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- PDB-2vn9: Crystal Structure of Human Calcium Calmodulin dependent Protein K... -

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Basic information

Entry
Database: PDB / ID: 2vn9
TitleCrystal Structure of Human Calcium Calmodulin dependent Protein Kinase II delta isoform 1, CAMKD
ComponentsCALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / SERINE-THREONINE KINASE / CELLULAR DIFFERENTIATION / VASCULAR SMOOTH MUSCLE / KINASE / ATP-BINDING / PHOSPHOPROTEIN / CALMODULIN-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / regulation of cardiac muscle cell action potential involved in regulation of contraction / calcium- and calmodulin-dependent protein kinase complex / regulation of cell communication by electrical coupling / Ca2+/calmodulin-dependent protein kinase / regulation of membrane depolarization / regulation of the force of heart contraction / Trafficking of AMPA receptors ...regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / regulation of cardiac muscle cell action potential involved in regulation of contraction / calcium- and calmodulin-dependent protein kinase complex / regulation of cell communication by electrical coupling / Ca2+/calmodulin-dependent protein kinase / regulation of membrane depolarization / regulation of the force of heart contraction / Trafficking of AMPA receptors / endoplasmic reticulum calcium ion homeostasis / sodium channel inhibitor activity / cardiac muscle cell contraction / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / relaxation of cardiac muscle / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / CaMK IV-mediated phosphorylation of CREB / positive regulation of cardiac muscle hypertrophy / regulation of cardiac muscle cell action potential / regulation of heart contraction / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / Regulation of MECP2 expression and activity / regulation of neuronal synaptic plasticity / HSF1-dependent transactivation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of cardiac muscle cell apoptotic process / regulation of protein localization to plasma membrane / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / sarcoplasmic reticulum membrane / Ras activation upon Ca2+ influx through NMDA receptor / cellular response to calcium ion / regulation of cell growth / RAF activation / sarcolemma / long-term synaptic potentiation / Interferon gamma signaling / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / RAF/MAP kinase cascade / transmembrane transporter binding / calmodulin binding / protein phosphorylation / neuron projection / postsynaptic density / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-GVD / PHOSPHATE ION / Calcium/calmodulin-dependent protein kinase type II subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRoos, A.K. / Rellos, P. / Salah, E. / Pike, A.C.W. / Fedorov, O. / Pilka, E.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Roos, A.K. / Rellos, P. / Salah, E. / Pike, A.C.W. / Fedorov, O. / Pilka, E.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Knapp, S.
CitationJournal: Plos Biol. / Year: 2010
Title: Structure of the Camkiidelta/Calmodulin Complex Reveals the Molecular Mechanism of Camkii Kinase Activation.
Authors: Rellos, P. / Pike, A.C.W. / Niesen, F.H. / Salah, E. / Lee, W.H. / von Delft, F. / Knapp, S.
History
DepositionJan 31, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.3Dec 13, 2017Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.gene_src_common_name ..._citation_author.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
B: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,92310
Polymers68,5072
Non-polymers1,4178
Water1,74797
1
A: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0996
Polymers34,2531
Non-polymers8455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8254
Polymers34,2531
Non-polymers5713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.276, 68.276, 313.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: -1 - 309 / Label seq-ID: 1 - 301

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

NCS oper: (Code: given
Matrix: (-0.501, -0.82, 0.275), (-0.865, 0.48, -0.145), (-0.013, -0.311, -0.95)
Vector: 13.43522, 58.73976, 58.85304)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN / CAM-KINASE II DELTA CHAIN / CAM KINASE II SUBUNIT DELTA / CAMK-II SUBUNIT DELTA / CALCIUM ...CAM-KINASE II DELTA CHAIN / CAM KINASE II SUBUNIT DELTA / CAMK-II SUBUNIT DELTA / CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE II DELTA ISOFORM 1


Mass: 34253.457 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 11-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-PRARE2
References: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase

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Non-polymers , 5 types, 105 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GVD / [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE


Mass: 381.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19N7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.85 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.5 / Details: 1.6 M NAKPO4 HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98248
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98248 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. obs: 39106 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V7O

2v7o


Resolution: 2.3→43.03 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 15.783 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1960 5 %RANDOM
Rwork0.211 ---
obs0.213 37042 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20.57 Å20 Å2
2--1.15 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 94 97 4912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224928
X-RAY DIFFRACTIONr_bond_other_d0.0020.023332
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9766686
X-RAY DIFFRACTIONr_angle_other_deg0.9763.0018071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02523.796216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52515820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5221530
X-RAY DIFFRACTIONr_chiral_restr0.080.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215440
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02980
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.68433000
X-RAY DIFFRACTIONr_mcbond_other0.8731210
X-RAY DIFFRACTIONr_mcangle_it2.48154823
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.49581928
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.576111857
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3959 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
1Atight thermal0.160.5
2Btight thermal0.160.5
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 140 -
Rwork0.298 2704 -
obs--99.89 %
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)
14.7580.43870.72318.4181.91611.652-0.3062-0.30870.5231-0.09870.13270.2238-0.7694-0.41470.1735-0.4185-0.03720.02420.1348-0.02220.059612.480237.930755.7746
26.7529-3.0149-0.35441.81970.94491.3251-0.1694-0.3660.45050.09630.07960.018-0.0176-0.12050.0898-0.4955-0.03430.00550.13710.0496-0.1308-0.275330.218553.5075
33.35980.505-0.23681.90791.25582.0951-0.27710.606-0.3184-0.42130.2423-0.11340.1423-0.07560.0348-0.2976-0.14460.07770.10630.023-0.17767.008415.675736.1947
47.46210.71621.00517.4556-0.382610.1546-0.2801-0.02990.4969-0.46170.29550.2677-0.3389-0.6191-0.01550.1722-0.2799-0.1864-0.09160.06210.0591-8.593957.9775-6.0806
50.21880.32490.72258.9965-2.13543.5945-0.35330.05360.2378-0.98190.11940.2851-0.12040.06870.23390.2174-0.337-0.1012-0.15210.0336-0.14193.795465.3807-1.354
61.55560.15491.60794.0334-2.59825.6129-0.2961-0.52240.11370.13630.1430.0182-0.4519-0.34150.1531-0.1601-0.12170.00390.0152-0.0134-0.25017.059754.94219.5083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 39
2X-RAY DIFFRACTION2A40 - 83
3X-RAY DIFFRACTION3A84 - 309
4X-RAY DIFFRACTION4B-1 - 39
5X-RAY DIFFRACTION5B40 - 83
6X-RAY DIFFRACTION6B84 - 309

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