ProtCID

ProtCID
Content
Description Similar interactions of homologous proteins in multiple crystal forms
Contact
Research center Fox Chase Cancer Center
Laboratory Institute for Cancer Research
Authors Qifang Xu, Roland Dunbrack
Primary citation Xu & Dunbrack (2011)[1]
Release date 2010
Access
Website http://dunbrack2.fccc.edu/protcid
Example of cluster of similar interfaces of homologous proteins identified by ProtCID -- similar homodimers of ERBB kinases (EGFR, ERBB2, ERBB4) associated with kinase activation.[2][3][4] Each monomer is colored from blue to red from N to C terminus. ProtCID provides PyMol scripts for each cluster to produce similar images.

The Protein Common Interface Database (ProtCID) is a database of similar protein-protein interfaces in crystal structures of homologous proteins.[1]

Its main goal is to identify and cluster homodimeric and heterodimeric interfaces observed in multiple crystal forms of homologous proteins. Such interfaces, especially of non-identical proteins or protein complexes, have been associated with biologically relevant interactions.[5]

A common interface in ProtCID indicates chain-chain interactions that occur in different crystal forms. All protein sequences of known structure in the Protein Data Bank (PDB)[6] are assigned a ”Pfam chain architecture”, which denotes the ordered Pfam[7] assignments for that sequence, e.g. (Pkinase) or (Cyclin_N)_(Cyclin_C). Homodimeric interfaces in all crystals that contain a particular architecture are compared, regardless of whether there are other protein types in the crystals. All interfaces between two different Pfam architectures in all PDB entries that contain them are also compared (e.g., (Pkinase) and (Cyclin_N)_(Cyclin_C) ). For both homodimers and heterodimers, the interfaces are clustered into common interfaces based on a similarity score.

ProtCID reports the number of crystal forms that contain a common interface, the number of PDB entries, the number of PDB and PISA[8] biological assembly annotations that contain the same interface, the average surface area, and the minimum sequence identity of proteins that contain the interface. ProtCID provides an independent check on publicly available annotations of biological interactions for PDB entries.

See also

References

  1. 1 2 Xu, Q.; Dunbrack, R. L. (2010). "The protein common interface database (ProtCID)—a comprehensive database of interactions of homologous proteins in multiple crystal forms". Nucleic Acids Research. 39 (Database issue): D761–70. doi:10.1093/nar/gkq1059. PMC 3013667Freely accessible. PMID 21036862.
  2. ↑ Zhang, X.; Gureasko, J.; Shen, K.; Cole, P. A.; Kuriyan, J. (2006). "An Allosteric Mechanism for Activation of the Kinase Domain of Epidermal Growth Factor Receptor". Cell. 125 (6): 1137–1149. doi:10.1016/j.cell.2006.05.013. PMID 16777603.
  3. ↑ Aertgeerts, K.; Skene, R.; Yano, J.; Sang, B. -C.; Zou, H.; Snell, G.; Jennings, A.; Iwamoto, K.; Habuka, N.; Hirokawa, A.; Ishikawa, T.; Tanaka, T.; Miki, H.; Ohta, Y.; Sogabe, S. (2011). "Structural Analysis of the Mechanism of Inhibition and Allosteric Activation of the Kinase Domain of HER2 Protein". Journal of Biological Chemistry. 286 (21): 18756–18765. doi:10.1074/jbc.M110.206193. PMC 3099692Freely accessible. PMID 21454582.
  4. ↑ Qiu, C.; Tarrant, M. K.; Choi, S. H.; Sathyamurthy, A.; Bose, R.; Banjade, S.; Pal, A.; Bornmann, W. G.; Lemmon, M. A.; Cole, P. A.; Leahy, D. J. (2008). "Mechanism of Activation and Inhibition of the HER4/ErbB4 Kinase". Structure. 16 (3): 460–467. doi:10.1016/j.str.2007.12.016. PMC 2858219Freely accessible. PMID 18334220.
  5. ↑ Xu, Qifang; Canutescu, Adrian A.; Wang, Guoli; Shapovalov, Maxim; Obradovic, Zoran; Dunbrack, Roland L. (2008). "Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins". Journal of Molecular Biology. 381 (2): 487–507. doi:10.1016/j.jmb.2008.06.002. PMC 2573399Freely accessible. PMID 18599072.
  6. ↑ Berman, H. M.; Battistuz, T.; Bhat, T. N.; Bluhm, W. F.; Bourne, P. E.; Burkhardt, K.; Feng, Z.; Gilliland, G. L.; Iype, L.; Jain, S.; Fagan, P.; Marvin, J.; Padilla, D.; Ravichandran, V.; Schneider, B.; Thanki, N.; Weissig, H.; Westbrook, J. D.; Zardecki, C. (2002). "The Protein Data Bank". Acta Crystallographica Section D. 58 (Pt 6 No 1): 899–907. doi:10.1107/S0907444902003451. PMID 12037327.
  7. ↑ Punta, M.; Coggill, P. C.; Eberhardt, R. Y.; Mistry, J.; Tate, J.; Boursnell, C.; Pang, N.; Forslund, K.; Ceric, G.; Clements, J.; Heger, A.; Holm, L.; Sonnhammer, E. L. L.; Eddy, S. R.; Bateman, A.; Finn, R. D. (2011). "The Pfam protein families database". Nucleic Acids Research. 40 (Database issue): D290–D301. doi:10.1093/nar/gkr1065. PMC 3245129Freely accessible. PMID 22127870.
  8. ↑ Krissinel, E.; Henrick, K. (2007). "Inference of Macromolecular Assemblies from Crystalline State". Journal of Molecular Biology. 372 (3): 774–797. doi:10.1016/j.jmb.2007.05.022. PMID 17681537.
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