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- PDB-1kgd: Crystal Structure of the Guanylate Kinase-like Domain of Human CASK -

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Basic information

Entry
Database: PDB / ID: 1kgd
TitleCrystal Structure of the Guanylate Kinase-like Domain of Human CASK
ComponentsPERIPHERAL PLASMA MEMBRANE CASK
KeywordsPROTEIN BINDING / MAGUK / CASK / GUANYLATE KINASE LIKE 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 / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding 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 ...CASK, SH3 domain / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding 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 / P-loop containing nucleotide triphosphate hydrolases / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.314 Å
AuthorsLi, Y. / Spangenberg, O. / Paarmann, I. / Konrad, M. / Lavie, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structural basis for nucleotide-dependent regulation of membrane-associated guanylate kinase-like domains.
Authors: Li, Y. / Spangenberg, O. / Paarmann, I. / Konrad, M. / Lavie, A.
History
DepositionNov 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PERIPHERAL PLASMA MEMBRANE CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9856
Polymers20,7551
Non-polymers2305
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.341, 70.341, 74.861
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PERIPHERAL PLASMA MEMBRANE CASK / CASK


Mass: 20754.535 Da / Num. of mol.: 1 / Fragment: guanylate kinase like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O14936
#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium formate, potassium chloride, magnesium chloride, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 Msodium formate1reservoir
215 mg/mlprotein1drop
350 mMTris-HCl1droppH7.5
4200 mM1dropKCl
55 mM1dropMgCl2
61 mMEDTA1drop
710 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.31→50 Å / Num. obs: 48853 / % possible obs: 94.2 % / Redundancy: 6.7 % / Rsym value: 0.034 / Net I/σ(I): 20.9
Reflection shellResolution: 1.31→1.4 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 8.31 / Rsym value: 0.145 / % possible all: 81
Reflection
*PLUS
Num. measured all: 327011 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 81 % / Rmerge(I) obs: 0.145

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.314→12 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.232 / SU ML: 0.04 / Isotropic thermal model: BABINET MODEL WITH MASK / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.064 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21244 4927 10.1 %RANDOM
Rwork0.18552 ---
obs0.18818 43926 95.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 25.768 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.24 Å20 Å2
2--0.49 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.314→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 0 233 1699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211466
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9521978
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2383173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33615268
X-RAY DIFFRACTIONr_chiral_restr0.090.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2490.3715
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3690.5204
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.355
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.522
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9371.5885
X-RAY DIFFRACTIONr_mcangle_it1.66821424
X-RAY DIFFRACTIONr_scbond_it2.1973581
X-RAY DIFFRACTIONr_scangle_it3.5594.5554
X-RAY DIFFRACTIONr_rigid_bond_restr1.10421466
X-RAY DIFFRACTIONr_sphericity_free1.3152219
X-RAY DIFFRACTIONr_sphericity_bonded1.58921440
LS refinement shellResolution: 1.314→1.348 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.236 281
Rwork0.209 2433
obs-48853
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10.1 % / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.0055
X-RAY DIFFRACTIONp_angle_d2.371
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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