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

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Basic information

Entry
Database: PDB / ID: 6nid
TitleCrystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain in complex with Neurexin-1 peptide
Components
  • Neurexin-1
  • Peripheral plasma membrane protein CASK
Keywordsprotein binding/peptide / PDZ domain / MAGUK protein family / peripheral plasma membrane protein / protein binding / c-terminal peptide binding / Neurexin / protein binding-peptide complex
Function / homology
Function and homology information


gephyrin clustering involved in postsynaptic density assembly / negative regulation of cellular response to growth factor stimulus / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / vocal learning / guanylate kinase activity / neuroligin family protein binding / positive regulation of synapse maturation / Dopamine Neurotransmitter Release Cycle ...gephyrin clustering involved in postsynaptic density assembly / negative regulation of cellular response to growth factor stimulus / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / vocal learning / guanylate kinase activity / neuroligin family protein binding / positive regulation of synapse maturation / Dopamine Neurotransmitter Release Cycle / neuron cell-cell adhesion / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / vocalization behavior / neurotransmitter secretion / calcium ion import / acetylcholine receptor binding / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / positive regulation of synapse assembly / 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 / adult behavior / negative regulation of cell-matrix adhesion / positive regulation of calcium ion import / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / Non-integrin membrane-ECM interactions / calcium channel regulator activity / basement membrane / negative regulation of keratinocyte proliferation / cell adhesion molecule binding / synapse assembly / positive regulation of synaptic transmission, glutamatergic / learning / cell projection / establishment of localization in cell / axon guidance / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / actin cytoskeleton / presynaptic membrane / signaling receptor activity / chemical synaptic transmission / basolateral plasma membrane / nuclear membrane / vesicle / non-specific serine/threonine protein kinase / calmodulin binding / cell adhesion / phosphorylation / protein serine kinase activity / focal adhesion / signaling receptor binding / protein serine/threonine kinase activity / neuronal cell body / calcium ion binding / nucleolus / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CASK, SH3 domain / Syndecan/Neurexin domain / Syndecan domain / L27 domain, C-terminal / L27 domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. ...CASK, SH3 domain / Syndecan/Neurexin domain / Syndecan domain / L27 domain, C-terminal / L27 domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G 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 / Pdz3 Domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / Epidermal growth factor-like domain. / EGF-like domain profile. / PDZ domain / EGF-like 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 / Concanavalin A-like lectin/glucanase domain superfamily / 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 / Neurexin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
D: Neurexin-1
E: Neurexin-1
F: Neurexin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3747
Polymers34,3126
Non-polymers621
Water3,801211
1
A: Peripheral plasma membrane protein CASK
E: Neurexin-1


Theoretical massNumber of molelcules
Total (without water)11,4372
Polymers11,4372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-4 kcal/mol
Surface area5650 Å2
MethodPISA
2
B: Peripheral plasma membrane protein CASK
D: Neurexin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4993
Polymers11,4372
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-4 kcal/mol
Surface area5860 Å2
MethodPISA
3
C: Peripheral plasma membrane protein CASK
F: Neurexin-1


Theoretical massNumber of molelcules
Total (without water)11,4372
Polymers11,4372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-4 kcal/mol
Surface area5750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.328, 51.177, 72.412
Angle α, β, γ (deg.)90.00, 97.72, 90.00
Int Tables number4
Space group name H-MP1211

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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: Protein/peptide Neurexin-1 / Neurexin I-alpha / Neurexin-1-alpha


Mass: 1318.517 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9ULB1
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.01M tri-sodium citrate 33% (w/v) PEG 6000

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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: May 12, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 1.86→51.18 Å / Num. obs: 21400 / % possible obs: 96.1 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.056 / Rrim(I) all: 0.081 / Net I/σ(I): 13.2
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2 / Num. unique obs: 2574 / CC1/2: 0.798 / Rpim(I) all: 0.361 / Rrim(I) all: 0.519 / % possible all: 80.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Blu-Icedata collection
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NH9

6nh9


Resolution: 1.86→41.666 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.37
RfactorNum. reflection% reflection
Rfree0.2396 1041 4.87 %
Rwork0.1918 --
obs0.1942 21376 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→41.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 4 211 2405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052295
X-RAY DIFFRACTIONf_angle_d0.6733086
X-RAY DIFFRACTIONf_dihedral_angle_d2.8741912
X-RAY DIFFRACTIONf_chiral_restr0.054346
X-RAY DIFFRACTIONf_plane_restr0.004403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.95810.34521070.24222393X-RAY DIFFRACTION79
1.9581-2.08080.24931470.20732849X-RAY DIFFRACTION95
2.0808-2.24140.26061560.19823020X-RAY DIFFRACTION100
2.2414-2.46690.26271700.2072982X-RAY DIFFRACTION100
2.4669-2.82380.27191490.20983022X-RAY DIFFRACTION100
2.8238-3.55750.21451500.18893018X-RAY DIFFRACTION99
3.5575-41.67610.20521620.16313051X-RAY DIFFRACTION98

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