Resources

Cellular Calcium Information Server

This server provides access to the following calcium-binding protein related databases:

Protein Structure Atomic Coordinates

1NWD NMR structure of Ca²⁺-calmodulin bound to the dimeric C-terminal domain of Petunia glutamate decarboxylase
Yap, K.L., Yuan, T., Mal, T.K., Vogel, H.J. and Ikura, M. (2003) Structural basis for simultaneous binding of two carboxy-terminal peptides of plant glutamate decarboxylase to calmodulin. J. Mol. Biol. 328,193-204.
1N4K Crystal Structure Of The Inositol 1,4,5-Trisphosphate Receptor Binding Core In Complex With IP₃
Bosanac, I., Alattia, J.R., Mal, T.K., Chan, J., Talarico, S., Tong, F.K., Tong, K.I., Yoshikawa, F., Furuichi, T., Iwai, M., Michikawa, T., Mikoshiba, K. and Ikura, M. (2002) Structure of the Inositol 1,4,5-Trisphosphate Receptor Binding Core in Complex with its Ligand. Nature 420, 696-700.
1MYW Crystal structure of a Yellow Fluorescent Protein With Improved Maturation and Reduced Environmental Sensitivity
Rekas, A., Alattia, J.R., Nagai, T., Miyawaki, A. and Ikura, M. (2002) Crystal structure of Venus, a Yellow Fluorescent Protein with Improved Maturation and Reduced Environmental Sensitivity. J. Biol. Chem. 277, 50573-50578.
1IQ5 Crystal structure of Ca²⁺/Calmodulin-CaMKK peptide Complex
Kurokawa, H., Osawa, M., Kurihara, H., Katayama, N., Tokumitsu, H., Swindells, M.B., Kainosho, M. and Ikura, M. (2001) Target-Induced Conformational Adaptation of Calmodulin Revealed by the Crystal Structure of a Complex with Nematode Ca²⁺/Calmodulin-Dependent Kinase Kinase Peptide. J. Mol. Biol. 312, 59-68.
1JOY Homodimeric Domain of EnvZ
Tomomori, C., Tanaka, T., Dutta, R., Park, H., Saha, S.K., Zhu, Y., Ishima, R., Liu, D., Tong, K.I., Kurokawa, H., Qian, H., Inouye, M. and Ikura, M. (1999) Solution Structure of the Homodimeric Domain of Escherichia Coli Histidine Kinase EnvZ. Nat. Struct. Biol. 6, 729-734.
1CKK NMR structure of Ca²⁺/Calmodulin-CaMKK peptide Complex
Osawa, M., Tokumitsu, H., Swindells, M.B., Kurihara, H., Orita, M., Shibanuma, T., Furuya, T., and Ikura, M. (1999) A Novel Target Recognition by Calmodulin Revealed by its Solution Structure in Complex with a Peptide Derived from Ca²⁺ Calmodulin Dependent Protein Kinase Kinase. Nature Struct. Biol. 6, 819-824.
1JBA Unmyristoylated GCAP-2
Ames, J.B., Dizhoor, A.M., Ikura, M., Palczewski, K., and Stryer, L. (1999) Three-dimensional Structure of GCAP-2, a Calcium Sensitive Modulator of Photoreceptor Guanylyl Cyclases. J. Biol. Chem. 274, 19329-19337.
1BXD Histidine Kinase Domain of EnvZ
Tanaka, T., Saha, S.K., Tomomori, C., Ishima, R., Liu, D., Tong, K.I., Park, H., Dutta, R., Qin, L., Swindells, M.B., Yamazaki, T., Ono, A.M., Kainosho, M., Inouye, M. and Ikura, M. (1998) NMR
Structure of the Histidine Kinase Domain of the E. Coli Osmosensor EnvZ. Nature 396, 88-92.
1TBA TBP-TAF_II230 Complex
Liu, D., Ishima, R., Tong, K.I., Bagby, S., Kokubo, T., Muhandiram, D.R., Kay, L.E., Nakatani, Y. and Ikura, M. (1998) Solution Structure of a TBP-TAFII230 Complex: Protein Mimicry of the Minor Groove Surface of the TATA Box Unwound by TBP. Cell 94, 573-583.
1MUX Ca²⁺/Calmodulin-W-7 Complex
Osawa M., Swindells, M.B., Tanikawa, J., Tanaka, T., Mase, T., Furuya, T. and Ikura, M. (1998) Solution Structure of Calmodulin-W-7 complex: Basis of Diversity NMRin Molecular Recognition. J. Mol. Biol. 276, 165-176.
1JSA Calcium-bound Myristoylated Recoverin
Ames, J.B., Ishima, R., Tanaka, T., Gordon, J.I., Stryer, L. and Ikura, M. (1997) Molecular Mechanics of Calcium-Myristoyl Switches. Nature 389,198-202.
1EDH E-Cadherin Domains 1 & 2 in Complex with Calcium
Nagar, B., Overduin, M., Ikura, M. and Rini, J.M. (1996) Structural Basis of Calcium-induced E-Cadherin Rigidification and Dimerization. Nature 380, 360-364.
1SUH Amino-Terminal Domain of Epithelial Cadherin in the Calcium Bound State
Overduin, M., Tong, K.I., Kay, C.M. and Ikura, M. (1996) 1H, 15N and 13C Resonance Assignments and Monomeric Structure of the Amino-Terminal Extracellular Domain of Epithelial Cadherin. J. Biomol. NMR 7, 173-189.
1TFB Human General Transcription Factor TFIIB Core Domain
Bagby, S., Kim, S., Maldonado, E., Tong, K.I., Reinberg, D. and Ikura, M. (1995) The Solution Structure of the Carboxy-terminal Core Domain of Human TFIIB: Similarity to Cyclin A and Interaction with the TATA Binding Protein Cell 82, 857-867.
1DMO Calcium-free Calmodulin
Zhang, M., Tanaka, T. and Ikura, M. (1995) Solution Structure of Apocalmodulin: Conformational Transition Induced by Calcium Binding. Nat. Struct. Biol. 2, 758-767.
1IKU Myristoylated Recoverin in the Calcium-free State
Tanaka, T., Ames, J.B., Harvey, T.S., Stryer, L., Ikura, M. (1995) Sequestration of the Membrane-targetting Myristoyl Group of Recoverin in the Calcium-free State. Nature 376, 444-448.
1PRS (30 structures) 1PRR (minimized average structure) Development-Specific Protein S (Spore Coat Protein S)
Bagby, S., Harvey, T.S., Eagle, S.G., Inouye, S. and Ikura, M. (1994) NMR-Derived Three-Dimensional Solution Structure of Protein S Complexed with Calcium. Structure 2, 107-122.
2BBN (21 structures) 2BBM (minimized average structure) Calmodulin (Calcium-bound) Complexed with Rabbit Skeletal Myosin Light Chain Kinase (Calmodulin-binding Domain)
Ikura, M., Clore, G.M., Gronenborn, A.M., Zhu, G., Klee, C.B. and Bax, A. (1992) Solution Structure of a Calmodulin-target Peptide Complex by Multidimensional NMR. Science 256, 632.

Visit the PDB website at http://www.rscb.org/.

NMR Chemical Shifts

Ca²⁺-free myristoylated recoverin (BMRB acc #4030)
Ca²⁺-bound calmodulin complexed with peptide M13 (not in BMRB format) backbone methyls
Ca²⁺-bound calmodulin: (BMRB acc #547) backbone & sidechain (Biochemistry 30:9216 supplement)
Ca²⁺-bound protein S
TFIIB core domain
Ca²⁺-free calmodulin (A) backbone
Ca²⁺-free calmodulin (B) backbone & sidechain
E-cadherin 1st repeat
Ca²⁺-bound calmodulin complexed with W-7 (4056)
Ca²⁺-bound myristoylated recoverin
Ca²⁺- calmodulin complexed with a dimeric peptide from glutamate decarboxylase (5770)

The following documents are made available for public use on condition that should they be used in your work, the author(s) of the documents will be acknowledged.

Algorithms

Weighted Chemical Shift Index using i-1, i and i+1 values
interhlx_orig.tar
C program to calculate the angle between two helices within a (PDB) protein, and the distance between the helices' midpoints. (formerly 'calc_all')
interhlx program with sign
pseudo_corr.tar
C program to correct pseudo-atom distances for X-PLOR distance constraint files.
Vector Geometry Mapping
C program to quantitatively and visually characterize the relative positions of two alpha-helices (such as in the EF-hand motif) in a set of structures.

Link to source code

Yap KL, Ames JB, Swindells MB, Ikura M.
"Diversity of conformational states and changes within the EF-hand protein superfamily" Proteins. 1999 Nov 15;37(3):499-507.

Yap KL, Ames JB, Swindells MB, Ikura M.
"Vector geometry mapping. A method to characterize the conformation of helix-loop-helix calcium-binding proteins" Methods Mol Biol. 2002;173:317-24.

Protocols

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Mitsu Ikura Lab

Connecting protein structures to signaling biology