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PDBsum entry 1c9h

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Immune system PDB id
1c9h
Jmol
Contents
Protein chain
107 a.a. *
Ligands
RAP
Waters ×101
* Residue conservation analysis
PDB id:
1c9h
Name: Immune system
Title: Crystal structure of fkbp12.6 in complex with rapamycin
Structure: Fkbp12.6. Chain: a. Fragment: fkbp12.6. Synonym: calcineurin. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: brain. Gene: cdna. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.205     R-free:   0.249
Authors: C.C.S.Deivanayagam,M.Carson,A.Thotakura,S.V.L.Narayana, C.S.Chodavarapu
Key ref:
C.C.Deivanayagam et al. (2000). Structure of FKBP12.6 in complex with rapamycin. Acta Crystallogr D Biol Crystallogr, 56, 266-271. PubMed id: 10713512 DOI: 10.1107/S0907444999016571
Date:
02-Aug-99     Release date:   03-Aug-00    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P68106  (FKB1B_HUMAN) -  Peptidyl-prolyl cis-trans isomerase FKBP1B
Seq:
Struc:
108 a.a.
107 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.2.1.8  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   8 terms 
  Biological process     calcium-mediated signaling using intracellular calcium source   35 terms 
  Biochemical function     ion channel binding     9 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444999016571 Acta Crystallogr D Biol Crystallogr 56:266-271 (2000)
PubMed id: 10713512  
 
 
Structure of FKBP12.6 in complex with rapamycin.
C.C.Deivanayagam, M.Carson, A.Thotakura, S.V.Narayana, R.S.Chodavarapu.
 
  ABSTRACT  
 
FKBP12.6 is a novel isoform of FKBP12, which selectively binds to the cardiac ryanodine receptor (RyR2). The crystal structure of FKBP12.6 in complex with rapamycin has now been determined at 2.0 A resolution. The structures of FKBP12.6 and FKBP12 are nearly identical, except for a displacement observed in the helical region of FKBP12.6 toward the hydrophobic pocket. This displacement was not predicted by homology modeling studies. Analyses of the residues that are likely to confer the RyR2-binding specificity are presented.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Stereo diagrams of the protein surfaces of rapamycin complexes of FKBP12.6 and FKBP12. The rapamycin is shown in ball-and-stick format, colored white, red and blue for carbon, oxygen and nitrogen, respectively. The protein surfaces are colored by chemical property: white is hydrophobic, red is negatively charged, blue is positively charged, orange is a hydrogen-bond acceptor, cyan is a hydrogen-bond donor and magenta can both accept and donate hydrogen bonds. Exposed surfaces of non-identical residues are textured with a mesh and labeled. The orientation is as in Fig. 1-(b), only 90% smaller. Above, FKBP12.6; below, FKBP12.
Figure 4.
Figure 4 Stereo diagrams of the hydrophobic binding pockets of FKBP12.6 and FKBP12. All residues and surfaces within 4 of rapamycin are shown. Ribbons and carbon are white in FKBP12.6 and gray in FKBP12. O atoms and N atoms are red and blue, respectively, in both. Hydrogen bonds are shown as dashed black lines.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 266-271) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20934451 D.W.Song, J.G.Lee, H.S.Youn, S.H.Eom, and d.o. .H.Kim (2011).
Ryanodine receptor assembly: A novel systems biology approach to 3D mapping.
  Prog Biophys Mol Biol, 105, 145-161.  
19277847 J.S.Woo, J.H.Hwang, J.K.Ko, d.o. .H.Kim, J.Ma, and E.H.Lee (2009).
Glutamate at position 227 of junctophilin-2 is involved in binding to TRPC3.
  Mol Cell Biochem, 328, 25-32.  
16481613 F.Huang, J.Shan, S.Reiken, X.H.Wehrens, and A.R.Marks (2006).
Analysis of calstabin2 (FKBP12.6)-ryanodine receptor interactions: rescue of heart failure by calstabin2 in mice.
  Proc Natl Acad Sci U S A, 103, 3456-3461.  
16214874 M.R.Sharma, L.H.Jeyakumar, S.Fleischer, and T.Wagenknecht (2006).
Three-dimensional visualization of FKBP12.6 binding to an open conformation of cardiac ryanodine receptor.
  Biophys J, 90, 164-172.  
15033987 E.H.Lee, S.H.Rho, S.J.Kwon, S.H.Eom, P.D.Allen, and d.o. .H.Kim (2004).
N-terminal region of FKBP12 is essential for binding to the skeletal ryanodine receptor.
  J Biol Chem, 279, 26481-26488.  
11751578 P.J.Pereira, M.C.Vega, E.González-Rey, R.Fernández-Carazo, S.Macedo-Ribeiro, F.X.Gomis-Rüth, A.González, and M.Coll (2002).
Trypanosoma cruzi macrophage infectivity potentiator has a rotamase core and a highly exposed alpha-helix.
  EMBO Rep, 3, 88-94.
PDB code: 1jvw
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