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PDBsum entry 1w15

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protein metals links
Metal binding protein PDB id
1w15
Jmol
Contents
Protein chain
132 a.a. *
Metals
_CL ×9
_CA ×3
_NA ×2
Waters ×93
* Residue conservation analysis
PDB id:
1w15
Name: Metal binding protein
Title: Rat synaptotagmin 4 c2b domain in the presence of calcium
Structure: Synaptotagmin iv. Chain: a. Fragment: c2b domain, residues 288-425. Engineered: yes
Source: Rattus norvegicus. Rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Trimer (from PDB file)
Resolution:
1.93Å     R-factor:   0.206     R-free:   0.233
Authors: H.Dai,O.-H.Shin,M.Machius,D.R.Tomchick,T.C.Sudhof,J.Rizo
Key ref:
H.Dai et al. (2004). Structural basis for the evolutionary inactivation of Ca2+ binding to synaptotagmin 4. Nat Struct Mol Biol, 11, 844-849. PubMed id: 15311271 DOI: 10.1038/nsmb817
Date:
16-Jun-04     Release date:   13-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P50232  (SYT4_RAT) -  Synaptotagmin-4
Seq:
Struc:
425 a.a.
132 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     transport   2 terms 
  Biochemical function     transporter activity     1 term  

 

 
DOI no: 10.1038/nsmb817 Nat Struct Mol Biol 11:844-849 (2004)
PubMed id: 15311271  
 
 
Structural basis for the evolutionary inactivation of Ca2+ binding to synaptotagmin 4.
H.Dai, O.H.Shin, M.Machius, D.R.Tomchick, T.C.Südhof, J.Rizo.
 
  ABSTRACT  
 
The neuronal protein synaptotagmin 1 functions as a Ca(2+) sensor in exocytosis via two Ca(2+)-binding C(2) domains. The very similar synaptotagmin 4, which includes all the predicted Ca(2+)-binding residues in the C(2)B domain but not in the C(2)A domain, is also thought to function as a neuronal Ca(2+) sensor. Here we show that, unexpectedly, both C(2) domains of fly synaptotagmin 4 exhibit Ca(2+)-dependent phospholipid binding, whereas neither C(2) domain of rat synaptotagmin 4 binds Ca(2+) or phospholipids efficiently. Crystallography reveals that changes in the orientations of critical Ca(2+) ligands, and perhaps their flexibility, render the rat synaptotagmin 4 C(2)B domain unable to form full Ca(2+)-binding sites. These results indicate that synaptotagmin 4 is a Ca(2+) sensor in the fly but not in the rat, that the Ca(2+)-binding properties of C(2) domains cannot be reliably predicted from sequence analyses, and that proteins clearly identified as orthologs may nevertheless have markedly different functional properties.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Intrinsic Ca^2+-binding properties of the synaptotagmin 4 and 11 C[2] domains. (a -f) 1H-15N HSQC spectra obtained at different Ca^2+ concentrations for the rat synaptotagmin 4 C[2]A (a) and C[2]B (b) domains, the D. melanogaster synaptotagmin 4 C[2]A (c) and C[2]B (d) domains, and the rat synaptotagmin 11 C[2]A (e) and C[2]B (f) domains. The protein concentrations were 120 M and the total Ca^2+ concentrations used (mM) were: a, 0, 0.2, 1, 5, 10, 20, 40, 80; b, 0, 20; c, 0, 5, 10, 20, 40, 80; d, 0, 0.2, 1, 3, 10, 20, 40; e, 0, 0.2, 1, 3, 5, 10, 20, 40, 80; f, 0, 20. The 1H-15N HSQC spectra acquired in the absence of Ca^2+ and the highest Ca^2+ concentrations are shown with multiple red contours and multiple black contours, respectively, whereas spectra obtained at intermediate Ca^2+ concentrations are shown with single black contours.
Figure 4.
Figure 4. Crystal structure of the rat synaptotagmin 4 C[2]B domain. (a) Ribbon diagram of the rat synaptotagmin 4 C[2]B domain. Strands (cyan) are labeled 1 -8 and the single helix (orange) is labeled HA. (b) Electron density map of the Ca^2+-binding site of the rat synaptotagmin 4 C[2]B domain. Contours are drawn at 1.0 the r.m.s. level of the map. Oxygen atoms are red, nitrogen atoms are blue and carbon atoms are yellow. The Ca^2+ ion is labeled Ca, the protein Ca^2+ ligands are labeled D2, D3 and E4, and a coordinating water molecule is labeled W. (c) Backbone superposition of the structures of the rat synaptotagmin 4 C[2]B domain (orange) and the rat synaptotagmin 1 C[2]B domain8 (cyan). (d) Superposition of the Ca^2+-binding loops of the rat synaptotagmin 4 C[2]B domain (orange) and the rat synaptotagmin 1 C[2]B domain (cyan). (e) Superposition of the Ca^2+-binding loops of the rat synaptotagmin 4 C[2]B domain (orange) and the rat synaptotagmin 1 C[2]A domain (dark blue). In d and e, the Ca^2+ ions are in the same color as the protein. The figure was generated with InsightII (MSI) and MolScript35.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 844-849) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21294713 G.Ankem, S.Mitra, F.Sun, A.C.Moreno, B.Chutvirasakul, H.F.Azurmendi, L.Li, and D.G.Capelluto (2011).
The C2 domain of Tollip, a Toll-like receptor signalling regulator, exhibits broad preference for phosphoinositides.
  Biochem J, 435, 597-608.  
21118669 V.Parpura, V.Grubišić, and A.Verkhratsky (2011).
Ca(2+) sources for the exocytotic release of glutamate from astrocytes.
  Biochim Biophys Acta, 1813, 984-991.  
20735850 J.M.Moore-Dotson, J.B.Papke, and A.B.Harkins (2010).
Upregulation of synaptotagmin IV inhibits transmitter release in PC12 cells with targeted synaptotagmin I knockdown.
  BMC Neurosci, 11, 104.  
  20824061 M.Xue, T.K.Craig, O.H.Shin, L.Li, C.A.Brautigam, D.R.Tomchick, T.C.Südhof, C.Rosenmund, and J.Rizo (2010).
Structural and mutational analysis of functional differentiation between synaptotagmins-1 and -7.
  PLoS One, 5, 0.
PDB code: 3n5a
20688915 Z.Wang, and E.R.Chapman (2010).
Rat and Drosophila synaptotagmin 4 have opposite effects during SNARE-catalyzed membrane fusion.
  J Biol Chem, 285, 30759-30766.  
19822673 C.F.Barber, R.A.Jorquera, J.E.Melom, and J.T.Littleton (2009).
Postsynaptic regulation of synaptic plasticity by synaptotagmin 4 requires both C2 domains.
  J Cell Biol, 187, 295-310.  
19805322 O.H.Shin, J.Xu, J.Rizo, and T.C.Südhof (2009).
Differential but convergent functions of Ca2+ binding to synaptotagmin-1 C2 domains mediate neurotransmitter release.
  Proc Natl Acad Sci U S A, 106, 16469-16474.  
18834310 T.A.Fiacco, C.Agulhon, and K.D.McCarthy (2009).
Sorting out astrocyte physiology from pharmacology.
  Annu Rev Pharmacol Toxicol, 49, 151-174.  
19030179 T.Mittelsteadt, G.Seifert, E.Alvárez-Barón, C.Steinhäuser, A.J.Becker, and S.Schoch (2009).
Differential mRNA expression patterns of the synaptotagmin gene family in the rodent brain.
  J Comp Neurol, 512, 514-528.  
19136969 Z.Zhang, A.Bhalla, C.Dean, E.R.Chapman, and M.B.Jackson (2009).
Synaptotagmin IV: a multifunctional regulator of peptidergic nerve terminals.
  Nat Neurosci, 12, 163-171.  
18308933 A.Maximov, Y.Lao, H.Li, X.Chen, J.Rizo, J.B.Sørensen, and T.C.Südhof (2008).
Genetic analysis of synaptotagmin-7 function in synaptic vesicle exocytosis.
  Proc Natl Acad Sci U S A, 105, 3986-3991.  
18508081 E.Connell, A.Giniatullina, J.Lai-Kee-Him, R.Tavare, E.Ferrari, A.Roseman, D.Cojoc, A.R.Brisson, and B.Davletov (2008).
Cross-linking of phospholipid membranes is a conserved property of calcium-sensitive synaptotagmins.
  J Mol Biol, 380, 42-50.  
18496517 S.Martens, and H.T.McMahon (2008).
Mechanisms of membrane fusion: disparate players and common principles.
  Nat Rev Mol Cell Biol, 9, 543-556.  
17521570 J.Xu, T.Mashimo, and T.C.Südhof (2007).
Synaptotagmin-1, -2, and -9: Ca(2+) sensors for fast release that specify distinct presynaptic properties in subsets of neurons.
  Neuron, 54, 567-581.  
17166855 P.Montaville, C.Schlicker, A.Leonov, M.Zweckstetter, G.M.Sheldrick, and S.Becker (2007).
The C2A-C2B linker defines the high affinity Ca(2+) binding mode of rabphilin-3A.
  J Biol Chem, 282, 5015-5025.
PDB codes: 2cm5 2cm6
17630786 R.Guan, H.Dai, D.R.Tomchick, I.Dulubova, M.Machius, T.C.Südhof, and J.Rizo (2007).
Crystal structure of the RIM1alpha C2B domain at 1.7 A resolution.
  Biochemistry, 46, 8988-8998.
PDB code: 2q3x
17360437 S.W.Min, W.P.Chang, and T.C.Südhof (2007).
E-Syts, a family of membranous Ca2+-sensor proteins with multiple C2 domains.
  Proc Natl Acad Sci U S A, 104, 3823-3828.  
17058190 A.Poopatanapong, I.Teramitsu, J.S.Byun, L.J.Vician, H.R.Herschman, and S.A.White (2006).
Singing, but not seizure, induces synaptotagmin IV in zebra finch song circuit nuclei.
  J Neurobiol, 66, 1613-1629.  
16774926 D.A.Nicoll, M.R.Sawaya, S.Kwon, D.Cascio, K.D.Philipson, and J.Abramson (2006).
The crystal structure of the primary Ca2+ sensor of the Na+/Ca2+ exchanger reveals a novel Ca2+ binding motif.
  J Biol Chem, 281, 21577-21581.
PDB code: 2dpk
16618809 M.Ahras, G.P.Otto, and S.A.Tooze (2006).
Synaptotagmin IV is necessary for the maturation of secretory granules in PC12 cells.
  J Cell Biol, 173, 241-251.  
17006898 V.Montana, E.B.Malarkey, C.Verderio, M.Matteoli, and V.Parpura (2006).
Vesicular transmitter release from astrocytes.
  Glia, 54, 700-715.  
15528213 O.H.Shin, W.Han, Y.Wang, and T.C.Südhof (2005).
Evolutionarily conserved multiple C2 domain proteins with two transmembrane regions (MCTPs) and unusual Ca2+ binding properties.
  J Biol Chem, 280, 1641-1651.  
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 code is shown on the right.