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- PDB-3mfu: CASK-4M CaM Kinase Domain, AMPPNP-Mn2+ -

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Basic information

Entry
Database: PDB / ID: 3mfu
TitleCASK-4M CaM Kinase Domain, AMPPNP-Mn2+
ComponentsPeripheral plasma membrane protein CASK
KeywordsTRANSFERASE / Catalytic mechanism / kinase catalysis / Mg2+-mediated phosphate transfer / protein kinase
Function / homology
Function and homology information


negative regulation of cellular response to growth factor stimulus / GMP kinase activity / neurexin family protein binding / Dopamine Neurotransmitter Release Cycle / negative regulation of wound healing / regulation of neurotransmitter secretion / nuclear lamina / calcium ion import / Nephrin family interactions / Assembly and cell surface presentation of NMDA receptors ...negative regulation of cellular response to growth factor stimulus / GMP kinase activity / neurexin family protein binding / Dopamine Neurotransmitter Release Cycle / negative regulation of wound healing / regulation of neurotransmitter secretion / nuclear lamina / calcium ion import / Nephrin family interactions / 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 / regulation of synaptic vesicle exocytosis / positive regulation of calcium ion import / basement membrane / negative regulation of cell-matrix adhesion / negative regulation of keratinocyte proliferation / establishment of localization in cell / Schaffer collateral - CA1 synapse / nuclear matrix / intracellular protein localization / cell-cell junction / actin cytoskeleton / presynaptic membrane / basolateral plasma membrane / vesicle / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / cell adhesion / signaling receptor binding / protein serine kinase activity / focal adhesion / 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. ...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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWahl, M.C. / Mukherjee, K.
CitationJournal: Sci.Signal. / Year: 2010
Title: Evolution of CASK into a Mg2+-sensitive kinase.
Authors: Mukherjee, K. / Sharma, M. / Jahn, R. / Wahl, M.C. / Sudhof, T.C.
History
DepositionApr 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8523
Polymers39,2911
Non-polymers5612
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.900, 62.005, 100.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 39291.047 Da / Num. of mol.: 1 / Fragment: CASK-4M CaM kinase domain, residues 1-337 / Mutation: Pro22Ala, His145Glu, Gly162Asp, Cys146Asn
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASK, LIN2 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14936, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.34 Å3/Da / Density % sol: 47.39 %
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: BESSY / Beamline: 14.2 / Wavelength: 1.87856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.87856 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 31627 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 51.1 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1968 / Rsym value: 0.497 / % possible all: 83.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C0I

3c0i


Resolution: 2.3→19.65 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 13.302 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.298 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23434 836 5 %RANDOM
Rwork0.17913 ---
all0.18192 16714 --
obs0.18192 15878 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20 Å2
2---1.04 Å20 Å2
3---1.85 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 32 190 2636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222519
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9833407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78823.009113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67315450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5971520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021883
X-RAY DIFFRACTIONr_nbd_refined0.20.21189
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21697
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2183
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.216
X-RAY DIFFRACTIONr_mcbond_it0.5891.51558
X-RAY DIFFRACTIONr_mcangle_it1.03322440
X-RAY DIFFRACTIONr_scbond_it1.52331092
X-RAY DIFFRACTIONr_scangle_it2.4934.5967
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 52 -
Rwork0.209 994 -
obs-1046 100 %
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)
17.1098-4.68270.49677.74690.71061.7348-0.0378-0.8071-0.00870.7970.16130.59160.0837-0.1731-0.1235-0.0683-0.05960.1107-0.1555-0.0859-0.0545-33.02215.0233.911
21.5383-0.39380.49785.2451-0.31243.00320.1803-0.114-0.1568-0.4396-0.09350.45730.3189-0.127-0.0868-0.0372-0.0158-0.0709-0.3013-0.0275-0.0803-25.844-5.265-11.203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 94
2X-RAY DIFFRACTION2A95 - 306

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