spacer
spacer

PDBsum entry 1f71
Go to PDB code: 
protein links
Transport protein PDB id
1f71

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
67 a.a. *
* Residue conservation analysis
PDB id:
1f71
Name: Transport protein
Title: Refined solution structure of calmodulin c-terminal domain
Structure: Calmodulin. Chain: a. Fragment: c-terminal domain. Engineered: yes
Source: Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 10 models
Authors: J.Chou,S.Li,A.Bax
Key ref: J.J.Chou et al. (2000). Study of conformational rearrangement and refinement of structural homology models by the use of heteronuclear dipolar couplings. J Biomol Nmr, 18, 217-227. PubMed id: 11142512
Date:
24-Jun-00     Release date:   22-Sep-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0DP33  (CALM1_XENLA) -  Calmodulin-1 from Xenopus laevis
Seq:
Struc: 		149 a.a.
67 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
J Biomol Nmr 18:217-227 (2000)
PubMed id: 11142512  
 
 
Study of conformational rearrangement and refinement of structural homology models by the use of heteronuclear dipolar couplings.
J.J.Chou, S.Li, A.Bax.
 
  ABSTRACT  
 
For an increasing fraction of proteins whose structures are being studied, sequence homology to known structures permits building of low resolution structural models. It is demonstrated that dipolar couplings, measured in a liquid crystalline medium, not only can validate such structural models, but also refine them. Here, experimental 1H-15N, 1Halpha-13Calpha, and 13C'-13Calpha dipolar couplings are shown to decrease the backbone rmsd between various homology models of calmodulin (CaM) and its crystal structure. Starting from a model of the Ca2+-saturated C-terminal domain of CaM, built from the structure of Ca2+-free recoverin on the basis of remote sequence homology, dipolar couplings are used to decrease the rmsd between the model and the crystal structure from 5.0 to 1.25 A. A better starting model, built from the crystal structure of Ca2+-saturated parvalbumin, decreases in rmsd from 1.25 to 0.93 A. Similarly, starting from the structure of the Ca2+-ligated CaM N-terminal domain, experimental dipolar couplings measured for the Ca2+-free form decrease the backbone rmsd relative to the refined solution structure of apo-CaM from 4.2 to 1.0 A.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21360154 J.L.Gifford, H.Ishida, and H.J.Vogel (2011).
Fast methionine-based solution structure determination of calcium-calmodulin complexes.
  J Biomol NMR, 50, 71-81.
PDB code: 2l7l
  20054830 H.Huang, H.Ishida, and H.J.Vogel (2010).
The solution structure of the Mg2+ form of soybean calmodulin isoform 4 reveals unique features of plant calmodulins in resting cells.
  Protein Sci, 19, 475-485.
PDB code: 2ksz
19023665 G.Verdone, A.Corazza, S.A.Colebrooke, D.Cicero, T.Eliseo, J.Boyd, R.Doliana, F.Fogolari, P.Viglino, A.Colombatti, I.D.Campbell, and G.Esposito (2009).
NMR-based homology model for the solution structure of the C-terminal globular domain of EMILIN1.
  J Biomol NMR, 43, 79-96.
PDB code: 2ka3
  19918063 W.K.Erbil, M.S.Price, D.E.Wemmer, and M.A.Marletta (2009).
A structural basis for H-NOX signaling in Shewanella oneidensis by trapping a histidine kinase inhibitory conformation.
  Proc Natl Acad Sci U S A, 106, 19753-19760.
PDB codes: 2kii 2kil
18463100 G.Verdone, R.Doliana, A.Corazza, S.A.Colebrooke, P.Spessotto, S.Bot, F.Bucciotti, A.Capuano, A.Silvestri, P.Viglino, I.D.Campbell, A.Colombatti, and G.Esposito (2008).
The solution structure of EMILIN1 globular C1q domain reveals a disordered insertion necessary for interaction with the alpha4beta1 integrin.
  J Biol Chem, 283, 18947-18956.  
18477568 H.Ishida, M.A.Borman, J.Ostrander, H.J.Vogel, and J.A.MacDonald (2008).
Solution structure of the calponin homology (CH) domain from the smoothelin-like 1 protein: a unique apocalmodulin-binding mode and the possible role of the C-terminal type-2 CH-domain in smooth muscle relaxation.
  J Biol Chem, 283, 20569-20578.
PDB codes: 2jv9 2k3s
18701719 P.Vallurupalli, D.F.Hansen, and L.E.Kay (2008).
Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy.
  Proc Natl Acad Sci U S A, 105, 11766-11771.
PDB code: 2k3b
18293296 T.Rathinavelan, and W.Im (2008).
A novel strategy to determine protein structures using exclusively residual dipolar coupling.
  J Comput Chem, 29, 1640-1649.  
18098352 C.M.Franzin, P.Teriete, and F.M.Marassi (2007).
Membrane orientation of the Na,K-ATPase regulatory membrane protein CHIF determined by solid-state NMR.
  Magn Reson Chem, 45, S192-S197.  
17074768 M.Pennestri, S.Melino, G.M.Contessa, E.C.Casavola, M.Paci, A.Ragnini-Wilson, and D.O.Cicero (2007).
Structural basis for the interaction of the myosin light chain Mlc1p with the myosin V Myo2p IQ motifs.
  J Biol Chem, 282, 667-679.
PDB codes: 2fcd 2fce
17511473 P.Teriete, C.M.Franzin, J.Choi, and F.M.Marassi (2007).
Structure of the Na,K-ATPase regulatory protein FXYD1 in micelles.
  Biochemistry, 46, 6774-6783.
PDB code: 2jo1
17299131 S.Niranjanakumari, J.J.Day-Storms, M.Ahmed, J.Hsieh, N.H.Zahler, R.A.Venters, and C.A.Fierke (2007).
Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage.
  RNA, 13, 521-535.  
16416140 F.Gabel, B.Simon, and M.Sattler (2006).
A target function for quaternary structural refinement from small angle scattering and NMR orientational restraints.
  Eur Biophys J, 35, 313-327.  
16927360 K.L.Mayer, Y.Qu, S.Bansal, P.D.LeBlond, F.E.Jenney, P.S.Brereton, M.W.Adams, Y.Xu, and J.H.Prestegard (2006).
Structure determination of a new protein from backbone-centered NMR data and NMR-assisted structure prediction.
  Proteins, 65, 480-489.
PDB code: 2f40
17093048 K.Makabe, D.McElheny, V.Tereshko, A.Hilyard, G.Gawlak, S.Yan, A.Koide, and S.Koide (2006).
Atomic structures of peptide self-assembly mimics.
  Proc Natl Acad Sci U S A, 103, 17753-17758.
PDB codes: 2af5 2fkg 2fkj 2hkd
16765893 R.R.Wei, J.R.Schnell, N.A.Larsen, P.K.Sorger, J.J.Chou, and S.C.Harrison (2006).
Structure of a central component of the yeast kinetochore: the Spc24p/Spc25p globular domain.
  Structure, 14, 1003-1009.
PDB code: 2fv4
16436213 X.Zhou, J.Chou, and S.T.Wong (2006).
Protein structure similarity from Principle Component Correlation analysis.
  BMC Bioinformatics, 7, 40.  
16043636 C.J.Park, J.H.Lee, and B.S.Choi (2005).
Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen.
  Nucleic Acids Res, 33, 4172-4181.
PDB code: 1ynx
16251268 H.Gong, P.J.Fleming, and G.D.Rose (2005).
Building native protein conformation from highly approximate backbone torsion angles.
  Proc Natl Acad Sci U S A, 102, 16227-16232.  
16131665 J.R.Schnell, G.P.Zhou, M.Zweckstetter, A.C.Rigby, and J.J.Chou (2005).
Rapid and accurate structure determination of coiled-coil domains using NMR dipolar couplings: application to cGMP-dependent protein kinase Ialpha.
  Protein Sci, 14, 2421-2428.
PDB code: 1zxa
16043693 K.Oxenoid, and J.J.Chou (2005).
The structure of phospholamban pentamer reveals a channel-like architecture in membranes.
  Proc Natl Acad Sci U S A, 102, 10870-10875.
PDB code: 1zll
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
15285893 C.J.Langmead, A.Yan, R.Lilien, L.Wang, and B.R.Donald (2004).
A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments.
  J Comput Biol, 11, 277-298.  
15630565 J.Song, Q.Zhao, S.Thao, R.O.Frederick, and J.L.Markley (2004).
Solution structure of a calmodulin-like calcium-binding domain from Arabidopsis thaliana.
  J Biomol NMR, 30, 451-456.
PDB code: 1tiz
15308674 R.D.Seidel, J.C.Amor, R.A.Kahn, and J.H.Prestegard (2004).
Conformational changes in human Arf1 on nucleotide exchange and deletion of membrane-binding elements.
  J Biol Chem, 279, 48307-48318.
PDB code: 1u81
12493823 A.Bax (2003).
Weak alignment offers new NMR opportunities to study protein structure and dynamics.
  Protein Sci, 12, 1.  
14648765 T.Haliloglu, A.Kolinski, and J.Skolnick (2003).
Use of residual dipolar couplings as restraints in ab initio protein structure prediction.
  Biopolymers, 70, 548-562.  
11972012 E.Oldfield (2002).
Chemical shifts in amino acids, peptides, and proteins: from quantum chemistry to drug design.
  Annu Rev Phys Chem, 53, 349-378.  
11959490 G.M.Clore, and C.D.Schwieters (2002).
Theoretical and computational advances in biomolecular NMR spectroscopy.
  Curr Opin Struct Biol, 12, 146-153.  
11685248 J.J.Chou, S.Li, C.B.Klee, and A.Bax (2001).
Solution structure of Ca(2+)-calmodulin reveals flexible hand-like properties of its domains.
  Nat Struct Biol, 8, 990-997.
PDB codes: 1j7o 1j7p
11785752 J.R.Tolman (2001).
Dipolar couplings as a probe of molecular dynamics and structure in solution.
  Curr Opin Struct Biol, 11, 532-539.  
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.

 

spacer
spacer