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- PDB-3bhh: Crystal structure of human calcium/calmodulin-dependent protein k... -

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Basic information

Entry
Database: PDB / ID: 3bhh
TitleCrystal structure of human calcium/calmodulin-dependent protein kinase IIB isoform 1 (CAMK2B)
ComponentsCalcium/calmodulin-dependent protein kinase type II beta chain
KeywordsTRANSFERASE / CAMK2B / CAM2 / CAMK2 / CaM kinase II beta chain / CAMK II beta subunit / Calcium/calmodulion dependent protein kinase II beta / EC:2.7.1.123 / MGC29528 / Proline rich calmodulin dependent protein kinase / Structural Genomics Consortium / SGC / ATP-binding / Calmodulin-binding / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


regulation of skeletal muscle adaptation / regulation of synapse structural plasticity / calcium- and calmodulin-dependent protein kinase complex / positive regulation of synapse maturation / regulation of dendritic spine development / Ca2+/calmodulin-dependent protein kinase / regulation of neuron migration / positive regulation of dendritic spine morphogenesis / Trafficking of AMPA receptors / calcium/calmodulin-dependent protein kinase activity ...regulation of skeletal muscle adaptation / regulation of synapse structural plasticity / calcium- and calmodulin-dependent protein kinase complex / positive regulation of synapse maturation / regulation of dendritic spine development / Ca2+/calmodulin-dependent protein kinase / regulation of neuron migration / positive regulation of dendritic spine morphogenesis / Trafficking of AMPA receptors / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / regulation of neuronal synaptic plasticity / regulation of calcium ion transport / Long-term potentiation / Regulation of MECP2 expression and activity / 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 / regulation of long-term neuronal synaptic plasticity / positive regulation of neuron projection development / 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 / Interferon gamma signaling / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / actin binding / nervous system development / RAF/MAP kinase cascade / protein autophosphorylation / cell differentiation / calmodulin binding / postsynaptic density / neuron projection / protein phosphorylation / protein serine kinase activity / centrosome / signal transduction / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-5CP / Calcium/calmodulin-dependent protein kinase type II subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsFilippakopoulos, P. / Rellos, P. / Niesen, F. / Burgess, N. / Bullock, A. / Berridge, G. / Pike, A.C.W. / Ugochukwu, E. / Pilka, E.S. / von Delft, F. ...Filippakopoulos, P. / Rellos, P. / Niesen, F. / Burgess, N. / Bullock, A. / Berridge, G. / Pike, A.C.W. / Ugochukwu, E. / Pilka, E.S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Calcium/Calmodulin-Dependent Protein Kinase IIB Isoform 1 (CAMK2B).
Authors: Filippakopoulos, P. / Rellos, P. / Niesen, F. / Burgess, N. / Bullock, A. / Berridge, G. / Pike, A.C.W. / Ugochukwu, E. / Pilka, E.S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Knapp, S.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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 beta chain
B: Calcium/calmodulin-dependent protein kinase type II beta chain
C: Calcium/calmodulin-dependent protein kinase type II beta chain
D: Calcium/calmodulin-dependent protein kinase type II beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,9796
Polymers134,2594
Non-polymers7212
Water4,720262
1
A: Calcium/calmodulin-dependent protein kinase type II beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9252
Polymers33,5651
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calcium/calmodulin-dependent protein kinase type II beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9252
Polymers33,5651
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Calcium/calmodulin-dependent protein kinase type II beta chain


Theoretical massNumber of molelcules
Total (without water)33,5651
Polymers33,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Calcium/calmodulin-dependent protein kinase type II beta chain


Theoretical massNumber of molelcules
Total (without water)33,5651
Polymers33,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.400, 79.200, 98.700
Angle α, β, γ (deg.)90.000, 104.500, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12C
22D
32C
42D
13A
23B
33C
43D

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETASPASPAA10 - 192 - 11
211METMETASPASPBB10 - 192 - 11
321SERSERTHRTHRAA26 - 9418 - 86
421SERSERTHRTHRBB26 - 9418 - 86
112METMETILEILECC10 - 202 - 12
212METMETILEILEDD10 - 202 - 12
322VALVALTHRTHRCC28 - 9420 - 86
422VALVALTHRTHRDD28 - 9420 - 86
113GLYGLYLEULEUAA95 - 30087 - 292
213GLYGLYLEULEUBB95 - 30087 - 292
313GLYGLYLEULEUCC95 - 30087 - 292
413GLYGLYLEULEUDD95 - 30087 - 292

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Calcium/calmodulin-dependent protein kinase type II beta chain / CaM-kinase II beta chain / CaM kinase II subunit beta / CaMK-II subunit beta


Mass: 33564.625 Da / Num. of mol.: 4 / Fragment: Residues 11-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2B, CAM2, CAMKB / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(R3)
References: UniProt: Q13554, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-5CP / [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-6-(methylamino)pyrimidin-2-yl}amino)phenyl]acetonitrile


Mass: 360.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 50% PEG 300, 0.2M NaCl, 0.1M Na/KPO4 pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97649 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97649 Å / Relative weight: 1
ReflectionResolution: 2.4→47.78 Å / Num. all: 50945 / Num. obs: 50690 / % possible obs: 99.5 % / Redundancy: 3.76 % / Rmerge(I) obs: 0.1157 / Rsym value: 0.1157 / Net I/σ(I): 9.77
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.4431 / Mean I/σ(I) obs: 2.69 / Num. unique all: 5776 / Rsym value: 0.4431 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.78 Å
Translation2.5 Å47.78 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 50687
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
11.3-10030.40.642507
8.53-11.325.10.86665
7.13-8.5333.90.874822
6.25-7.1343.50.845964
5.63-6.2545.60.8241064
5.17-5.6346.50.8521171
4.8-5.1741.70.8881261
4.51-4.838.20.8891339
4.26-4.5135.60.91431
4.05-4.2635.80.8971515
3.86-4.0536.40.8871568
3.7-3.8637.10.8781639
3.56-3.737.20.8711689
3.43-3.5636.30.8741778
3.32-3.4338.40.871852
3.22-3.3237.90.8681901
3.12-3.2237.90.8681964
3.04-3.12370.8662034
2.96-3.04390.8572044
2.88-2.9638.90.8762111
2.81-2.88400.8742185
2.75-2.8139.40.8722237
2.69-2.7537.10.8712289
2.64-2.6937.30.8612304
2.58-2.6438.20.8662373
2.53-2.5838.20.8652425
2.49-2.5338.40.8712466
2.44-2.4937.30.8672547
2.4-2.4439.40.8492542

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Processing

Software
NameVersionClassificationNB
PHASERphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2V7O

2v7o


Resolution: 2.4→47.78 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.862 / SU B: 20.258 / SU ML: 0.238 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.462 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2575 5.1 %RANDOM
Rwork0.223 ---
all0.225 48113 --
obs0.225 48113 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-2.35 Å2
2---1.01 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8617 0 54 262 8933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0218880
X-RAY DIFFRACTIONr_bond_other_d0.0030.025650
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.94712112
X-RAY DIFFRACTIONr_angle_other_deg1.1223.00113740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07751141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06223.526363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36151291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8871543
X-RAY DIFFRACTIONr_chiral_restr0.0810.21379
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210088
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021824
X-RAY DIFFRACTIONr_nbd_refined0.1850.21673
X-RAY DIFFRACTIONr_nbd_other0.20.25769
X-RAY DIFFRACTIONr_nbtor_refined0.1770.24161
X-RAY DIFFRACTIONr_nbtor_other0.0930.24487
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2284
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0620.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4020.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.213
X-RAY DIFFRACTIONr_mcbond_it1.71235837
X-RAY DIFFRACTIONr_mcbond_other1.24532312
X-RAY DIFFRACTIONr_mcangle_it2.18659063
X-RAY DIFFRACTIONr_scbond_it4.58583498
X-RAY DIFFRACTIONr_scangle_it5.597113043
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A471TIGHT POSITIONAL0.050.05
11B503MEDIUM POSITIONAL0.050.5
11C471TIGHT THERMAL0.190.5
11D503MEDIUM THERMAL0.152
22A465TIGHT POSITIONAL0.060.05
22B430MEDIUM POSITIONAL0.070.5
22C465TIGHT THERMAL0.170.5
22D430MEDIUM THERMAL0.172
33A1212TIGHT POSITIONAL0.050.05
33B1212TIGHT POSITIONAL0.050
33C1212TIGHT POSITIONAL0.060
33D1212TIGHT POSITIONAL0.060
33A1214MEDIUM POSITIONAL0.060.5
33B1214MEDIUM POSITIONAL0.050
33C1214MEDIUM POSITIONAL0.060
33D1214MEDIUM POSITIONAL0.060
33A1212TIGHT THERMAL0.170.5
33B1212TIGHT THERMAL0.170
33C1212TIGHT THERMAL0.190
33D1212TIGHT THERMAL0.170
33A1214MEDIUM THERMAL0.152
33B1214MEDIUM THERMAL0.140
33C1214MEDIUM THERMAL0.170
33D1214MEDIUM THERMAL0.150
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 171 -
Rwork0.278 3435 -
all-3606 -
obs--96.24 %
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)
10.7544-0.24740.31982.01820.66312.0164-0.0814-0.09760.08890.1760.0069-0.071-0.1173-0.0370.07450.0334-0.02930.00970.0378-0.00570.064726.327463.397631.0364
22.5057-0.41050.8813.4645-0.82283.20780.04420.0563-0.1237-0.16950.00980.20670.0815-0.0968-0.0540.0155-0.0337-0.0111-0.0311-0.0449-0.009217.54949.330416.3436
32.0048-0.66371.35961.506-0.28892.06030.02110.0812-0.02450.04480.0281-0.06020.01830.1494-0.04930.0168-0.02310.04350.02730.01960.011330.809630.227-11.6798
42.01470.08250.79293.0238-0.0844.5481-0.18820.05640.1609-0.09050.0393-0.0878-0.32790.0820.1488-0.00990.0214-0.0141-0.00770.0530.012321.439243.9177-26.3117
50.4913-0.17570.95060.9756-0.66241.9534-0.0847-0.15240.03030.23570.0821-0.1172-0.10340.05970.00260.0389-0.00010.00230.06230.00380.085815.683814.175726.0144
62.0422-0.8532-0.41111.95630.42221.83230.0253-0.02120.0544-0.0875-0.0376-0.1036-0.08210.05770.0123-0.0526-0.0221-0.0158-0.06040.0104-0.028110.825222.10726.1194
71.0067-0.26681.44241.09660.11132.3044-0.04640.1599-0.15610.05930.11060.07770.0488-0.0203-0.06420.03540.00090.04090.05370.00320.055555.816340.143823.167
82.67220.75260.49962.60410.07232.54670.14220.152-0.21330.10070.104-0.30750.28370.1992-0.24620.00850.0514-0.0395-0.032-0.03730.004772.47332.457835.363
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 1631 - 155
2X-RAY DIFFRACTION2AA164 - 301156 - 293
3X-RAY DIFFRACTION3BB10 - 1632 - 155
4X-RAY DIFFRACTION4BB164 - 301156 - 293
5X-RAY DIFFRACTION5CC10 - 1632 - 155
6X-RAY DIFFRACTION6CC164 - 300156 - 292
7X-RAY DIFFRACTION7DD10 - 1632 - 155
8X-RAY DIFFRACTION8DD164 - 300156 - 292

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