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- PDB-9kys: the Ca2+/CaM-CASK-ARD complex -

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Basic information

Entry
Database: PDB / ID: 9kys
Titlethe Ca2+/CaM-CASK-ARD complex
Components
  • Calmodulin-1
  • Peripheral plasma membrane protein CASK
KeywordsSTRUCTURAL PROTEIN / Ca2+ / calmodulin / CASK-ARD
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
Peripheral plasma membrane protein CASK / Calmodulin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsLi, W. / Wang, Y. / Feng, W.
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
DepositionDec 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,24512
Polymers45,9254
Non-polymers3218
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-166 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.662, 76.786, 130.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calmodulin-1


Mass: 17150.842 Da / Num. of mol.: 2
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 (E. coli) / References: UniProt: P0DP29
#2: Protein Peripheral plasma membrane protein CASK / hCASK / Calcium/calmodulin-dependent serine protein kinase / Protein lin-2 homolog


Mass: 5811.497 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASK, LIN2 / Production host: Escherichia coli (E. coli)
References: UniProt: O14936, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: magnesium chloride, PEG 3350

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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: Dec 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 37870 / % possible obs: 98.4 % / Redundancy: 10.7 % / CC1/2: 0.998 / Net I/σ(I): 3.9
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 10.6 % / Num. unique obs: 3659 / CC1/2: 0.976 / CC star: 0.994 / % possible all: 96.8

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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: 1CDL

1cdl


Resolution: 1.76→32.73 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 2000 5.29 %
Rwork0.1974 --
obs0.1992 37825 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 8 352 3088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072759
X-RAY DIFFRACTIONf_angle_d0.883695
X-RAY DIFFRACTIONf_dihedral_angle_d32.0871047
X-RAY DIFFRACTIONf_chiral_restr0.053401
X-RAY DIFFRACTIONf_plane_restr0.005499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.34931340.28642405X-RAY DIFFRACTION94
1.8-1.850.31421400.24042510X-RAY DIFFRACTION98
1.85-1.910.26211410.21792526X-RAY DIFFRACTION99
1.91-1.970.25421410.20382533X-RAY DIFFRACTION99
1.97-2.040.22741410.19682517X-RAY DIFFRACTION99
2.04-2.120.241430.1912567X-RAY DIFFRACTION99
2.12-2.220.20751430.18692556X-RAY DIFFRACTION99
2.22-2.330.22831420.18742548X-RAY DIFFRACTION99
2.33-2.480.24781440.19742566X-RAY DIFFRACTION99
2.48-2.670.24681430.20762579X-RAY DIFFRACTION99
2.67-2.940.24641460.21642596X-RAY DIFFRACTION100
2.94-3.360.23491460.20832623X-RAY DIFFRACTION100
3.36-4.240.19561480.17192645X-RAY DIFFRACTION99
4.24-32.730.21761480.19242654X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -6.1333 Å / Origin y: -13.1907 Å / Origin z: 28.9538 Å
111213212223313233
T0.2055 Å2-0.0058 Å2-0.0165 Å2-0.1932 Å2-0.0051 Å2--0.208 Å2
L0.0508 °2-0.0379 °20.4419 °2-0.5602 °20.1523 °2--2.4354 °2
S0.062 Å °0.0242 Å °-0.0222 Å °0.0454 Å °-0.0538 Å °0.0842 Å °0.1268 Å °-0.0046 Å °-0.0083 Å °
Refinement TLS groupSelection details: all

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