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- PDB-9m6g: the crystal structure of the Ca2+/CaM-CASK-CaMK-Mint1-CID complex -

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Basic information

Entry
Database: PDB / ID: 9m6g
Titlethe crystal structure of the Ca2+/CaM-CASK-CaMK-Mint1-CID complex
Components
  • Amyloid-beta A4 precursor protein-binding family A member 1
  • Calmodulin-1
  • Peripheral plasma membrane protein CASK
KeywordsSTRUCTURAL PROTEIN / Ca2+/CaM / CASK-CaMK / Mint1-CID / AMPPNP
Function / homology
Function and homology information


negative regulation of cellular response to growth factor stimulus / neurexin family protein binding / gamma-aminobutyric acid secretion / GMP kinase activity / Dopamine Neurotransmitter Release Cycle / negative regulation of wound healing / Dopamine Neurotransmitter Release Cycle / regulation of neurotransmitter secretion / nuclear lamina / establishment of protein localization to mitochondrial membrane ...negative regulation of cellular response to growth factor stimulus / neurexin family protein binding / gamma-aminobutyric acid secretion / GMP kinase activity / Dopamine Neurotransmitter Release Cycle / 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 / glutamate secretion / 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 / synaptic vesicle exocytosis / 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 / presynaptic active zone membrane / regulation of calcium-mediated signaling / phosphatidylinositol-4,5-bisphosphate binding / voltage-gated potassium channel complex / calcium channel complex / presynaptic modulation of chemical synaptic transmission / 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 / PDZ domain binding / locomotory behavior / intracellular protein transport / 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 / multicellular organism growth / nuclear matrix / spindle pole / calcium-dependent protein binding / cell-cell junction / intracellular protein localization / myelin sheath / actin cytoskeleton / amyloid-beta binding / presynaptic membrane / growth cone / regulation of gene expression / basolateral plasma membrane / vesicle / chemical synaptic transmission / dendritic spine / in utero embryonic development / transmembrane transporter binding / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / signaling receptor binding / protein domain specific binding / protein serine kinase activity
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 / Phosphotyrosine interaction domain (PTB/PID) ...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 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / 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 / PH-like domain superfamily / 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 / MALONATE ION / Peripheral plasma membrane protein CASK / Amyloid-beta A4 precursor protein-binding family A member 1 / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 7, 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
C: Amyloid-beta A4 precursor protein-binding family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2567
Polymers61,5683
Non-polymers6884
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-49 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.214, 80.562, 109.173
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 , 3 types, 3 molecules ABC

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


Mass: 36682.469 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
#3: Protein Amyloid-beta A4 precursor protein-binding family A member 1 / Adapter protein X11alpha / Neuron-specific X11 protein / Neuronal Munc18-1-interacting protein 1 / Mint-1


Mass: 7734.669 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Apba1, Mint1, X11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O35430

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Non-polymers , 4 types, 367 molecules

#4: 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
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Sodium malonate, pH 5.0, 12% (v/v) 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: May 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 60114 / % possible obs: 99.9 % / Redundancy: 10.8 % / CC1/2: 0.998 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.7610.70.61459350.9220.980.1950.6451.136100
1.76-1.8310.80.4559270.9490.9870.1430.4721.145100
1.83-1.9110.80.30459470.9780.9940.0960.3191.118100
1.91-2.0210.90.259430.990.9970.0630.211.082100
2.02-2.1410.90.13859450.9950.9990.0440.1451.069100
2.14-2.31110.10459790.9970.9990.0330.1091.001100
2.31-2.54110.08360230.9970.9990.0260.0870.936100
2.54-2.91110.08760260.9960.9990.0270.0921.038100
2.91-3.6610.80.08160890.9970.9990.0260.0851.048100
3.66-5010.40.04863000.99810.0160.0510.91299.4

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9M5Y

9m5y


Resolution: 1.7→40.74 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1871 2918 4.86 %
Rwork0.1654 --
obs0.1665 60043 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 40 363 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153224
X-RAY DIFFRACTIONf_angle_d1.3414356
X-RAY DIFFRACTIONf_dihedral_angle_d23.3541212
X-RAY DIFFRACTIONf_chiral_restr0.097471
X-RAY DIFFRACTIONf_plane_restr0.009560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.23421210.20932640X-RAY DIFFRACTION98
1.73-1.760.21891370.1922695X-RAY DIFFRACTION100
1.76-1.790.19061340.18342694X-RAY DIFFRACTION100
1.79-1.820.19911480.18082671X-RAY DIFFRACTION100
1.82-1.860.19351340.18322702X-RAY DIFFRACTION100
1.86-1.90.22681410.17332666X-RAY DIFFRACTION100
1.9-1.950.18211480.15852682X-RAY DIFFRACTION100
1.95-1.990.17611220.15582707X-RAY DIFFRACTION100
1.99-2.050.1541450.15472704X-RAY DIFFRACTION100
2.05-2.110.18131220.15342742X-RAY DIFFRACTION100
2.11-2.180.21051380.15562698X-RAY DIFFRACTION100
2.18-2.250.17771260.15672721X-RAY DIFFRACTION100
2.25-2.340.18681380.15272708X-RAY DIFFRACTION100
2.34-2.450.17441630.15692701X-RAY DIFFRACTION100
2.45-2.580.18461340.16982717X-RAY DIFFRACTION100
2.58-2.740.19451360.17682741X-RAY DIFFRACTION100
2.74-2.950.19181300.17562740X-RAY DIFFRACTION100
2.95-3.250.22231360.17442765X-RAY DIFFRACTION100
3.25-3.720.16621490.15772752X-RAY DIFFRACTION100
3.72-4.690.14891410.14192809X-RAY DIFFRACTION100
4.69-40.740.22151750.18682870X-RAY DIFFRACTION99
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)
13.02560.61141.39925.878-0.27523.136-0.0739-0.05320.25610.3268-0.00070.0695-0.0323-0.19520.07950.16620.0341-0.02020.18520.00690.1453-49.321221.9966-3.1552
25.4662-4.8188-4.05674.51353.56575.22290.05750.03151.0773-0.0654-0.215-0.1771-0.847-0.34020.19750.48230.065-0.08140.3203-0.00220.4173-40.90934.04225.7187
30.9812-0.01470.63360.8983-0.23671.52950.04940.112-0.1503-0.17960.07820.15840.0556-0.0942-0.12450.1459-0.003-0.02390.14560.0010.136-38.295714.81399.2514
42.2414-0.1354-0.15943.65131.68422.9177-0.01790.02320.13070.00850.0810.1947-0.016-0.0375-0.03750.1274-0.0026-0.02150.11270.04610.1076-38.179725.073517.2213
51.7843-0.1860.13683.0985-0.20611.4237-0.0301-0.3026-0.09990.24550.09050.2415-0.0252-0.1048-0.03660.1238-0.00550.01290.14940.03170.0928-35.600614.989529.0281
66.8338-4.85152.98668.5581-2.78034.5164-0.1368-0.1108-0.05970.14320.20520.6104-0.2843-0.4809-0.11540.1519-0.0521-0.00680.29240.08920.3462-53.025811.194421.4274
71.93091.71850.42612.31911.24483.7395-0.1775-0.67331.43670.68240.1041-0.6988-1.80150.31330.19260.7047-0.0298-0.16170.5831-0.01130.8328-64.767724.268625.0662
85.2377-0.54230.20186.1233-1.33456.82380.0686-0.4316-0.32-0.1451-0.1638-0.50640.41250.1170.02820.23370.0113-0.02460.36690.08090.4226-70.107512.022117.8936
91.32260.60420.28933.3756-1.28443.47580.12590.59620.1623-0.47490.28230.0351-0.3310.3363-0.34511.25450.13770.27390.97060.30081.2365-60.45178.706211.196
108.3776-2.2861-0.58988.58475.23968.2427-0.35770.3176-0.71310.688-0.2027-1.23221.53261.35550.47480.6190.1564-0.05020.60020.17761.1262-61.80543.187521.6291
114.87483.4188-2.70493.0944-0.39614.72880.2681-0.7828-1.08160.64930.16390.33570.8052-0.4424-0.44390.4469-0.0886-0.11330.74320.24260.5986-68.81297.640530.3274
126.4845-0.18063.16345.2866-1.16064.7552-0.5933-0.90720.24430.10160.2004-0.01370.4699-0.27890.19360.33080.0391-0.02290.63190.04310.3313-60.682715.605330.174
138.4725.1815-2.69449.2489-5.38423.32880.0710.0266-0.9321-0.5666-0.4186-0.76790.93020.24270.38410.38780.0302-0.10340.2591-0.02430.3872-36.5074-4.764315.6825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 134 )
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 197 )
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 288 )
6X-RAY DIFFRACTION6chain 'A' and (resid 289 through 312 )
7X-RAY DIFFRACTION7chain 'B' and (resid 80 through 93 )
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 112 )
9X-RAY DIFFRACTION9chain 'B' and (resid 113 through 118 )
10X-RAY DIFFRACTION10chain 'B' and (resid 119 through 129 )
11X-RAY DIFFRACTION11chain 'B' and (resid 130 through 138 )
12X-RAY DIFFRACTION12chain 'B' and (resid 139 through 149 )
13X-RAY DIFFRACTION13chain 'C' and (resid 378 through 385 )

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