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- PDB-9m5y: the crystal structure of the Ca2+/CaM-CASK-CaMK complex -

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Basic information

Entry
Database: PDB / ID: 9m5y
Titlethe crystal structure of the Ca2+/CaM-CASK-CaMK complex
Components
  • Calmodulin-1
  • Peripheral plasma membrane protein CASK
KeywordsSTRUCTURAL PROTEIN / Ca2+/CaM / CASK-CaMK / AMPPNP
Function / homology
Function and homology information


negative regulation of cellular response to growth factor stimulus / neurexin family protein binding / GMP kinase activity / negative regulation of wound healing / Dopamine Neurotransmitter Release Cycle / regulation of neurotransmitter secretion / nuclear lamina / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane ...negative regulation of cellular response to growth factor stimulus / neurexin family protein binding / GMP kinase activity / negative regulation of wound healing / Dopamine Neurotransmitter Release Cycle / regulation of neurotransmitter secretion / nuclear lamina / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / calcium ion import / Nephrin family interactions / Assembly and cell surface presentation of NMDA receptors / Sensory processing of sound by outer hair cells of the cochlea / Neurexins and neuroligins / Sensory processing of sound by inner hair cells of the cochlea / ciliary membrane / Syndecan interactions / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / positive regulation of calcium ion import / presynaptic endocytosis / nitric-oxide synthase binding / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / basement membrane / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / negative regulation of cell-matrix adhesion / detection of calcium ion / catalytic complex / regulation of synaptic vesicle endocytosis / negative regulation of keratinocyte proliferation / regulation of cardiac muscle contraction / postsynaptic cytosol / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / presynaptic cytosol / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / regulation of heart rate / calyx of Held / response to amphetamine / adenylate cyclase activator activity / sarcomere / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / calcium channel regulator activity / positive regulation of receptor signaling pathway via JAK-STAT / establishment of localization in cell / response to calcium ion / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Schaffer collateral - CA1 synapse / nuclear matrix / spindle pole / calcium-dependent protein binding / cell-cell junction / intracellular protein localization / myelin sheath / actin cytoskeleton / presynaptic membrane / growth cone / basolateral plasma membrane / vesicle / transmembrane transporter binding / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / signaling receptor binding / protein domain specific binding / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / calcium ion binding / centrosome / protein kinase binding / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CASK, SH3 domain / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. ...CASK, SH3 domain / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / : / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / Peripheral plasma membrane protein CASK / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, W. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071191 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural basis for the Ca 2+ /CaM-mediated regulation of CASK-CaMK.
Authors: Li, W. / Wang, Y. / Feng, W.
History
DepositionMar 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peripheral plasma membrane protein CASK
B: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0096
Polymers55,3282
Non-polymers6814
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-43 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.010, 80.137, 110.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Peripheral plasma membrane protein CASK / hCASK / Calcium/calmodulin-dependent serine protein kinase / Protein lin-2 homolog


Mass: 38177.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASK, LIN2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O14936, non-specific serine/threonine protein kinase
#2: Protein Calmodulin-1


Mass: 17150.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calm1, Calm, Cam, Cam1, CaMI
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0DP29

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Non-polymers , 4 types, 348 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M Sodium citrate tribasic dihydrate, pH 5.0, 10% (v/v) PEG 6000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 50795 / % possible obs: 99.7 % / Redundancy: 5.8 % / CC1/2: 0.993 / Net I/σ(I): 4.4
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 2593 / CC1/2: 0.93 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3COI

3coi


Resolution: 1.8→36.48 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 2502 4.93 %
Rwork0.1667 --
obs0.1682 50733 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→36.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 38 344 3386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163121
X-RAY DIFFRACTIONf_angle_d1.2794215
X-RAY DIFFRACTIONf_dihedral_angle_d27.0181175
X-RAY DIFFRACTIONf_chiral_restr0.092457
X-RAY DIFFRACTIONf_plane_restr0.008541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.31941370.2812593X-RAY DIFFRACTION98
1.84-1.870.27861300.25292645X-RAY DIFFRACTION99
1.87-1.910.27471320.23022658X-RAY DIFFRACTION99
1.91-1.960.25011410.19972618X-RAY DIFFRACTION100
1.96-2.010.2011270.18732681X-RAY DIFFRACTION100
2.01-2.060.20741370.1762647X-RAY DIFFRACTION100
2.06-2.120.20011310.17042660X-RAY DIFFRACTION100
2.12-2.190.21441250.16892685X-RAY DIFFRACTION100
2.19-2.270.20041340.1632663X-RAY DIFFRACTION100
2.27-2.360.23711170.15912691X-RAY DIFFRACTION100
2.36-2.470.17491400.16532675X-RAY DIFFRACTION100
2.47-2.60.20911610.16412652X-RAY DIFFRACTION100
2.6-2.760.1971390.15962704X-RAY DIFFRACTION100
2.76-2.970.2091430.16322697X-RAY DIFFRACTION100
2.97-3.270.1871600.15662681X-RAY DIFFRACTION100
3.27-3.740.18621650.15362717X-RAY DIFFRACTION100
3.74-4.710.15191430.1362755X-RAY DIFFRACTION100
4.72-36.480.19971400.18222809X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.1566-0.0221-0.72843.8239-0.63416.34210.10710.10210.2839-0.0611-0.0115-0.0867-0.23790.0913-0.06270.21350.012-0.01380.1771-0.00720.1549134.4218101.5223104.9769
24.4251-0.19141.95312.1810.60382.4359-0.2334-0.06880.4553-0.0541-0.0170.1822-0.5073-0.15420.17940.30060.0126-0.0450.20890.00840.1582139.993106.6054112.9704
32.13321.1953-0.74592.6101-1.21561.80870.07510.0623-0.1991-0.07350.07970.22120.1304-0.0992-0.14590.1628-0.016-0.04580.16140.00910.1691147.360289.9842127.0868
43.2897-0.43530.55483.70721.37423.1631-0.02410.0993-0.0464-0.09290.09790.27160.0134-0.0035-0.05810.1522-0.0194-0.01250.1570.04130.096146.2383101.8008123.5163
51.8045-0.40310.18783.2056-0.41250.9422-0.0695-0.3058-0.06450.31030.14620.2823-0.038-0.096-0.05250.13270.00140.02570.16510.0220.0833146.396798.4408139.2103
65.7035-3.14222.4835.093-2.13684.543-0.3176-0.1705-0.02880.05420.41650.5723-0.2361-0.7069-0.03770.1835-0.052-0.03230.30660.11410.4041130.414891.3241131.876
72.05071.01581.12998.1702-0.4458.3976-0.09-0.76130.72120.5318-0.4834-0.5515-1.4142-0.01830.29570.5343-0.0405-0.09920.53380.03680.5963118.1258103.2375134.168
85.4506-0.4427-0.61814.275-0.57146.66030.1282-0.3771-0.2435-0.1739-0.3552-0.33160.4089-0.28490.27880.34470.0139-0.01180.45350.05510.4181113.220992.2622128.3053
92.1490.317-2.39373.67321.19265.2765-0.27550.1287-0.4956-0.68770.2122-0.29251.06240.83840.03150.74640.07580.12210.66690.24231.1359121.945685.0595128.7526
107.9431.51020.95521.7620.062.6225-0.2086-0.8458-0.5313-0.16640.16670.13230.6234-0.6412-0.07780.4778-0.0341-0.05230.69230.10060.4784119.482392.8256140.7569
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 135 )
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 175 )
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 288 )
6X-RAY DIFFRACTION6chain 'A' and (resid 289 through 312 )
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 93 )
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 112 )
9X-RAY DIFFRACTION9chain 'B' and (resid 113 through 129 )
10X-RAY DIFFRACTION10chain 'B' and (resid 130 through 149 )

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