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PDBsum entry 1dro

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protein links
Cytoskeleton PDB id
1dro
Jmol
Contents
Protein chain
122 a.a. *
* Residue conservation analysis
PDB id:
1dro
Name: Cytoskeleton
Title: Nmr structure of the cytoskeleton/signal transduction protein
Structure: Beta-spectrin. Chain: a. Fragment: pleckstrin homology domain. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Organ: fruit. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: expression vector used was pgex-2t
NMR struc: 15 models
Authors: P.Zhang,S.Talluri,H.Deng,D.Branton,G.Wagner
Key ref:
P.Zhang et al. (1995). Solution structure of the pleckstrin homology domain of Drosophila beta-spectrin. Structure, 3, 1185-1195. PubMed id: 8591029 DOI: 10.1016/S0969-2126(01)00254-4
Date:
29-Sep-95     Release date:   03-Apr-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q00963  (SPTCB_DROME) -  Spectrin beta chain
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2291 a.a.
122 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     phospholipid binding     1 term  

 

 
DOI no: 10.1016/S0969-2126(01)00254-4 Structure 3:1185-1195 (1995)
PubMed id: 8591029  
 
 
Solution structure of the pleckstrin homology domain of Drosophila beta-spectrin.
P.Zhang, S.Talluri, H.Deng, D.Branton, G.Wagner.
 
  ABSTRACT  
 
BACKGROUND: The pleckstrin homology (PH) domain, which is approximately 100 amino acids long, has been found in about 70 proteins involved in signal transduction and cytoskeletal function, a frequency comparable to SH2 (src homology 2) and SH3 domains. PH domains have been shown to bind the beta gamma-subunits of G-proteins and phosphatidylinositol 4,5-bisphosphate (PIP2). It is conceivable that the PH domain of beta-spectrin plays a part in the association of spectrin with the plasma membrane of cells. RESULTS: We have solved the solution structure of the 122-residue PH domain of Drosophila beta-spectrin. The overall fold consists of two antiparallel beta-sheets packing against each other at an angle of approximately 60 degrees to form a beta-sandwich, a two-turn alpha-helix unique to spectrin PH domains, and a four-turn C-terminal alpha-helix. One of the major insertions in beta-spectrin PH domains forms a long, basic surface loop and appears to undergo slow conformational exchange in solution. This loop shows big spectral changes upon addition of D-myo-inositol 1,4,5-trisphosphate (IP3). CONCLUSIONS: We propose that the groove at the outer surface of the second beta-sheet is an important site of association with other proteins. This site and the possible lipid-binding site can serve to localize the spectrin network under the plasma membrane. More generally, it has to be considered that the common fold observed for the PH domain structures solved so far does not necessarily mean that all PH domains have similar functions. In fact, the residues constituting potential binding sites for ligands or other proteins are only slightly conserved between different PH domains.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. A stereo view of the superposition of the 15 DspPH structures. At the top is the groove formed by the outer surface of the second β-sheet and the ill-defined β1/β2 loop and β5/β6 loop. At the right, at the open edge of the β-sandwich is the proposed PIP[2]-binding pocket. All backbone heavy atoms are shown. Figure 7. A stereo view of the superposition of the 15 DspPH structures. At the top is the groove formed by the outer surface of the second β-sheet and the ill-defined β1/β2 loop and β5/β6 loop. At the right, at the open edge of the β-sandwich is the proposed PIP[2]-binding pocket. All backbone heavy atoms are shown.
Figure 8.
Figure 8. Head-on view of the molecular surface of DspPH into the groove on the outer surface of the second β-sheet, color coded by electrostatic potential. The positive electrostatic potential is shown in blue, the negative in red, and the neutral in white. The β1/β2 loop is at the bottom, the β5/β6 loop is at the top, and in between is the groove at the outer surface of the second β-sheet. The figure was generated with the program GRASP [42]. Figure 8. Head-on view of the molecular surface of DspPH into the groove on the outer surface of the second β-sheet, color coded by electrostatic potential. The positive electrostatic potential is shown in blue, the negative in red, and the neutral in white. The β1/β2 loop is at the bottom, the β5/β6 loop is at the top, and in between is the groove at the outer surface of the second β-sheet. The figure was generated with the program GRASP [[3]42].
 
  The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 1185-1195) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20668894 A.J.Baines (2010).
The spectrin-ankyrin-4.1-adducin membrane skeleton: adapting eukaryotic cells to the demands of animal life.
  Protoplasma, 244, 99.  
  20457566 V.Bennett, and J.Healy (2009).
Membrane domains based on ankyrin and spectrin associated with cell-cell interactions.
  Cold Spring Harb Perspect Biol, 1, a003012.  
18287096 A.Das, C.Base, D.Manna, W.Cho, and R.R.Dubreuil (2008).
Unexpected complexity in the mechanisms that target assembly of the spectrin cytoskeleton.
  J Biol Chem, 283, 12643-12653.  
18675341 R.Luo, L.M.Miller Jenkins, P.A.Randazzo, and J.Gruschus (2008).
Dynamic interaction between Arf GAP and PH domains of ASAP1 in the regulation of GAP activity.
  Cell Signal, 20, 1968-1977.  
17339315 D.F.Ceccarelli, I.M.Blasutig, M.Goudreault, Z.Li, J.Ruston, T.Pawson, and F.Sicheri (2007).
Non-canonical interaction of phosphoinositides with pleckstrin homology domains of Tiam1 and ArhGAP9.
  J Biol Chem, 282, 13864-13874.
PDB codes: 2p0d 2p0f 2p0h
17060500 A.Das, C.Base, S.Dhulipala, and R.R.Dubreuil (2006).
Spectrin functions upstream of ankyrin in a spectrin cytoskeleton assembly pathway.
  J Cell Biol, 175, 325-335.  
15366709 P.A.Janmey, and U.Lindberg (2004).
Cytoskeletal regulation: rich in lipids.
  Nat Rev Mol Cell Biol, 5, 658-666.  
12885767 G.E.Cozier, D.Bouyoucef, and P.J.Cullen (2003).
Engineering the phosphoinositide-binding profile of a class I pleckstrin homology domain.
  J Biol Chem, 278, 39489-39496.  
10940243 J.H.Hurley, and S.Misra (2000).
Signaling and subcellular targeting by membrane-binding domains.
  Annu Rev Biophys Biomol Struct, 29, 49-79.  
11080629 N.Blomberg, E.Baraldi, M.Sattler, M.Saraste, and M.Nilges (2000).
Structure of a PH domain from the C. elegans muscle protein UNC-89 suggests a novel function.
  Structure, 8, 1079-1087.
PDB code: 1fho
11050430 T.Doerks, M.Strauss, M.Brendel, and P.Bork (2000).
GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins.
  Trends Biochem Sci, 25, 483-485.  
10591098 N.Blomberg, R.R.Gabdoulline, M.Nilges, and R.C.Wade (1999).
Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity.
  Proteins, 37, 379-387.  
9759500 J.A.Pitcher, N.J.Freedman, and R.J.Lefkowitz (1998).
G protein-coupled receptor kinases.
  Annu Rev Biochem, 67, 653-692.  
9838094 M.J.Bottomley, K.Salim, and G.Panayotou (1998).
Phospholipid-binding protein domains.
  Biochim Biophys Acta, 1436, 165-183.  
9646876 M.J.Rebecchi, and S.Scarlata (1998).
Pleckstrin homology domains: a common fold with diverse functions.
  Annu Rev Biophys Biomol Struct, 27, 503-528.  
9566119 D.C.Dalgarno, M.C.Botfield, and R.J.Rickles (1997).
SH3 domains and drug design: ligands, structure, and biological function.
  Biopolymers, 43, 383-400.  
8791400 A.Viel, and D.Branton (1996).
Spectrin: on the path from structure to function.
  Curr Opin Cell Biol, 8, 49-55.  
  8947047 K.Salim, M.J.Bottomley, E.Querfurth, M.J.Zvelebil, I.Gout, R.Scaife, R.L.Margolis, R.Gigg, C.I.Smith, P.C.Driscoll, M.D.Waterfield, and G.Panayotou (1996).
Distinct specificity in the recognition of phosphoinositides by the pleckstrin homology domains of dynamin and Bruton's tyrosine kinase.
  EMBO J, 15, 6241-6250.  
8599766 M.M.Zhou, B.Huang, E.T.Olejniczak, R.P.Meadows, S.B.Shuker, M.Miyazaki, T.Trüb, S.E.Shoelson, and S.W.Fesik (1996).
Structural basis for IL-4 receptor phosphopeptide recognition by the IRS-1 PTB domain.
  Nat Struct Biol, 3, 388-393.
PDB code: 1irs
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.