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Structural protein PDB id
1ag4
Jmol
Contents
Protein chain
103 a.a. *
* Residue conservation analysis
PDB id:
1ag4
Name: Structural protein
Title: Nmr structure of spherulin 3a (s3a) from physarum polycephalum, minimized average structure
Structure: Spherulin 3a. Chain: a. Synonym: s3a. Engineered: yes. Other_details: reduced form of s3a, with calcium
Source: Physarum polycephalum. Organism_taxid: 5791. Cellular_location: cytoplasm. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 1 models
Authors: B.Rosinke,C.Renner,E.-M.Mayr,R.Jaenicke,T.A.Holak
Key ref:
B.Rosinke et al. (1997). Ca2+-loaded spherulin 3a from Physarum polycephalum adopts the prototype gamma-crystallin fold in aqueous solution. J Mol Biol, 271, 645-655. PubMed id: 9281431 DOI: 10.1006/jmbi.1997.1184
Date:
01-Apr-97     Release date:   08-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09353  (SR3A_PHYPO) -  Spherulin-3A
Seq:
Struc: 		103 a.a.
103 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 

 

 
DOI no: 10.1006/jmbi.1997.1184 J Mol Biol 271:645-655 (1997)
PubMed id: 9281431  
 
 
Ca2+-loaded spherulin 3a from Physarum polycephalum adopts the prototype gamma-crystallin fold in aqueous solution.
B.Rosinke, C.Renner, E.M.Mayr, R.Jaenicke, T.A.Holak.
 
  ABSTRACT  
 
Spherulin 3a is the most abundantly expressed cytosolic protein in spherulating plasmodia of the slime mold Physarum polycephalum. High yields of unlabeled, uniformly 15N and uniformly 13C/15N-labeled recombinant spherulin 3a from Escherichia coli could be produced by a simple protocol described here. The three-dimensional solution structure of Ca2+-loaded spherulin 3a was determined by homo- and heteronuclear NMR spectroscopy. The structure of monomeric spherulin 3a consists of two pleated beta-sheets plus a short alpha-helix arranged into the gamma-crystallin fold. The beta-sheets comprise two intertwined Greek-key motifs. An additional N-terminal beta-strand is unique to spherulin 3a. Complexation of calcium ions greatly enhances overall conformational stability of the protein. The average atomic root-mean-square deviations (r.m.s.d.) for heavy atoms in beta-strands were 0.34(+/-0.16) A for the backbone atoms and 0.73(+/-0.40) A for all atoms. The corresponding r.m.s.d. values for heavy atoms in the whole protein were 0.62(+/-0.42) A for the backbone atoms and 0.99(+/-0.65) A for all atoms. We show the structural relationship between spherulin 3a, a myxomycete dormancy protein, and crystallins from the vertebrate eye lens. Since spherulin 3a has a structure corresponding to one domain of bovine gammaB(II)-crystallin, it represents a hypothetical ancestral gamma-crystallin precursor structure.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. The 3D structure of S3a. (a) Ribbon drawing of S3a with β-strands in blue and the mini α-helix in red. The two foldovers are colored pink. The Figure was created with the program MOLSCRIPT [Kraulis 1991]. (b) Stereo view of the backbone atoms (N, C^α, C and O) of the final ensemble of 20 S3a structures best fit to N, C^α and carbonyl atoms of the residues in the β-sheets. The Figure was created with the program WHATIF [Vriend 1991]. In (a) and (b) S3a is deliberately shown from different perspectives to convey as many structural details as possible. 		Figure 11.
Figure 11. A modified scheme of the putative evolution of the β, γ-crystallin superfamily (according to [Wistow 1990] and supplemented with our data).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 271, 645-655) copyright 1997.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17651443 M.K.Jobby, and Y.Sharma (2007).
Calcium-binding to lens betaB2- and betaA3-crystallins suggests that all beta-crystallins are calcium-binding proteins.
  FEBS J, 274, 4135-4147.  
  16511323 P.Aravind, B.Rajini, Y.Sharma, and R.Sankaranarayanan (2006).
Crystallization and preliminary X-ray crystallographic investigations on a betagamma-crystallin domain of absent in melanoma 1 (AIM1), a protein from Homo sapiens.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 282-284.  
15691335 C.Giancola, E.Pizzo, A.Di Maro, M.V.Cubellis, and G.D'Alessio (2005).
Preparation and characterization of geodin. A betagamma-crystallin-type protein from a sponge.
  FEBS J, 272, 1023-1035.  
15668020 C.Stephens, K.Kazan, K.C.Goulter, D.J.Maclean, and J.M.Manners (2005).
The mode of action of the plant antimicrobial peptide MiAMP1 differs from that of its structural homologue, the yeast killer toxin WmKT.
  FEMS Microbiol Lett, 243, 205-210.  
15700139 C.Stephens, S.J.Harrison, K.Kazan, F.W.Smith, K.C.Goulter, D.J.Maclean, and J.M.Manners (2005).
Altered fungal sensitivity to a plant antimicrobial peptide through over-expression of yeast cDNAs.
  Curr Genet, 47, 194-201.  
15536081 M.K.Jobby, and Y.Sharma (2005).
Calcium-binding crystallins from Yersinia pestis. Characterization of two single betagamma-crystallin domains of a putative exported protein.
  J Biol Chem, 280, 1209-1216.  
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
12084052 G.D'Alessio (2002).
The evolution of monomeric and oligomeric betagamma-type crystallins. Facts and hypotheses.
  Eur J Biochem, 269, 3122-3130.  
11502736 B.Rajini, P.Shridas, C.S.Sundari, D.Muralidhar, S.Chandani, F.Thomas, and Y.Sharma (2001).
Calcium binding properties of gamma-crystallin: calcium ion binds at the Greek key beta gamma-crystallin fold.
  J Biol Chem, 276, 38464-38471.  
10231565 C.W.Chan, Y.Saimi, and C.Kung (1999).
A new multigene family encoding calcium-dependent calmodulin-binding membrane proteins of Paramecium tetraurelia.
  Gene, 231, 21-32.  
10064142 M.Kretschmar, E.M.Mayr, and R.Jaenicke (1999).
Homo-dimeric spherulin 3a: a single-domain member of the beta gamma-crystallin superfamily.
  Biol Chem, 380, 89-94.  
9461075 S.Krapp, G.Kelly, J.Reischl, R.O.Weinzierl, and S.Matthews (1998).
Eukaryotic RNA polymerase subunit RPB8 is a new relative of the OB family.
  Nat Struct Biol, 5, 110-114.
PDB code: 1a1d
  9541393 S.Palme, R.Jaenicke, and C.Slingsby (1998).
X-ray structures of three interface mutants of gammaB-crystallin from bovine eye lens.
  Protein Sci, 7, 611-618.  
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.