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- PDB-6nh9: Crystal structure of a human calcium/calmodulin dependent serine ... -

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Basic information

Entry
Database: PDB / ID: 6nh9
TitleCrystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain
ComponentsPeripheral plasma membrane protein CASK
KeywordsPROTEIN BINDING / PDZ domain / MAGUK protein family / peripheral plasma membrane protein / c-terminal peptide binding
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 / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / calcium ion import / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins ...negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / calcium ion import / Assembly and cell surface presentation of NMDA receptors / 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 / Pdz3 Domain / 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 / Roll / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsSun, Y.J. / Gakhar, L. / Fuentes, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association15GRNT25740021 United States
CitationJournal: To be published
Title: CASK PDZ domain specificity
Authors: Sun, Y.J. / Hou, T. / Fuentes, E.J.
History
DepositionDec 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peripheral plasma membrane protein CASK
B: Peripheral plasma membrane protein CASK
C: Peripheral plasma membrane protein CASK


Theoretical massNumber of molelcules
Total (without water)30,3573
Polymers30,3573
Non-polymers00
Water2,720151
1
A: Peripheral plasma membrane protein CASK


Theoretical massNumber of molelcules
Total (without water)10,1191
Polymers10,1191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peripheral plasma membrane protein CASK


Theoretical massNumber of molelcules
Total (without water)10,1191
Polymers10,1191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peripheral plasma membrane protein CASK


Theoretical massNumber of molelcules
Total (without water)10,1191
Polymers10,1191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.052, 35.400, 119.487
Angle α, β, γ (deg.)90.00, 90.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

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Components

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


Mass: 10118.886 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: M 485 Expression artifact G 486 Expression artifact
Source: (gene. exp.) Homo sapiens (human) / Gene: CASK, LIN2 / Production host: Escherichia coli (E. coli)
References: UniProt: O14936, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10.5 / Details: 30% v/v PEG 400 0.1M CAPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 23, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 1.85→59.77 Å / Num. obs: 20769 / % possible obs: 93.7 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.021 / Rpim(I) all: 0.021 / Rrim(I) all: 0.03 / Net I/σ(I): 10.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1910 / CC1/2: 0.911 / Rpim(I) all: 0.284 / Rrim(I) all: 0.402 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Blu-Icedata collection
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 1.85→59.743 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.65
RfactorNum. reflection% reflection
Rfree0.263 964 4.65 %
Rwork0.2261 --
obs0.2278 20739 93.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→59.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 0 151 2141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062032
X-RAY DIFFRACTIONf_angle_d0.5742728
X-RAY DIFFRACTIONf_dihedral_angle_d5.3091403
X-RAY DIFFRACTIONf_chiral_restr0.05314
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.94760.40041330.36042705X-RAY DIFFRACTION90
1.9476-2.06960.36151420.28312791X-RAY DIFFRACTION94
2.0696-2.22940.30071460.26152839X-RAY DIFFRACTION95
2.2294-2.45370.29981530.25872863X-RAY DIFFRACTION96
2.4537-2.80880.28781110.25882931X-RAY DIFFRACTION96
2.8088-3.53880.26351470.21852846X-RAY DIFFRACTION93
3.5388-59.77380.21441320.18692800X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 12.001 Å / Origin y: 5.2988 Å / Origin z: 30.4494 Å
111213212223313233
T0.2571 Å2-0.0563 Å20.0145 Å2-0.2675 Å20.0088 Å2--0.2529 Å2
L0.3174 °20.1129 °20.8788 °2-0.4363 °20.9417 °2--4.3481 °2
S0.0027 Å °0.1893 Å °-0.0367 Å °0.0701 Å °0.0965 Å °-0.0483 Å °-0.0379 Å °0.3184 Å °-0.0803 Å °
Refinement TLS groupSelection details: all

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