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- PDB-9blh: Crystal structure of calcium/calmodulin-dependent protein kinase ... -

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Basic information

Entry
Database: PDB / ID: 9blh
TitleCrystal structure of calcium/calmodulin-dependent protein kinase type II subunit delta complexed with ribociclib
ComponentsCalcium/calmodulin-dependent protein kinase type II subunit delta
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE / PROTEIN KINASE / PHOSPHORYLATION / CALCIUM/CALMODULIN / CYTOSOLIC / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / RIBOCICLIB / TRANSFERASE
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 ...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 / cardiac muscle cell contraction / sodium channel inhibitor activity / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / relaxation of cardiac muscle / CaMK IV-mediated phosphorylation of CREB / regulation of cardiac muscle cell action potential / regulation of heart contraction / regulation of cell communication by electrical coupling involved in cardiac conduction / positive regulation of cardiac muscle hypertrophy / 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 neuronal synaptic plasticity / Long-term potentiation / Regulation of MECP2 expression and activity / regulation of ryanodine-sensitive calcium-release channel activity / HSF1-dependent transactivation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of protein localization to plasma membrane / positive regulation of cardiac muscle cell apoptotic process / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / sarcoplasmic reticulum membrane / peptidyl-threonine phosphorylation / 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 / Signaling by BRAF and RAF1 fusions / endocytic vesicle membrane / peptidyl-serine phosphorylation / RAF/MAP kinase cascade / protein autophosphorylation / transmembrane transporter binding / calmodulin binding / neuron projection / postsynaptic density / protein phosphorylation / 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 / 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 / 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. ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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
Similarity search - Domain/homology
Chem-6ZZ / Calcium/calmodulin-dependent protein kinase type II subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsTomchick, D.R. / Majumdar, A. / Tagliabracci, V.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137419 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM147532 United States
Robert A. Welch FoundationI-1911 United States
Robert A. Welch FoundationI-1704 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Bacterial ubiquitin ligase engineered for small molecule and protein target identification
Authors: Ye, J.S. / Majumdar, A. / Park, B.C. / Black, M.H. / Hsieh, T.-S. / Osinski, A. / Servage, K.A. / Kulkarni, K. / Naidoo, J. / Alto, N.M. / Stratton, M.M. / Ready, J.M. / Pawlowski, K. / ...Authors: Ye, J.S. / Majumdar, A. / Park, B.C. / Black, M.H. / Hsieh, T.-S. / Osinski, A. / Servage, K.A. / Kulkarni, K. / Naidoo, J. / Alto, N.M. / Stratton, M.M. / Ready, J.M. / Pawlowski, K. / Tomchick, D.R. / Tagliabracci, V.
History
DepositionApr 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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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 subunit delta
B: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2344
Polymers68,3652
Non-polymers8692
Water1,31573
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A: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6172
Polymers34,1821
Non-polymers4351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6172
Polymers34,1821
Non-polymers4351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.322, 82.817, 172.914
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 34182.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2D, CAMKD / Production host: Escherichia coli (E. coli)
References: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-6ZZ / 7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide / Ribociclib


Mass: 434.537 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H30N8O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M CaCl2, 0.15 M NaCl, 12% (w/v) PEG 3350, 0.7 mM ribociclib and 35% (w/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 28133 / % possible obs: 98.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.76 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.024 / Rrim(I) all: 0.066 / Χ2: 0.918 / Net I/σ(I): 9.1 / Num. measured all: 193322
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.35-2.394.90.79111680.7420.9230.3570.8720.84482.6
2.39-2.435.30.71513220.7640.9310.3110.7830.86292.4
2.43-2.485.70.68413260.8480.9580.2920.7460.8397.4
2.48-2.536.20.61913890.8890.970.2540.6710.82999.3
2.53-2.596.60.5614270.9150.9780.2270.6060.84699.3
2.59-2.656.60.51413600.9320.9820.210.5560.87999.9
2.65-2.716.20.44214250.930.9820.1890.4820.89699.8
2.71-2.797.50.3414000.970.9920.130.3650.88899.9
2.79-2.877.80.27214250.9810.9950.1010.290.92399.9
2.87-2.967.70.21614150.9850.9960.0810.2310.92999.9
2.96-3.077.70.18114120.9870.9970.0680.1940.98599.9
3.07-3.197.50.13713970.9930.9980.0520.1471.033100
3.19-3.337.50.10314370.9950.9990.040.111.02899.9
3.33-3.517.30.07414210.9970.9990.0290.081.04699.7
3.51-3.737.10.05814190.9980.9990.0230.0631.07999.9
3.73-4.026.30.04214160.99810.0180.0461.03598.7
4.02-4.427.70.03414480.99910.0130.0360.93499.9
4.42-5.067.60.02914700.99910.0110.0310.87599.9
5.06-6.377.30.0314830.99910.0120.0320.79100
6.37-506.50.02215730.99910.0090.0240.72998.6

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39.37 Å / SU ML: 0.291 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 1900 7.26 %
Rwork0.1968 24275 -
obs0.2009 26175 91.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.52 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 64 73 4785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244836
X-RAY DIFFRACTIONf_angle_d0.55766548
X-RAY DIFFRACTIONf_chiral_restr0.0409697
X-RAY DIFFRACTIONf_plane_restr0.0082838
X-RAY DIFFRACTIONf_dihedral_angle_d16.87321816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.3391670.2511823X-RAY DIFFRACTION44.48
2.41-2.480.3192900.24851146X-RAY DIFFRACTION61.99
2.48-2.550.29741190.24171522X-RAY DIFFRACTION81.85
2.55-2.630.25871380.23421785X-RAY DIFFRACTION95.43
2.63-2.720.33371460.22661875X-RAY DIFFRACTION99.8
2.72-2.830.33361440.23211842X-RAY DIFFRACTION99.85
2.83-2.960.26381480.21381888X-RAY DIFFRACTION99.9
2.96-3.120.28761450.21241864X-RAY DIFFRACTION99.95
3.12-3.310.26821480.2161885X-RAY DIFFRACTION99.95
3.31-3.570.25971480.20991884X-RAY DIFFRACTION99.66
3.57-3.930.26311460.18131879X-RAY DIFFRACTION99.17
3.93-4.50.19651500.1551904X-RAY DIFFRACTION99.9
4.5-5.660.18871520.16611940X-RAY DIFFRACTION99.95
5.66-39.370.23341590.1892038X-RAY DIFFRACTION99.37
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)
11.026415509890.469475768015-0.5337933485060.461156573982-1.033605758092.781427203980.0661310704736-0.1424707328940.2727445278130.06051695549020.2101108818540.46530014603-0.318610951241-0.773768870269-0.1351056804440.2543980337850.0711875545530.01581075940830.4185922257110.08305555700960.632004056846-23.990416084612.8496695347-31.775935129
22.13760180379-0.267368896933-0.1449951477591.64022970392-0.3581551731853.05977289483-0.0208782600811-0.05711276525680.16579953134-0.03495207369640.2057430135840.535422555812-0.285904917564-0.440572868593-0.1515159927870.2849603698480.0855509227914-0.06945375289040.1841874462450.05598788225370.431033905168-16.239301896119.0398909278-42.1927940098
31.57440266155-0.599770302627-0.4129738392793.25129226098-1.303144432022.50805070149-0.09179092213350.117886587766-0.0799061667584-0.2849190075690.003039723757880.0138696521860.1497309148160.0402148459090.05641722151980.265438709310.00859427007654-0.05242806930690.09406532639620.04311380632420.277913925679-4.3852361940411.1447371624-49.5687125639
44.43711402325-2.09902130474-1.664200525352.636673404284.322013030078.24346263356-0.0560966891208-0.2788297310160.4783370350960.1037843183810.308067319526-0.540841259046-0.1892600294540.36602863007-0.09053505435820.2995344577810.0211533774155-0.05399634455410.1837723980840.03712233847940.380130970833-0.6342300451466.86150884137-33.2496860073
50.5577634540920.145788500611-0.9166842586191.4817785671.102464265064.93534481839-0.1597941699780.0001245558996540.176185189768-0.2233883031910.17826238433-0.113074550747-0.9875536933421.15677317976-0.04183662214810.59034673638-0.144961535373-0.06552045925810.5540752983790.1418977927410.294434979877.887507201618.9727515278-70.3600051098
61.46528258070.1093083050870.6463802048282.431058568720.8640656592864.99043525436-0.240726355455-0.136993877137-0.3851196444220.0561589065719-0.1674954015310.607156326125-0.561367081177-0.6094435306040.03033987926490.2305619079910.05989386440320.002746977391690.4599562120120.08217780594510.464707986217-5.17850719986.68129090929-82.7556475104
72.738572999320.0248991547453-0.07613105005321.88600918391.683695456974.45004412213-0.1018439931070.11390999225-0.746767858460.1328793918520.013992652260.2418671812770.1857877979410.2963741359860.09720206285360.153563719174-0.02047947956650.02992038235750.4104872932310.1043162348240.5113769189752.01402894133-2.16015075639-90.212021131
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 130 )AA11 - 1301 - 120
22chain 'A' and (resid 131 through 192 )AA131 - 192121 - 182
33chain 'A' and (resid 193 through 284 )AA193 - 284183 - 274
44chain 'A' and (resid 285 through 301 )AA285 - 301275 - 291
55chain 'B' and (resid 11 through 91 )BC11 - 911 - 81
66chain 'B' and (resid 92 through 152 )BC92 - 15282 - 142
77chain 'B' and (resid 153 through 298 )BC153 - 298143 - 288

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