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- PDB-2ux0: Structure of the oligomerisation domain of calcium-calmodulin dep... -

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Basic information

Entry
Database: PDB / ID: 2ux0
TitleStructure of the oligomerisation domain of calcium-calmodulin dependent protein kinase II gamma
ComponentsCALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
KeywordsTRANSFERASE / CALMODULIN / PROTEIN KINASE / OLIGOMERISATION DOMAIN / SERINE- THREONINE KINASE / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE.
Function / homology
Function and homology information


regulation of skeletal muscle adaptation / calcium-dependent protein serine/threonine phosphatase activity / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / Trafficking of AMPA receptors / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / insulin secretion / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB ...regulation of skeletal muscle adaptation / calcium-dependent protein serine/threonine phosphatase activity / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / Trafficking of AMPA receptors / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / insulin secretion / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / regulation of neuron projection development / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of calcium ion transport / Ion transport by P-type ATPases / Long-term potentiation / Regulation of MECP2 expression and activity / regulation of neuronal synaptic plasticity / HSF1-dependent transactivation / regulation of protein localization to plasma membrane / Ion homeostasis / sarcoplasmic reticulum membrane / Ras activation upon Ca2+ influx through NMDA receptor / RAF activation / 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 / nervous system development / RAF/MAP kinase cascade / cell differentiation / calmodulin binding / neuron projection / postsynaptic density / protein serine kinase activity / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
GLYCINE / Calcium/calmodulin-dependent protein kinase type II subunit gamma / Calcium/calmodulin-dependent protein kinase type II subunit gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsBunkoczi, G. / Debreczeni, J.E. / Salah, E. / Gileadi, O. / Rellos, P. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / von Delft, F. ...Bunkoczi, G. / Debreczeni, J.E. / Salah, E. / Gileadi, O. / Rellos, P. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / von Delft, F. / Turnbull, A. / Pike, A.C.W. / 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
DepositionMar 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
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_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_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 (CAM KINASE) II GAMMA
B: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
C: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
D: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
E: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
F: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,62811
Polymers98,2526
Non-polymers3755
Water1,78399
1
A: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
B: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
C: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
D: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
E: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
F: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
hetero molecules

A: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
B: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
C: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
D: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
E: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
F: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,25522
Polymers196,50512
Non-polymers75110
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area26160 Å2
ΔGint-213.5 kcal/mol
Surface area70370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.954, 158.363, 103.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A389 - 452
2112B389 - 452
3112C389 - 452
4112D389 - 452
5112E389 - 452
6112F389 - 452
1214A453 - 456
2214B453 - 456
3214C453 - 456
4214D453 - 456
5214E453 - 456
6214F453 - 456
1312A457 - 488
2312B457 - 488
3312C457 - 488
4312D457 - 488
5312E457 - 488
6312F457 - 488
1414A489 - 491
2414B489 - 491
3414C489 - 491
4414D489 - 491
5414E489 - 491
6414F489 - 491
1512A492 - 521
2512B492 - 521
3512C492 - 521
4512D492 - 521
5512E492 - 521
6512F492 - 521

NCS oper:
IDCodeMatrixVector
1given(0.60631, -0.7661, -0.21328), (0.7701, 0.49876, 0.39772), (-0.19832, -0.40539, 0.89237)-25.2648, -30.38748, -13.51065
2given(-0.19034, -0.77142, -0.6072), (0.76619, -0.50342, 0.39939), (-0.61377, -0.38921, 0.68687)-15.23708, -70.81217, -7.40988
3given(-0.58854, 0.00228, -0.80847), (-0.0039, -0.99999, 2.0E-5), (-0.80846, 0.00316, 0.58854)20.91674, -80.33826, 10.94072
4given(-0.18421, 0.77312, -0.60692), (-0.76885, -0.49802, -0.40105), (-0.61232, 0.39275, 0.68615)46.91051, -49.61198, 23.78858
5given(0.6034, 0.77188, -0.20029), (-0.77113, 0.50079, -0.39316), (-0.20317, 0.39168, 0.89739)36.28653, -9.81225, 18.48212

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Components

#1: Protein
CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA


Mass: 16375.393 Da / Num. of mol.: 6 / Fragment: OLIGOMERISATION DOMAIN, RESIDUES 387-527 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8N4I3, UniProt: Q13555*PLUS, EC: 2.7.1.123
#2: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN B, LEU 526 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN B, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN C, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN D, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN E, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN F, LEU 526 TO ARG
Sequence detailsTHE L526R MUTATION IS FROM THE ENTRY CLONE THAT HAS BEEN SEQUENCED AFTER IDENTIFICATION OF THE MASS DIFFERENCE

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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: 2.64 Å3/Da / Density % sol: 53 %
Crystal growpH: 7 / Details: 0.1 M SPG PH 7.0, 60% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 21, 2006
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.46→39.7 Å / Num. obs: 29117 / % possible obs: 78.2 % / Observed criterion σ(I): 0 / Redundancy: 2.63 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.4
Reflection shellResolution: 2.46→2.56 Å / Redundancy: 0.13 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.45 / % possible all: 10.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HKX

1hkx


Resolution: 2.46→39.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 21.332 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.982 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1467 5 %RANDOM
Rwork0.184 ---
obs0.186 27628 78.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20 Å2
2---0.54 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.46→39.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6360 0 25 99 6484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216530
X-RAY DIFFRACTIONr_bond_other_d0.0020.024202
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9318880
X-RAY DIFFRACTIONr_angle_other_deg0.91310256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1015809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.55624.63324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.891151013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5571530
X-RAY DIFFRACTIONr_chiral_restr0.0710.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027405
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021313
X-RAY DIFFRACTIONr_nbd_refined0.2090.21152
X-RAY DIFFRACTIONr_nbd_other0.1880.23942
X-RAY DIFFRACTIONr_nbtor_refined0.1770.23072
X-RAY DIFFRACTIONr_nbtor_other0.0850.23530
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.252
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8234222
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.41656545
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.98582674
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.668112335
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 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A738tight positional0.040.05
2B738tight positional0.040.05
3C738tight positional0.040.05
4D738tight positional0.030.05
5E738tight positional0.030.05
6F738tight positional0.030.05
1A909medium positional0.410.5
2B909medium positional0.320.5
3C909medium positional0.30.5
4D909medium positional0.370.5
5E909medium positional0.350.5
6F909medium positional0.290.5
1A738tight thermal0.080.5
2B738tight thermal0.080.5
3C738tight thermal0.080.5
4D738tight thermal0.070.5
5E738tight thermal0.070.5
6F738tight thermal0.070.5
1A909medium thermal0.82
2B909medium thermal0.82
3C909medium thermal0.682
4D909medium thermal0.692
5E909medium thermal0.682
6F909medium thermal0.72
LS refinement shellResolution: 2.46→2.52 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.405 6
Rwork0.475 195
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)
10.8671-0.46110.19574.75230.13662.6830.09540.29560.0263-0.5306-0.21740.00380.0404-0.01280.122-0.01170.0308-0.01620.0385-0.0663-0.0074-19.9583-60.07843.44
24.8976-1.14482.26961.0795-0.35764.29110.29350.7231-0.3206-0.296-0.1607-0.16820.51480.5194-0.13270.05010.1164-0.02080.0216-0.0442-0.03278.0281-74.518918.1934
32.48961.01330.34322.7970.95782.20590.01110.30830.0183-0.3548-0.077-0.5031-0.04580.73640.0659-0.0577-0.01050.01110.26860.1180.104232.8026-54.535330.8115
42.2781-0.9349-1.35015.2144-0.51141.95250.12470.34770.2399-0.4258-0.162-1.0571-0.28360.27920.03740.0659-0.12930.0510.13170.12650.312729.4705-20.527328.7426
53.8401-0.5910.92241.7424-1.07452.7759-0.01360.46420.2853-0.3601-0.2132-0.0801-0.21880.29380.22680.06290.03710.00380.220.0730.05531.9976-5.616614.8346
61.58941.58990.06614.16530.02822.6536-0.11710.34970.0817-0.82010.05050.2833-0.1594-0.12270.06670.14530.0935-0.15460.1644-0.04220.1326-22.1673-26.11212.3191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A385 - 521
2X-RAY DIFFRACTION2B385 - 521
3X-RAY DIFFRACTION3C385 - 521
4X-RAY DIFFRACTION4D385 - 521
5X-RAY DIFFRACTION5E385 - 521
6X-RAY DIFFRACTION6F385 - 521

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