PDBsum entry 3g5b

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Apoptosis PDB id
Protein chain
383 a.a. *
PO4 ×3
Waters ×226
* Residue conservation analysis
PDB id:
Name: Apoptosis
Title: The structure of unc5b cytoplasmic domain
Structure: Netrin receptor unc5b. Chain: a. Fragment: unp residues 541-945. Synonym: protein unc-5 homolog b, unc-5 homolog 2. Engineered: yes. Mutation: yes
Source: Rattus norvegicus. Rat. Organism_taxid: 10116. Gene: unc5b. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.00Å     R-factor:   0.196     R-free:   0.250
Authors: R.Wang,Z.Wei,M.Zhang
Key ref:
R.Wang et al. (2009). Autoinhibition of UNC5b revealed by the cytoplasmic domain structure of the receptor. Mol Cell, 33, 692-703. PubMed id: 19328064 DOI: 10.1016/j.molcel.2009.02.016
04-Feb-09     Release date:   07-Apr-09    
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Protein chain
Pfam   ArchSchema ?
O08722  (UNC5B_RAT) -  Netrin receptor UNC5B
945 a.a.
383 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     signal transduction   1 term 


DOI no: 10.1016/j.molcel.2009.02.016 Mol Cell 33:692-703 (2009)
PubMed id: 19328064  
Autoinhibition of UNC5b revealed by the cytoplasmic domain structure of the receptor.
R.Wang, Z.Wei, H.Jin, H.Wu, C.Yu, W.Wen, L.N.Chan, Z.Wen, M.Zhang.
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.
  Selected figure(s)  
Figure 4.
Figure 4. The UNC5b ZU5-UPA-DD Supramodule Adopts a Closed Conformation
(A) Schematic diagram showing the engineering of a HRV 3C protease cutting site between UPA and DD.
(B)The HRV 3C protease-cleaved ZU5-UPA-DD mutant remained as a monomer as shown by gel filtration chromatography. Each of the relevant fractions is shown in the lower panel by SDS-PAGE. The elution volumes of standard size markers are indicated by arrowheads.
(C) Gel filtration profile of the HRV 3C protease-cleaved ZU5-UPA-DD mutant after prolonged incubation. The cleaved ZU5-UPA formed oligomer, and DD formed homodimer.
(D) Gel filtration profiles of various point mutations of ZU5-UPA-DD supramodule mutants used in this study.
(E) Gel filtration profiles of the isolated DD mutants described in this study.
Figure 6.
Figure 6. The Open Conformation of UNC5b ZU5-UPA-DD Has Higher Activity in Promoting PAV Vessel Formation in Zebrafish
(A–F) Whole-mount fluorescene image of 48 hpf fli1:eGFP transgenic embryo injected with 8 ng control MO (A), 4 ng unc5b MO (B), 4 ng unc5b MO plus a high dose of wild-type rat UNC5b mRNA (220 pg) (C), 4 ng unc5b MO plus a low dose of wild-type UNC5b mRNA (30 pg) (D), 4 ng unc5b MO plus 250 pg UNC5bΔZU5 mRNA (E), 4 ng unc5b MO plus 280 pg UNC5bΔDD mRNA (F). (A′–F′) Confocal projections showing the lateral views of somties 8–13 of fli1:eGFP transgenics shown in (A)–(F). Red arrows indicate that PAV spans the entire hemisegment. Blue arrows indicate that PAV spans only part of the hemisegment. DA, dorsal aorta; PCV, posterior cardinal vein.
(G) Summary of PAV formation scored as fraction of hemisegment per embryo in various conditions. In this study, two hemisegments with partial PAV formation were counted as one. The number of embryos examined in each condition are as follows: n[Ctrl MO] = 100; n[unc5b MO] = 186; n[unc5b MO+WT(high)] = 104; n[unc5b MO+WT(low)] = 46; n[unc5b MO+ΔZU5] = 69; n[unc5b MO+ΔDD] = 78. ^***p < 0.0001. Scale bars, mean ± SEM.
  The above figures are reprinted by permission from Cell Press: Mol Cell (2009, 33, 692-703) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20966961 A.Tinel, M.J.Eckert, E.Logette, S.Lippens, S.Janssens, B.Jaccard, M.Quadroni, and J.Tschopp (2011).
Regulation of PIDD auto-proteolysis and activity by the molecular chaperone Hsp90.
  Cell Death Differ, 18, 506-515.  
21186323 G.Ayalon, J.D.Hostettler, J.Hoffman, K.Kizhatil, J.Q.Davis, and V.Bennett (2011).
Ankyrin-B Interactions with Spectrin and Dynactin-4 Are Required for Dystrophin-based Protection of Skeletal Muscle from Exercise Injury.
  J Biol Chem, 286, 7370-7378.  
21240187 L.Huo, W.Wen, R.Wang, C.Kam, J.Xia, W.Feng, and M.Zhang (2011).
Cdc42-dependent formation of the ZO-1/MRCKβ complex at the leading edge controls cell migration.
  EMBO J, 30, 665-678.
PDB codes: 2kxr 2kxs
21326323 P.Mehlen, C.Delloye-Bourgeois, and A.Chédotal (2011).
Novel roles for Slits and netrins: axon guidance cues as anticancer targets?
  Nat Rev Cancer, 11, 188-197.  
21172648 A.Bagri, and A.Ashkenazi (2010).
UNCovering the molecular machinery of dependence receptor signaling.
  Mol Cell, 40, 851-853.  
20411297 A.Czogalla, and A.F.Sikorski (2010).
Do we already know how spectrin attracts ankyrin?
  Cell Mol Life Sci, 67, 2679-2683.  
21172653 C.Guenebeaud, D.Goldschneider, M.Castets, C.Guix, G.Chazot, C.Delloye-Bourgeois, A.Eisenberg-Lerner, G.Shohat, M.Zhang, V.Laudet, A.Kimchi, A.Bernet, and P.Mehlen (2010).
The dependence receptor UNC5H2/B triggers apoptosis via PP2A-mediated dephosphorylation of DAP kinase.
  Mol Cell, 40, 863-876.  
20173780 D.Goldschneider, and P.Mehlen (2010).
Dependence receptors: a new paradigm in cell signaling and cancer therapy.
  Oncogene, 29, 1865-1882.  
20101027 J.J.Ipsaro, and A.Mondragón (2010).
Structural basis for spectrin recognition by ankyrin.
  Blood, 115, 4093-4101.
PDB codes: 3kbt 3kbu
  20452960 R.H.Adams, and A.Eichmann (2010).
Axon guidance molecules in vascular patterning.
  Cold Spring Harb Perspect Biol, 2, a001875.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.