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PDBsum entry 1cm4

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protein metals Protein-protein interface(s) links
Calcium-binding/transferase PDB id
1cm4
Jmol
Contents
Protein chains
143 a.a. *
18 a.a. *
Metals
_CA ×17
Waters ×58
* Residue conservation analysis
PDB id:
1cm4
Name: Calcium-binding/transferase
Title: Motions of calmodulin-four-conformer refinement
Structure: Calmodulin. Chain: a. Calmodulin-dependent protein kinase ii-alpha. Chain: b. Fragment: calmodulin binding domain, residues 290 - 314. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: brain. Other_details: sigma lot 54h9558. Synthetic: yes
Biol. unit: Not given
Resolution:
2.00Å     R-factor:   0.166     R-free:   0.262
Authors: M.E.Wall,G.N.Phillips Jr.
Key ref:
M.E.Wall et al. (1997). Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. Structure, 5, 1599-1612. PubMed id: 9438860 DOI: 10.1016/S0969-2126(97)00308-0
Date:
23-Sep-97     Release date:   04-Mar-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62157  (CALM_BOVIN) -  Calmodulin
Seq:
Struc:
149 a.a.
143 a.a.
Protein chain
Pfam   ArchSchema ?
P11275  (KCC2A_RAT) -  Calcium/calmodulin-dependent protein kinase type II subunit alpha
Seq:
Struc:
478 a.a.
18 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain B: E.C.2.7.11.17  - Calcium/calmodulin-dependent protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
= ADP
+ phosphoprotein
      Cofactor: Ca(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   9 terms 
  Biological process     regulation of cytokinesis   12 terms 
  Biochemical function     ion channel binding     10 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(97)00308-0 Structure 5:1599-1612 (1997)
PubMed id: 9438860  
 
 
Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering.
M.E.Wall, J.B.Clarage, G.N.Phillips.
 
  ABSTRACT  
 
BACKGROUND: Calmodulin is a calcium-activated regulatory protein which can bind to many different targets. The protein resembles a highly flexible dumbbell, and bends in the middle as it binds. This and other motions must be understood to formulate a realistic model of calmodulin function. RESULTS: Using the Bragg reflections from X-ray crystallography, a multiple-conformer refinement of a calmodulin-peptide complex shows anisotropic displacements, with high variations of dihedral angles in several nonhelical domains: the flexible linker; three of the four calcium-binding sites (including both of the N-terminal sites); and a turn connecting the C-terminal EF-hand calcium-binding domains. Three-dimensional maps of the large scale diffuse X-ray scattering data show isotropic liquid-like motions with an unusually small correlation length. Three-dimensional maps of the small scale diffuse streaks show highly coupled, anisotropic motions along the head-to-tail molecular packing direction in the unit cell. There is also weak coupling perpendicular to the head-to-tail packing direction, particularly across a cavity occupied by the disordered linker domain of the molecule. CONCLUSIONS: Together, the Bragg and diffuse scattering present a self-consistent description of the motions in the flexible linker of calmodulin. The other mobile regions of the protein are also of great interest. In particular, the high variations in the calcium-binding sites are likely to influence how strongly they bind ions. This is especially important in the N-terminal sites, which regulate the activity of the molecule.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Dynamics in calmodulin binding. The linker of calmodulin (white) bends as the ends of the protein engulf the target (red stick model); there are also significant motions within the globular ends. Experiments to characterize these motions are necessary to understand how calmodulin works (see text for details). Within the globular ends, helices are shown in cyan, b strands in green and loops in orange; Ca^2+ ions are depicted as white spheres. (The figure was made using the program RIBBONS [41].)
 
  The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 1599-1612) copyright 1997.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21156208 J.Snijder, R.J.Rose, R.Raijmakers, and A.J.Heck (2011).
Site-specific methionine oxidation in calmodulin affects structural integrity and interaction with Ca2+/calmodulin-dependent protein kinase II.
  J Struct Biol, 174, 187-195.  
20544963 M.D.Feldkamp, S.E.O'Donnell, L.Yu, and M.A.Shea (2010).
Allosteric effects of the antipsychotic drug trifluoperazine on the energetics of calcium binding by calmodulin.
  Proteins, 78, 2265-2282.  
19998355 Y.Zhang, H.Tan, G.Chen, and Z.Jia (2010).
Investigating the disorder-order transition of calmodulin binding domain upon binding calmodulin using molecular dynamics simulation.
  J Mol Recognit, 23, 360-368.  
19395800 P.Kraft, A.Bergamaschi, C.h.Broennimann, R.Dinapoli, E.F.Eikenberry, B.Henrich, I.Johnson, A.Mozzanica, C.M.Schlepütz, P.R.Willmott, and B.Schmitt (2009).
Performance of single-photon-counting PILATUS detector modules.
  J Synchrotron Radiat, 16, 368-375.  
19583261 S.J.Abraham, R.P.Nolet, R.J.Calvert, L.M.Anderson, and V.Gaponenko (2009).
The hypervariable region of K-Ras4B is responsible for its specific interactions with calmodulin.
  Biochemistry, 48, 7575-7583.  
18089570 A.Scheschonka, S.Findlow, R.Schemm, O.El Far, J.H.Caldwell, M.P.Crump, K.Holden-Dye, V.O'Connor, H.Betz, and J.M.Werner (2008).
Structural determinants of calmodulin binding to the intracellular C-terminal domain of the metabotropic glutamate receptor 7A.
  J Biol Chem, 283, 5577-5588.  
18078545 C.D.Putnam, M.Hammel, G.L.Hura, and J.A.Tainer (2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
  Q Rev Biophys, 40, 191-285.  
17850744 E.J.Levin, D.A.Kondrashov, G.E.Wesenberg, and G.N.Phillips (2007).
Ensemble refinement of protein crystal structures: validation and application.
  Structure, 15, 1040-1052.
PDB codes: 2q3m 2q3o 2q3p 2q3q 2q3r 2q3s 2q3t 2q3u 2q3v 2q3w 2q40 2q41 2q42 2q43 2q44 2q45 2q46 2q47 2q48 2q49 2q4a 2q4b 2q4c 2q4d 2q4e 2q4f 2q4h 2q4i 2q4j 2q4k 2q4l 2q4m 2q4n 2q4o 2q4p 2q4q 2q4r 2q4s 2q4t 2q4u 2q4v 2q4x 2q4y 2q4z 2q50 2q51 2q52
17154425 L.Meinhold, and J.C.Smith (2007).
Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns.
  Proteins, 66, 941-953.  
16721661 K.Chen, J.Ruan, and L.A.Kurgan (2006).
Prediction of three dimensional structure of calmodulin.
  Protein J, 25, 57-70.  
16493654 P.Radivojac, S.Vucetic, T.R.O'Connor, V.N.Uversky, Z.Obradovic, and A.K.Dunker (2006).
Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition.
  Proteins, 63, 398-410.  
15822100 D.Ming, and M.E.Wall (2005).
Quantifying allosteric effects in proteins.
  Proteins, 59, 697-707.  
15596444 I.Horváth, V.Harmat, A.Perczel, V.Pálfi, L.Nyitray, A.Nagy, E.Hlavanda, G.Náray-Szabó, and J.Ovádi (2005).
The structure of the complex of calmodulin with KAR-2: a novel mode of binding explains the unique pharmacology of the drug.
  J Biol Chem, 280, 8266-8274.
PDB code: 1xa5
15817398 O.Carugo, and K.Djinović Carugo (2005).
When X-rays modify the protein structure: radiation damage at work.
  Trends Biochem Sci, 30, 213-219.  
14501118 M.A.Wilson, and A.T.Brunger (2003).
Domain flexibility in the 1.75 A resolution structure of Pb2+-calmodulin.
  Acta Crystallogr D Biol Crystallogr, 59, 1782-1792.
PDB code: 1n0y
12542690 S.W.Vetter, and E.Leclerc (2003).
Novel aspects of calmodulin target recognition and activation.
  Eur J Biochem, 270, 404-414.  
11340055 A.G.Palmer (2001).
Nmr probes of molecular dynamics: overview and comparison with other techniques.
  Annu Rev Biophys Biomol Struct, 30, 129-155.  
11031286 M.E.Wall, S.C.Gallagher, and J.Trewhella (2000).
Large-scale shape changes in proteins and macromolecular complexes.
  Annu Rev Phys Chem, 51, 355-380.  
  10631988 M.E.Wall, S.Subramaniam, and G.N.Phillips (1999).
Protein structure determination using a database of interatomic distance probabilities.
  Protein Sci, 8, 2720-2727.  
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.