Motion in Calmodulin [cm]

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Classification Known Domain Motion, Hinge Mechanism [D-h-2]

Structures
1CDL Closed (mammelian, recomb., X-ray) [ PartsList ]
1CLL Open (human, X-ray, refined) [ PartsList ]
1CTR Closed [ PartsList ]
2BBM fly, NMR, closed with peptideClosed [ PartsList ]
2BBN fly, NMR, closed with 2nd peptideClosed conf. 3 [ PartsList ]
4CLN fly, X-rayOpen [ PartsList ]

Description
Basically, this hinge motion involves a long helix splitting into 2 helices (inclined at ~100 degrees) with a strand in between.
The unligated form of calmodulin contains two globular domains, connected by a long helix. NMR and X-ray structures of ligated calmodulin show the molecule binding to peptide helices with different sequences and the two domains closing around the peptide far enough to make contact with each other. In this motion, the long interdomain helix, which is known to have only marginal stability in solution, partly unfolds to break into two helical segments connected by a 4-residue hinge region in an extended conformation. The angle between the axes of the two helical segments is ~100 degrees. As there is an additional twist around the helix axes, the total rotation of one domain relative to the other is upwards of 150 degrees. Calmodulin can bind peptides with different sequences because of flexibility in the side chains that make contact with the peptide and by slightly shifting the relative placement of the domains through changes in the extent of the hinge region, which has consequently been dubbed a variable 'expansion joint.'
Specifically, in comparing 4cln with 2bbm, the largest torsion angle differences are in residues 72 to 82, where the protein changes from an alpha helix to an extended structure. This contains at most 20 changing torsions.

Particular values describing motion
Annotation Level (1..10) = 7
Domain 1 (residue selection) = 2-80
Domain 2 (residue selection) = 81-147
Location of a Hinge (residue selection) = 72 - 82 (4cln v. 2bbm)
Maximum CA displacement (A) = 60 (After sieve-fitting on domain-1)
Maximum Rotation (degrees) = 148.02
Experimental Methods = xn (Traditional X-ray and NMR)
Number of Inter-domain connections = 1
Number of hinges = 1
Number of Significant Torsion Angle Changes = 18 (Greater than 20 degrees)
Creation Date = 19970822
Modification Date = 19970822

References
L Stryer (1995). Biochemistry. New York, W H Freeman and Company. [Medline info for 11455603]
M Ikura, G M Clore, A M Gronenborn, G Zhu, C B Klee and A Bax (1992). Solution structureof a Calmodulin-Target peptide complex by multidimensional NMR. Science. 256: 632-644. [Medline info for 92263094]
W E Meador, A R Means and F A Quiocho (1992). Target enzyme recognition by Calmodulin: 2.4 Å structure of a Calmodulin-Peptide Complex. Science. 257: 1251-1255. [Medline info for 92390716]
W E Meador, A R Means and F A Quiocho (1993). Modulation of calmodulin plasticity in molecular recognition on the basis of x-ray structures. Science. 262: 1718-1721. [Medline info for 94082290]

Data and Graphics
Closed Form Adapted from Biochemistry, Copyright 1995, Lubert Stryer.
Open Form Adapted from Biochemistry, Copyright 1995, Lubert Stryer.
Torsion Changes + Atom Deviations Columns are, respectively: residue, phi-O, psi-O, sidechain-rotamer-O, phi-C, psi-C, rotamer-C, dphi, dpsi, dCA (after doing a fit) (O=open-form, C=closed-form).
The closing of calmodulin in 3 steps From another viewpoint, showing open, closed, and partially open.
4x4 Transformation Matrix The following 4x4 matrix [1 .. 16] orients the opened form so that the axis of rotation is along the z-axis and the origin is at the molecular centroid.

GO terms associated with structures
Molecular functionATP binding, calcium ion binding, protein kinase activity, protein serine/threonine kinase activity
Biological processprotein amino acid phosphorylation

Morphs

[ show all images ]
Best representative
Morph Morph name Structure #1 Structure #2 Residues
Calmodulin (with and 1ctr [ A ] 1cll [ A ] 148

User-submitted morphs
Morph Morph name Structure #1 Structure #2 Residues
477761-2679 Apo-Calmodulin Calcium Binding 1cfd [ A ] 1cll [ A ] 148
641930-21772 B. taurus calmodulin C-terminal 1cmg [ A ] 1cmf [ A ] 73
649090-23994 B. taurus calmodulin C-terminal 1cmg [ A ] 1cmf [ A ] 73
666277-11822 B. taurus calmodulin C-terminal 1cmf [ A ] 1cmg [ A ] 73
167979-23268 C-ter calmodulin 1cmf [ A ] 1cmg [ A ] 73
01725-7276 Calmodulin 1ctr [ A ] 1cll [ A ] 148
08377-17773 calmodulin 4cln [ A ] 2bbm [ A ] 148
08578-22059 Calmodulin 1ctr [ A ] 1cll [ A ] 148
14394-5469 Calmodulin 1ctr [ A ] 1cll [ A ] 148
23657-12736 Calmodulin 4cln [ A ] 2bbn [ A ] 148
61251-1272 Calmodulin upload [ ] upload [ ] 28
66972-25487 Calmodulin 1cmf [ A ] 1cmg [ A ] 73
67232-26216 Calmodulin 1sym [ A ] 1qlk [ A ] 92
69012-30322 Calmodulin upload [ ] upload [ ] 148
73416-26571 Calmodulin 4cln [ A ] 2bbn [ A ] 148
73439-26600 Calmodulin 4cln [ A ] 2bbn [ A ] 148
73518-21188 calmodulin upload [ A ] upload [ A ] 143
73766-27856 Calmodulin 4cln [ A ] 1cll [ A ] 148
77498-30128 calmodulin 1ctr [ A ] 2bbn [ A ] 148
77545-30151 calmodulin 1ctr [ A ] 4cln [ A ] 148
78252-5656 calmodulin 1cfd [ A ] 3cln [ A ] 148
81853-1359 Calmodulin 1dmo [ A ] 1cll [ A ] 148
82276-8935 calmodulin 1cll [ A ] 1ctr [ A ] 148
82342-9043 Calmodulin 1cll [ A ] 1cdl [ A ] 147
83269-14268 calmodulin 1cfd [ A ] 3cln [ A ] 148
84296-3082 Calmodulin upload [ A ] upload [ A ] 148
738147-20827 Calmodulin 1ctr [ A ] 1cll [ A ] 148
737022-20167 calmodulin 1ctr [ A ] 2bbm [ A ] 148
821501-16363 calmodulin 1cll [ A ] 1ctr [ A ] 148
813239-13890 Calmodulin 2bbn [ A ] 2bbm [ A ] 148
814007-14919 calmodulin 1cdl [ A ] 1cll [ A ] 148
722383-24233 Calmodulin 1dmo [ A ] 1cfc [ A ] 148
050329-435 calmodulin 1cdl [ A ] 1cll [ A ] 148
166179-9404 calmodulin 1exr [ A ] 2bbm [ A ] 148
404133-20907 calmodulin 1cdl [ A ] 1cll [ A ] 148
978471-24430 calmodulin 1cdl [ A ] 1cll [ A ] 148
916801-17919 calmodulin 1cll [ A ] upload [ A ] 147
223295-13614 Calmodulin 1cdl [ A ] 1cll [ A ] 148
229625-15151 Calmodulin 1cll [ A ] 1ctr [ A ] 148
657199-1899 Calmodulin upload [ A ] upload [ A ] 148
618370-9637 calmodulin 3cln [ A ] 1mxe [ A ] 148
75659-20457 Calmodulin 1cll [ A ] 1ctr [ A ] 148
024867-19131 calmodulin 1cdm [ A ] 1cfc [ A ] 148
129351-21747 calmodulin upload [ A ] upload [ A ] 148
384266-3122 Calmodulin 1cfd [ A ] 1cll [ A ] 148
521859-12503 calmodulin upload [ A ] upload [ A ] 148
535425-27929 calmodulin upload [ A ] upload [ A ] 148
545906-29509 Calmodulin 1cfd [ A ] 1cll [ A ] 148
545942-29547 Calmodulin 1cfd [ A ] 1a29 [ A ] 148
545975-29582 Calmodulin 1cfd [ A ] 1cm1 [ A ] 148
545993-29640 Calmodulin 1cfd [ A ] 2bbm [ A ] 148
632354-16196 calmodulin 1cfc [ A ] 1mux [ A ] 148
638094-18965 Calmodulin 4cln [ A ] 2bbm [ A ] 148
899144-27090 calmodulin upload [ A ] upload [ A ] 148
904106-3071 calmodulin upload [ A ] upload [ A ] 148
905492-6470 calmodulin upload [ A ] upload [ A ] 148
841619-2829 calmodulin upload [ A ] upload [ A ] 147
842005-3518 calmodulin upload [ A ] upload [ A ] 147
842622-5162 calmodulin upload [ A ] upload [ A ] 147
205667-26622 Calmodulin 1cfd [ A ] 3cln [ A ] 148
810320-27219 calmodulin 1a29 [ A ] 1cll [ A ] 148
441256-21753 Calmodulin upload [ A ] upload [ A ] 144
618263-27664 Calmodulin 4cln [ A ] 2bbn [ A ] 148
618341-27759 Calmodulin 1ctr [ A ] 1cll [ A ] 148
687989-18060 Calmodulin 1ctr [ A ] 3cln [ A ] 148
063848-16677 calmodulin upload [ A ] upload [ A ] 148
644870-11497 Calmodulin 1ctr [ A ] 1cll [ A ] 148
032798-11904 Calmodulin 1cfd [ A ] 1cll [ A ] 148
372215-4458 Calmodulin upload [ A ] upload [ A ] 148
374466-14065 Calmodulin upload [ A ] upload [ A ] 144
733212-22868 Calmodulin 1ctr [ A ] 1cll [ A ] 148
062151-16187 calmodulin 1a29 [ A ] 1cll [ A ] 148
784437-30999 Calmodulin 1ctr [ A ] 1prw [ A ] 147
786058-32088 Calmodulin 1ctr [ A ] 1prw [ A ] 147
042394-23653 Calmodulin 1exr [ A ] 2bbm [ A ] 148
042487-24114 Calmodulin 1ctr [ A ] 1prw [ A ] 147
201851-29662 Calmodulin 2bbm [ A ] 1exr [ A ] 148
201903-29830 Calmodulin 1ctr [ A ] 1prw [ A ] 147
201957-30117 Calmodulin 1prw [ A ] 1ctr [ A ] 148
204738-1312 Calmodulin 1cfd [ A ] 1osa [ A ] 148
204788-1428 Calmodulin 1osa [ A ] 1cfd [ A ] 148
459682-24148 Calmodulin 1prw [ A ] 1osa [ A ] 148
459728-24243 Calmodulin 1exr [ A ] 1ctr [ A ] 148
045573-6180 Calmodulin (DM test) 1cll [ A ] 1ctr [ A ] 148
18924-32697 Calmodulin (without 1cll [ A ] 1ctr [ A ] 148
032937-12485 Calmodulin - N terminal upload [ A ] upload [ A ] 148
372158-4425 Calmodulin - N terminal upload [ A ] upload [ A ] 148
373794-10887 Calmodulin - N terminal upload [ A ] upload [ A ] 72
97035-30938 Calmodulin C-termina 1cmf [ A ] 1cmg [ A ] 73
26716-25592 calmodulin c-terminal domain 1cmf [ ] 1cmg [ ] 73
74562-27769 calmodulin check 1cll [ A ] 1ctr [ A ] 148
171077-24555 calmodulin compact form 1cfd [ A ] 1prw [ A ] 147
028776-21461 Calmodulin conformational change when bi 1ctr [ A ] 1ctl [ A ] 85
171106-24592 calmodulin extended form 1cfd [ A ] 1cll [ A ] 148
066132-17985 calmodulin-n upload [ A ] upload [ A ] 148
637463-17713 Drosophila calmodulin 4cln [ A ] 2bbm [ A ] 148
230054-16152 fly calmodulin 4cln [ A ] 2bbm [ A ] 148
329178-1319 Human calmodulin 1cll [ A ] 1ctr [ A ] 148
161217-21573 Nter yeast calmodulin 1f54 [ A ] 1f55 [ A ] 77
396657-13022 X. laevis calmodulin 1cfc [ A ] 1cff [ A ] 148
603443-28645 X. laevis calmodulin 1cfc [ A ] 1cff [ A ] 148
636528-16077 X. laevis calmodulin upload [ A ] upload [ A ] 148
653789-28203 X. laevis calmodulin 1cfc [ A ] 1mux [ A ] 148
12912-1182 Zinc Finger 4cln [ A ] 2bbn [ A ] 148
12924-1256 Zinc Finger 4cln [ A ] 2bbm [ A ] 148

Automatic morphs
Morph Morph name Structure #1 Structure #2 Residues
va1ak8A-1dmoA Calmodulin 1ak8 [ A ] 1dmo [ A ] 148
va1ak8A-1f70A Calmodulin 1ak8 [ A ] 1f70 [ A ] 76
va1cfcA-1cffA Calmodulin 1cfc [ A ] 1cff [ A ] 148
va1cfdA-1cffA Calmodulin 1cfd [ A ] 1cff [ A ] 148
va1cffA-1ckkA Calmodulin 1cff [ A ] 1ckk [ A ] 148
va1dmoA-1cffA Calmodulin 1dmo [ A ] 1cff [ A ] 148
va1cffA-1ajiA Calmodulin 1cff [ A ] 1aji [ A ] 144
va1ak8A-1cfdA Calmodulin 1ak8 [ A ] 1cfd [ A ] 148
va1ak8A-1cfcA Calmodulin 1ak8 [ A ] 1cfc [ A ] 148
va1dmoA-1ckkA Calmodulin 1dmo [ A ] 1ckk [ A ] 148
va1ajiA-1muxA Calmodulin 1aji [ A ] 1mux [ A ] 148
va1f70A-1ckkA Calmodulin 1f70 [ A ] 1ckk [ A ] 148
va1ajiA-1dmoA Calmodulin 1aji [ A ] 1dmo [ A ] 148
va1cffA-2clnA Calmodulin 1cff [ A ] 2cln [ A ] 148
va1ajiA-2clnA Calmodulin 1aji [ A ] 2cln [ A ] 148
va1muxA-1dmoA Calmodulin 1mux [ A ] 1dmo [ A ] 148
va1muxA-1ckkA Calmodulin 1mux [ A ] 1ckk [ A ] 148
va1muxA-1cfcA Calmodulin 1mux [ A ] 1cfc [ A ] 148
va1muxA-1cffA Calmodulin 1mux [ A ] 1cff [ A ] 148
va1muxA-1cfdA Calmodulin 1mux [ A ] 1cfd [ A ] 148
va1dmoA-1cfcA Calmodulin 1dmo [ A ] 1cfc [ A ] 148
va1dmoA-1cfdA Calmodulin 1dmo [ A ] 1cfd [ A ] 148
va1ajiA-1cfdA Calmodulin 1aji [ A ] 1cfd [ A ] 148
va1ajiA-1ckkA Calmodulin 1aji [ A ] 1ckk [ A ] 148
va1dmoA-1degA Calmodulin 1dmo [ A ] 1deg [ A ] 142
va1cfdA-1cfcA Calmodulin 1cfd [ A ] 1cfc [ A ] 148
va1cfdA-1ckkA Calmodulin 1cfd [ A ] 1ckk [ A ] 148
va1ajiA-1cfcA Calmodulin 1aji [ A ] 1cfc [ A ] 148
va1cfcA-1ckkA Calmodulin 1cfc [ A ] 1ckk [ A ] 148
va1f70A-4clnA Calmodulin 1f70 [ A ] 4cln [ A ] 148
va1ahrA-1f70A Calmodulin 1ahr [ A ] 1f70 [ A ] 76
va1cffA-1ak8A Calmodulin 1cff [ A ] 1ak8 [ A ] 76
va1j7pA-1f71A Calmodulin 1j7p [ A ] 1f71 [ A ] 67
va1j7oA-1ajiA Calmodulin 1j7o [ A ] 1aji [ A ] 144
va1j7oA-1cfcA Calmodulin 1j7o [ A ] 1cfc [ A ] 148
va1j7oA-1cfdA Calmodulin 1j7o [ A ] 1cfd [ A ] 148
va1ak8A-4clnA Calmodulin 1ak8 [ A ] 4cln [ A ] 148
va1ak8A-1ajiA Calmodulin 1ak8 [ A ] 1aji [ A ] 144
va1muxA-1f70A Calmodulin 1mux [ A ] 1f70 [ A ] 76
va1f70A-1degA Calmodulin 1f70 [ A ] 1deg [ A ] 142
va1j7oA-1dmoA Calmodulin 1j7o [ A ] 1dmo [ A ] 148
va1j7oA-1f70A Calmodulin 1j7o [ A ] 1f70 [ A ] 76
va1ak8A-1ahrA Calmodulin 1ak8 [ A ] 1ahr [ A ] 146
va1muxA-1ak8A Calmodulin 1mux [ A ] 1ak8 [ A ] 76
va1j7oA-1ak8A Calmodulin 1j7o [ A ] 1ak8 [ A ] 76
va1j7oA-1ckkA Calmodulin 1j7o [ A ] 1ckk [ A ] 148
va1cffA-1j7oA Calmodulin 1cff [ A ] 1j7o [ A ] 76
va1j7oA-1muxA Calmodulin 1j7o [ A ] 1mux [ A ] 148
va1j7oA-1degA Calmodulin 1j7o [ A ] 1deg [ A ] 142
va1ak8A-1ckkA Calmodulin 1ak8 [ A ] 1ckk [ A ] 148
va1f70A-1dmoA Calmodulin 1f70 [ A ] 1dmo [ A ] 148
va1j7oA-4clnA Calmodulin 1j7o [ A ] 4cln [ A ] 148
va1j7oA-1ahrA Calmodulin 1j7o [ A ] 1ahr [ A ] 146
va2bbmA-4clnA Calmodulin (Calcium-Bound) Com 2bbm [ A ] 4cln [ A ] 148
va2bbmA-1f70A Calmodulin (Calcium-Bound) Com 2bbm [ A ] 1f70 [ A ] 76
va2bbnA-1f70A Calmodulin (Calcium-Bound) Com 2bbn [ A ] 1f70 [ A ] 76
va2bbmA-1j7oA Calmodulin (Calcium-Bound) Com 2bbm [ A ] 1j7o [ A ] 76
va2bbnA-1ak8A Calmodulin (Calcium-Bound) Com 2bbn [ A ] 1ak8 [ A ] 76
va2bbnA-1j7oA Calmodulin (Calcium-Bound) Com 2bbn [ A ] 1j7o [ A ] 76
va2bbmA-1ak8A Calmodulin (Calcium-Bound) Com 2bbm [ A ] 1ak8 [ A ] 76
va2bbmB-2bbnB Calmodulin (Calcium-Bound) Com 2bbm [ B ] 2bbn [ B ] 26
va1cmgA-1cmfA Calmodulin (Vertebrate) 1cmg [ A ] 1cmf [ A ] 73
va4clnA-2bbnA Calmodulin - Chain _ 4cln [ A ] 2bbn [ A ] 148
va1degA-2clnA Calmodulin Mutant With Glu 84 1deg [ A ] 2cln [ A ] 148
va1degA-1ak8A Calmodulin Mutant With Glu 84 1deg [ A ] 1ak8 [ A ] 76
va2clnA-1ckkA N==Z115== Trimethylcalmodulin 2cln [ A ] 1ckk [ A ] 148
va2clnA-1cfcA N==Z115== Trimethylcalmodulin 2cln [ A ] 1cfc [ A ] 148
va2clnA-1dmoA N==Z115== Trimethylcalmodulin 2cln [ A ] 1dmo [ A ] 148
va2clnA-1cfdA N==Z115== Trimethylcalmodulin 2cln [ A ] 1cfd [ A ] 148
va2clnA-1muxA N==Z115== Trimethylcalmodulin 2cln [ A ] 1mux [ A ] 148
va2clnA-1f70A N==Z115== Trimethylcalmodulin 2cln [ A ] 1f70 [ A ] 76
va2clnA-1ak8A N==Z115== Trimethylcalmodulin 2cln [ A ] 1ak8 [ A ] 76
va2clnA-1j7oA N==Z115== Trimethylcalmodulin 2cln [ A ] 1j7o [ A ] 76

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Copyright 1995-2005 M. Gerstein, W. Krebs, S. Flores, N. Echols, and others
Email: Mark.Gerstein _at_ yale.edu