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- PDB-3c0g: CASK CaM-Kinase Domain- 3'-AMP complex, P1 form -

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Basic information

Entry
Database: PDB / ID: 3c0g
TitleCASK CaM-Kinase Domain- 3'-AMP complex, P1 form
ComponentsPeripheral plasma membrane protein CASK
KeywordsTRANSFERASE / CASK / neurexin / Ca2+/calmodulin dependent protein kinase / Mg2+ / synaptic plasticity / pseudokinase / MAGUK / membrane-associated guanylate kinase / ATP-binding / Calmodulin-binding / Magnesium / Metal-binding / Nucleotide-binding / Nucleus / Serine/threonine-protein kinase / SH3 domain
Function / homology
Function and homology information


negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / nuclear lamina / regulation of neurotransmitter secretion / negative regulation of wound healing / Assembly and cell surface presentation of NMDA receptors / calcium ion import / Neurexins and neuroligins ...negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / nuclear lamina / regulation of neurotransmitter secretion / negative regulation of wound healing / Assembly and cell surface presentation of NMDA receptors / calcium ion import / Neurexins and neuroligins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / ciliary membrane / regulation of synaptic vesicle exocytosis / Syndecan interactions / negative regulation of cell-matrix adhesion / positive regulation of calcium ion import / basement membrane / negative regulation of keratinocyte proliferation / establishment of localization in cell / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / actin cytoskeleton / presynaptic membrane / basolateral plasma membrane / vesicle / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / phosphorylation / signaling receptor binding / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytosol / cytoplasm
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. / Guanylate kinase-like domain profile. ...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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3AM / Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsWahl, M.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: CASK Functions as a Mg2+-independent neurexin kinase
Authors: Mukherjee, K. / Sharma, M. / Urlaub, H. / Bourenkov, G.P. / Jahn, R. / Sudhof, T.C. / Wahl, M.C.
History
DepositionJan 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2094
Polymers78,5142
Non-polymers6942
Water4,540252
1
A: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6042
Polymers39,2571
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6042
Polymers39,2571
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.328, 60.267, 60.553
Angle α, β, γ (deg.)90.00, 106.49, 105.80
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 6 - 304 / Label seq-ID: 20 - 318

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 39257.121 Da / Num. of mol.: 2 / Fragment: CaM-Kinase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASK / Plasmid: pGEX-6T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: O14936, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3AM / [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate / 3'-AMP


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 12.5%(v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 29, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.19→30 Å / Num. obs: 32667 / % possible obs: 89.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 48 Å2 / Rsym value: 0.112 / Net I/σ(I): 12.4
Reflection shellResolution: 2.19→2.3 Å / Mean I/σ(I) obs: 1.5 / Num. unique all: 4046 / Rsym value: 0.427 / % possible all: 76.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: rat CamKI

Resolution: 2.19→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 17.385 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.375 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26969 1576 4.9 %RANDOM
Rwork0.20754 ---
obs0.21074 30426 86.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.058 Å2
Baniso -1Baniso -2Baniso -3
1-3.79 Å20.42 Å20.57 Å2
2---1.04 Å20.06 Å2
3----2.2 Å2
Refinement stepCycle: LAST / Resolution: 2.19→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 46 252 5308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225237
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9767079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96622.739230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92315926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8181540
X-RAY DIFFRACTIONr_chiral_restr0.0810.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023927
X-RAY DIFFRACTIONr_nbd_refined0.1880.22443
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23533
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2325
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.215
X-RAY DIFFRACTIONr_mcbond_it3.03643245
X-RAY DIFFRACTIONr_mcangle_it4.17765097
X-RAY DIFFRACTIONr_scbond_it3.27242257
X-RAY DIFFRACTIONr_scangle_it4.28261982
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2388 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.290.5
medium thermal0.552
LS refinement shellResolution: 2.188→2.244 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 84 -
Rwork0.278 1414 -
obs--54.51 %
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)
11.46030.3329-0.97072.7703-1.55293.9810.0833-0.08330.13450.34360.01260.1193-0.4485-0.3284-0.0958-0.11310.0762-0.0155-0.1686-0.0356-0.15520.78911.9885-0.0971
21.7818-0.6148-1.45632.46411.29944.67290.19030.15550.0883-0.5479-0.0227-0.0564-0.69210.1087-0.1676-0.04410.0018-0.0172-0.21980.0331-0.180128.1734-21.0164-24.9295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 9520 - 109
2X-RAY DIFFRACTION1AA96 - 322110 - 336
3X-RAY DIFFRACTION2BB5 - 9519 - 109
4X-RAY DIFFRACTION2BB96 - 324110 - 338

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