PDBsum entry 1mzw

Go to PDB code: 
protein Protein-protein interface(s) links
Isomerase PDB id
Protein chains
173 a.a. *
31 a.a. *
Waters ×260
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of a u4/u6 snrnp complex between human spliceosomal cyclophilin h and a u4/u6-60k peptide
Structure: U-snrnp-associated cyclophilin. Chain: a. Synonym: cyclophilin h. Engineered: yes. U4/u6 snrnp 60kda protein. Chain: b. Fragment: residues 107-137, internal domain. Synonym: wd splicing factor prp4, hprp4, u4/u6 small nuclear ribonucleo protein prp4.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: peptide b106-b136 was chemically synthesized
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.195     R-free:   0.212
Authors: U.Reidt,M.C.Wahl,D.S.Horowitz,R.Luehrmann,R.Ficner
Key ref:
U.Reidt et al. (2003). Crystal structure of a complex between human spliceosomal cyclophilin H and a U4/U6 snRNP-60K peptide. J Mol Biol, 331, 45-56. PubMed id: 12875835 DOI: 10.1016/S0022-2836(03)00684-3
10-Oct-02     Release date:   19-Aug-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O43447  (PPIH_HUMAN) -  Peptidyl-prolyl cis-trans isomerase H
177 a.a.
173 a.a.
Protein chain
Pfam   ArchSchema ?
O43172  (PRP4_HUMAN) -  U4/U6 small nuclear ribonucleoprotein Prp4
522 a.a.
31 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.  - 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     U4/U6 snRNP   6 terms 
  Biological process     protein complex assembly   7 terms 
  Biochemical function     protein binding     5 terms  


    Added reference    
DOI no: 10.1016/S0022-2836(03)00684-3 J Mol Biol 331:45-56 (2003)
PubMed id: 12875835  
Crystal structure of a complex between human spliceosomal cyclophilin H and a U4/U6 snRNP-60K peptide.
U.Reidt, M.C.Wahl, D.Fasshauer, D.S.Horowitz, R.Lührmann, R.Ficner.
The spliceosomal cyclophilin H is a specific component of the human U4/U6 small nuclear ribonucleoprotein particle, interacting with homologous sequences in the proteins U4/U6-60K and hPrp18 during pre-mRNA splicing. We determined the crystal structure of the complex comprising cyclophilin H and the cognate domain of U4/U6-60K. The 31 amino acid fragment of U4/U6-60K is bound to a region remote from the cyclophilin active site. Residues Ile118-Phe121 of U4/U6-60K expand the central beta-sheet of cyclophilin H and the side-chain of Phe121 inserts into a hydrophobic cavity. Concomitantly, in the crystal the cyclophilin H active site is occupied by the N terminus of a neighboring cyclophilin H molecule in a substrate-like manner, indicating the capacity of joint binding to a substrate and to U4/U6-60K. Free and complexed cyclophilin H have virtually identical conformations suggesting that the U4/U6-60K binding site is pre-shaped and the peptidyl-prolyl-cis/trans isomerase activity is unaffected by complex formation. The complex defines a novel protein-protein interaction mode for a cyclophilin, allowing cyclophilin H to mediate interactions between different proteins inside the spliceosome or to initiate from its binding platforms isomerization or chaperoning activities.
  Selected figure(s)  
Figure 2.
Figure 2. Sequence alignments. (A) Alignment of human and other putative CypH sequences and human CypA. Residues identical across the groups are on a red background, conserved residues are on a yellow background. Residues, which are only identical within the group of CypH-like cyclophilins are on a blue background, those conserved only within a subgroup are on gray. Secondary structure elements as seen in the present structure are indicated below the alignment. Regions binding the U4/U6-60K peptide are marked with a cyan bar above the alignment. Magenta arrows above the alignment point out the active site residues Arg67 and His138, contacting the substrate-like peptide through water-mediated hydrogen bonds. His104, which upon mutation yields an inactive enzyme but does not seem to contact the substrate directly, is indicated with a green arrow. A region in which the CypH-class and human CypA show significant sequence diversity, but which is remote from either of the identified functional sites on CypH in three dimensions, is indicated with an orange bar above the sequences. The protein used in the present study (human CypH) is labeled in red. H. sapiens, Homo sapiens; M. muscullus, Mus muscullus; D. melanogaster, Drosophila melanogaster; C. elegans, Caenorhabditis elegans; A. thaliana, Arabidopsis thaliana. (B) Alignment of regions corresponding to the U4/U6-60K peptide from the present structure. The first group aligns the corresponding regions from U4/U6-60K proteins, the second group aligns the homologous regions from Prp18 proteins. Observed secondary structure elements are indicated below the alignment. Phe121, which is most critical for binding to CypH, is labeled with a black arrow above the alignment. Color-coding is as in (A). The Figure was prepared with Alscript.[38]
Figure 6.
Figure 6. Thermodynamics of the interaction of CypH and the U4/U6-60K peptide. Isothermal titration calorimetric analysis of the interaction of CypH (28.9 µM) with the U4/U6-60K peptide (900 µM) at 25 °C. Raw data were obtained over a series of injections of U4/U6-60K peptide and plotted as power (µcal/seconds) versus time (minutes). Upper panel: The negative peaks (black line) indicate an exothermic reaction with the peak area proportional to the heat released at each injection (red line: base line). Lower panel: Binding isotherms created by plotting the areas under the peaks in the upper panel against the molar ratio of the U4/U6-60K peptide injected to CypH. The best-fit line through the values was obtained by least-squares regression using a one-site model and yields the enthalpy (DH[a]), stoichiometry (n), and the equilibrium dissociation constant (K[d]). For the interaction of CypH with the U4/U6-60K peptide n=1.022, DH[a]= -17.08 kcal mol -1, and K[d]=1.97 µM.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 331, 45-56) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20602248 A.Galat, and J.Bua (2010).
Molecular aspects of cyclophilins mediating therapeutic actions of their ligands.
  Cell Mol Life Sci, 67, 3467-3488.  
20368803 C.M.Stegmann, R.Lührmann, and M.C.Wahl (2010).
The crystal structure of PPIL1 bound to cyclosporine A suggests a binding mode for a linear epitope of the SKIP protein.
  PLoS One, 5, e10013.
PDB code: 2x7k
20676357 T.L.Davis, J.R.Walker, V.Campagna-Slater, P.J.Finerty, R.Paramanathan, G.Bernstein, F.MacKenzie, W.Tempel, H.Ouyang, W.H.Lee, E.Z.Eisenmesser, and S.Dhe-Paganon (2010).
Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases.
  PLoS Biol, 8, e1000439.  
19239890 M.C.Wahl, C.L.Will, and R.Lührmann (2009).
The spliceosome: design principles of a dynamic RNP machine.
  Cell, 136, 701-718.  
18544344 A.Mesa, J.A.Somarelli, and R.J.Herrera (2008).
Spliceosomal immunophilins.
  FEBS Lett, 582, 2345-2351.  
19000813 J.Sperling, M.Azubel, and R.Sperling (2008).
Structure and function of the Pre-mRNA splicing machine.
  Structure, 16, 1605-1615.  
18397323 T.L.Davis, J.R.Walker, H.Ouyang, F.MacKenzie, C.Butler-Cole, E.M.Newman, E.Z.Eisenmesser, and S.Dhe-Paganon (2008).
The crystal structure of human WD40 repeat-containing peptidylprolyl isomerase (PPWD1).
  FEBS J, 275, 2283-2295.
PDB code: 2a2n
18342330 V.Thai, P.Renesto, C.A.Fowler, D.J.Brown, T.Davis, W.Gu, D.D.Pollock, D.Kern, D.Raoult, and E.Z.Eisenmesser (2008).
Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus.
  J Mol Biol, 378, 71-86.
PDB code: 2ose
16595688 C.Xu, J.Zhang, X.Huang, J.Sun, Y.Xu, Y.Tang, J.Wu, Y.Shi, Q.Huang, and Q.Zhang (2006).
Solution structure of human peptidyl prolyl isomerase-like protein 1 and insights into its interaction with SKIP.
  J Biol Chem, 281, 15900-15908.
PDB code: 1xwn
16689644 H.Stark, and R.Lührmann (2006).
Cryo-electron microscopy of spliceosomal components.
  Annu Rev Biophys Biomol Struct, 35, 435-457.  
15735342 L.L.Huang, X.M.Zhao, C.Q.Huang, L.Yu, and Z.X.Xia (2005).
Structure of recombinant human cyclophilin J, a novel member of the cyclophilin family.
  Acta Crystallogr D Biol Crystallogr, 61, 316-321.
PDB code: 1xyh
16134115 T.J.Pemberton, and J.E.Kay (2005).
The cyclophilin repertoire of the fission yeast Schizosaccharomyces pombe.
  Yeast, 22, 927-945.  
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.