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PDBsum entry 1b4c
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Metal binding protein PDB id
1b4c

 

 

 

 

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Contents
Protein chains
92 a.a. *
* Residue conservation analysis
PDB id:
1b4c
Name: Metal binding protein
Title: Solution structure of rat apo-s100b using dipolar couplings
Structure: Protein (s-100 protein, beta chain). Chain: a, b. Synonym: s100b, s100beta. Engineered: yes. Other_details: s100b is a homodimer of s100beta subunits
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: s100beta from rattus norvegicus (rat). Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: see main reference
NMR struc: 21 models
Authors: D.J.Weber,A.C.Drohat,N.Tjandra,D.M.Baldisseri
Key ref: A.C.Drohat et al. (1999). The use of dipolar couplings for determining the solution structure of rat apo-S100B(betabeta). Protein Sci, 8, 800-809. PubMed id: 10211826 DOI: 10.1110/ps.8.4.800
Date:
17-Dec-98     Release date:   30-Dec-98    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04631  (S100B_RAT) -  Protein S100-B from Rattus norvegicus
Seq:
Struc: 		92 a.a.
92 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1110/ps.8.4.800 Protein Sci 8:800-809 (1999)
PubMed id: 10211826  
 
 
The use of dipolar couplings for determining the solution structure of rat apo-S100B(betabeta).
A.C.Drohat, N.Tjandra, D.M.Baldisseri, D.J.Weber.
 
  ABSTRACT  
 
The relative orientations of adjacent structural elements without many well-defined NOE contacts between them are typically poorly defined in NMR structures. For apo-S100B(betabeta) and the structurally homologous protein calcyclin, the solution structures determined by conventional NMR exhibited considerable differences and made it impossible to draw unambiguous conclusions regarding the Ca2+-induced conformational change required for target protein binding. The structure of rat apo-S100B(betabeta) was recalculated using a large number of constraints derived from dipolar couplings that were measured in a dilute liquid crystalline phase. The dipolar couplings orient bond vectors relative to a single-axis system, and thereby remove much of the uncertainty in NOE-based structures. The structure of apo-S100B(betabeta) indicates a minimal change in the first, pseudo-EF-hand Ca2+ binding site, but a large reorientation of helix 3 in the second, classical EF-hand upon Ca2+ binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20827422 D.B.Zimmer, and D.J.Weber (2010).
The Calcium-Dependent Interaction of S100B with Its Protein Targets.
  Cardiovasc Psychiatry Neurol, 2010, 0.  
20053360 T.H.Charpentier, L.E.Thompson, M.A.Liriano, K.M.Varney, P.T.Wilder, E.Pozharski, E.A.Toth, and D.J.Weber (2010).
The effects of CapZ peptide (TRTK-12) binding to S100B-Ca2+ as examined by NMR and X-ray crystallography.
  J Mol Biol, 396, 1227-1243.
PDB codes: 3iqo 3iqq
19700353 K.Berlin, D.P.O'Leary, and D.Fushman (2009).
Improvement and analysis of computational methods for prediction of residual dipolar couplings.
  J Magn Reson, 201, 25-33.  
18795951 A.C.Rintala-Dempsey, A.Rezvanpour, and G.S.Shaw (2008).
S100-annexin complexes--structural insights.
  FEBS J, 275, 4956-4966.  
18037438 D.Rifat, N.T.Wright, K.M.Varney, D.J.Weber, and L.W.Black (2008).
Restriction endonuclease inhibitor IPI* of bacteriophage T4: a novel structure for a dedicated target.
  J Mol Biol, 375, 720-734.
PDB code: 2jub
18650434 N.T.Wright, B.L.Prosser, K.M.Varney, D.B.Zimmer, M.F.Schneider, and D.J.Weber (2008).
S100A1 and calmodulin compete for the same binding site on ryanodine receptor.
  J Biol Chem, 283, 26676-26683.
PDB code: 2k2f
18949447 N.T.Wright, K.G.Inman, J.A.Levine, B.R.Cannon, K.M.Varney, and D.J.Weber (2008).
Refinement of the solution structure and dynamic properties of Ca(2+)-bound rat S100B.
  J Biomol NMR, 42, 279-286.
PDB code: 2k7o
18384084 S.Malik, M.Revington, S.P.Smith, and G.S.Shaw (2008).
Analysis of the structure of human apo-S100B at low temperature indicates a unimodal conformational distribution is adopted by calcium-free S100 proteins.
  Proteins, 73, 28-42.
PDB code: 2pru
17180551 C.Eichmüller, and N.R.Skrynnikov (2007).
Observation of microsecond time-scale protein dynamics in the presence of Ln3+ ions: application to the N-terminal domain of cardiac troponin C.
  J Biomol NMR, 37, 79-95.  
17986189 J.J.Velarde, K.M.Varney, K.G.Inman, M.Farfan, E.Dudley, J.Fletcher, D.J.Weber, and J.P.Nataro (2007).
Solution structure of the novel dispersin protein of enteroaggregative Escherichia coli.
  Mol Microbiol, 66, 1123-1135.
PDB code: 2jvu
17660747 T.Ostendorp, E.Leclerc, A.Galichet, M.Koch, N.Demling, B.Weigle, C.W.Heizmann, P.M.Kroneck, and G.Fritz (2007).
Structural and functional insights into RAGE activation by multimeric S100B.
  EMBO J, 26, 3868-3878.
PDB code: 2h61
15937283 D.V.Venkitaramani, D.B.Fulton, A.H.Andreotti, K.M.Johansen, and J.Johansen (2005).
Solution structure and backbone dynamics of Calsensin, an invertebrate neuronal calcium-binding protein.
  Protein Sci, 14, 1894-1901.
PDB codes: 1yx7 1yx8
16258827 K.Simon, J.Xu, C.Kim, and N.R.Skrynnikov (2005).
Estimating the accuracy of protein structures using residual dipolar couplings.
  J Biomol NMR, 33, 83-93.  
16222559 N.T.Wright, J.W.Margolis, F.L.Margolis, and D.J.Weber (2005).
Refinement of the solution structure of rat olfactory marker protein (OMP).
  J Biomol NMR, 33, 63-68.
PDB code: 1zri
16260758 Z.Wu, F.Delaglio, K.Wyatt, G.Wistow, and A.Bax (2005).
Solution structure of (gamma)S-crystallin by molecular fragment replacement NMR.
  Protein Sci, 14, 3101-3114.
PDB codes: 1zwm 1zwo
15139819 R.S.Lipsitz, and N.Tjandra (2004).
Residual dipolar couplings in NMR structure analysis.
  Annu Rev Biophys Biomol Struct, 33, 387-413.  
14744980 Y.Qu, J.T.Guo, V.Olman, and Y.Xu (2004).
Protein structure prediction using sparse dipolar coupling data.
  Nucleic Acids Res, 32, 551-561.  
12493823 A.Bax (2003).
Weak alignment offers new NMR opportunities to study protein structure and dynamics.
  Protein Sci, 12, 1.  
12645003 D.B.Zimmer, P.Wright Sadosky, and D.J.Weber (2003).
Molecular mechanisms of S100-target protein interactions.
  Microsc Res Tech, 60, 552-559.  
12645004 J.C.Deloulme, B.J.Gentil, and J.Baudier (2003).
Monitoring of S100 homodimerization and heterodimeric interactions by the yeast two-hybrid system.
  Microsc Res Tech, 60, 560-568.  
14668443 J.Meiler, and D.Baker (2003).
Rapid protein fold determination using unassigned NMR data.
  Proc Natl Acad Sci U S A, 100, 15404-15409.  
12493841 M.Palczewska, P.Groves, G.Batta, B.Heise, and J.Kuźnicki (2003).
Calretinin and calbindin D28k have different domain organizations.
  Protein Sci, 12, 180-184.  
12136135 P.R.Mittl, G.Fritz, D.F.Sargent, T.J.Richmond, C.W.Heizmann, and M.G.Grütter (2002).
Metal-free MIRAS phasing: structure of apo-S100A3.
  Acta Crystallogr D Biol Crystallogr, 58, 1255-1261.
PDB code: 1kso
11297409 K.G.Inman, D.M.Baldisseri, K.E.Miller, and D.J.Weber (2001).
Backbone dynamics of the calcium-signaling protein apo-S100B as determined by 15N NMR relaxation.
  Biochemistry, 40, 3439-3448.  
  11152126 B.E.Ramirez, O.N.Voloshin, R.D.Camerini-Otero, and A.Bax (2000).
Solution structure of DinI provides insight into its mode of RecA inactivation.
  Protein Sci, 9, 2161-2169.
PDB codes: 1f0a 1ghh
10591109 K.L.Yap, J.B.Ames, M.B.Swindells, and M.Ikura (1999).
Diversity of conformational states and changes within the EF-hand protein superfamily.
  Proteins, 37, 499-507.  
  10493575 R.R.Rustandi, D.M.Baldisseri, A.C.Drohat, and D.J.Weber (1999).
Structural changes in the C-terminus of Ca2+-bound rat S100B (beta beta) upon binding to a peptide derived from the C-terminal regulatory domain of p53.
  Protein Sci, 8, 1743-1751.  
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.

 

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