosis and blood vessel patterning. Finally, we provide evidence showing that the supramodular nature of UNC5 ZU5-UPA-DD is likely to be shared by the ankyrin and PIDD families of scaffold proteins.

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Organizational Affiliation: 

Department of Biochemistry, Molecular Neuroscience Center, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin receptor UNC5B	A	405	Rattus norvegicus	Mutation(s): 2  Gene Names: Unc5b, Unc5h2 Membrane Entity: Yes
UniProt
Find proteins for O08722 (Rattus norvegicus) Explore O08722  Go to UniProtKB:  O08722

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [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: 0.250 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.243	α = 90
b = 62.71	β = 90
c = 118.11	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-04 
• Released Date: 2009-04-07 
Deposition Author(s): Wang, R., Wei, Z., Zhang, M.

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations