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- PDB-3kl8: CaMKIINtide Inhibitor Complex -

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Basic information

Entry
Database: PDB / ID: 3kl8
TitleCaMKIINtide Inhibitor Complex
Components
  • Calcium/calmodulin dependent protein kinase II
  • Calcium/calmodulin-dependent protein kinase II inhibitor 1
KeywordsTRANSFERASE/ TRANSFERASE INHIBITOR / CaMKII / CaMKIINtide / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Cell junction / Cell membrane / Membrane / Postsynaptic cell membrane / Protein kinase inhibitor / Synapse / Synaptosome / TRANSFERASE- TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


medium-term memory / Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / Ion homeostasis / Ca2+ pathway / HSF1-dependent transactivation / calcium-dependent protein kinase inhibitor activity / negative regulation of cyclin-dependent protein kinase activity / serotonin biosynthetic process / Ca2+/calmodulin-dependent protein kinase ...medium-term memory / Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / Ion homeostasis / Ca2+ pathway / HSF1-dependent transactivation / calcium-dependent protein kinase inhibitor activity / negative regulation of cyclin-dependent protein kinase activity / serotonin biosynthetic process / Ca2+/calmodulin-dependent protein kinase / positive regulation of systemic arterial blood pressure / calmodulin-dependent protein kinase activity / protein kinase inhibitor activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of cell cycle / calcium ion homeostasis / axon cytoplasm / negative regulation of proteolysis / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / MAPK cascade / chemical synaptic transmission / perikaryon / peptidyl-serine phosphorylation / transmembrane transporter binding / postsynaptic density / calmodulin binding / neuron projection / negative regulation of cell population proliferation / phosphorylation / protein phosphorylation / protein serine kinase activity / dendrite / neuronal cell body / synapse / positive regulation of gene expression / protein kinase binding / ATP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II inhibitor / Calcium/calmodulin-dependent protein kinase II inhibitor / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Calcium/calmodulin-dependent protein kinase II inhibitor / Calcium/calmodulin-dependent protein kinase II inhibitor / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Calcium/calmodulin-dependent protein kinase type II / Calcium/calmodulin-dependent protein kinase II inhibitor 1 / Calcium/calmodulin-dependent protein kinase type II
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.372 Å
AuthorsKuriyan, J. / Chao, L.H. / Pellicena, P. / Deindl, S. / Barclay, L.A. / Schulman, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation.
Authors: Chao, L.H. / Pellicena, P. / Deindl, S. / Barclay, L.A. / Schulman, H. / Kuriyan, J.
History
DepositionNov 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium/calmodulin dependent protein kinase II
B: Calcium/calmodulin-dependent protein kinase II inhibitor 1
C: Calcium/calmodulin dependent protein kinase II
D: Calcium/calmodulin-dependent protein kinase II inhibitor 1
E: Calcium/calmodulin dependent protein kinase II
F: Calcium/calmodulin-dependent protein kinase II inhibitor 1
G: Calcium/calmodulin dependent protein kinase II
H: Calcium/calmodulin-dependent protein kinase II inhibitor 1
I: Calcium/calmodulin dependent protein kinase II
J: Calcium/calmodulin-dependent protein kinase II inhibitor 1


Theoretical massNumber of molelcules
Total (without water)162,32110
Polymers162,32110
Non-polymers00
Water1,38777
1
A: Calcium/calmodulin dependent protein kinase II

D: Calcium/calmodulin-dependent protein kinase II inhibitor 1


Theoretical massNumber of molelcules
Total (without water)32,4642
Polymers32,4642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area2040 Å2
ΔGint-7 kcal/mol
Surface area13610 Å2
MethodPISA
2
I: Calcium/calmodulin dependent protein kinase II

B: Calcium/calmodulin-dependent protein kinase II inhibitor 1


Theoretical massNumber of molelcules
Total (without water)32,4642
Polymers32,4642
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2160 Å2
ΔGint-9 kcal/mol
Surface area13280 Å2
MethodPISA
3
C: Calcium/calmodulin dependent protein kinase II
H: Calcium/calmodulin-dependent protein kinase II inhibitor 1


Theoretical massNumber of molelcules
Total (without water)32,4642
Polymers32,4642
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-8 kcal/mol
Surface area13460 Å2
MethodPISA
4
E: Calcium/calmodulin dependent protein kinase II

J: Calcium/calmodulin-dependent protein kinase II inhibitor 1


Theoretical massNumber of molelcules
Total (without water)32,4642
Polymers32,4642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
Buried area1960 Å2
ΔGint-10 kcal/mol
Surface area13520 Å2
MethodPISA
5
F: Calcium/calmodulin-dependent protein kinase II inhibitor 1
G: Calcium/calmodulin dependent protein kinase II


Theoretical massNumber of molelcules
Total (without water)32,4642
Polymers32,4642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-9 kcal/mol
Surface area13490 Å2
MethodPISA
6
B: Calcium/calmodulin-dependent protein kinase II inhibitor 1


Theoretical massNumber of molelcules
Total (without water)2,0091
Polymers2,0091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
D: Calcium/calmodulin-dependent protein kinase II inhibitor 1


Theoretical massNumber of molelcules
Total (without water)2,0091
Polymers2,0091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
J: Calcium/calmodulin-dependent protein kinase II inhibitor 1


Theoretical massNumber of molelcules
Total (without water)2,0091
Polymers2,0091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.410, 83.080, 145.130
Angle α, β, γ (deg.)90.00, 101.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31B
41C
51E
12D
22A
32B
42C
52E

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain D and (resseq 6:6 or resseq 8:21 or resseq 25:49 or resseq 51:271 )D6
121chain D and (resseq 6:6 or resseq 8:21 or resseq 25:49 or resseq 51:271 )D8 - 21
131chain D and (resseq 6:6 or resseq 8:21 or resseq 25:49 or resseq 51:271 )D25 - 49
141chain D and (resseq 6:6 or resseq 8:21 or resseq 25:49 or resseq 51:271 )D51 - 271
211chain A and (resseq 9:9 or resseq 11:18 or resseq 27:272 )A9
221chain A and (resseq 9:9 or resseq 11:18 or resseq 27:272 )A11 - 18
231chain A and (resseq 9:9 or resseq 11:18 or resseq 27:272 )A27 - 272
311chain B and (resseq 8:19 or resseq 25:46 or resseq 52:272 )B8 - 19
321chain B and (resseq 8:19 or resseq 25:46 or resseq 52:272 )B25 - 46
331chain B and (resseq 8:19 or resseq 25:46 or resseq 52:272 )B52 - 272
411chain C and (resseq 8:18 or resseq 25:45 or resseq 51:272 )C8 - 18
421chain C and (resseq 8:18 or resseq 25:45 or resseq 51:272 )C25 - 45
431chain C and (resseq 8:18 or resseq 25:45 or resseq 51:272 )C51 - 272
511chain E and (resseq 6:6 or resseq 8:21 or resseq 25:46 or resseq 55:272 )E6
521chain E and (resseq 6:6 or resseq 8:21 or resseq 25:46 or resseq 55:272 )E8 - 21
531chain E and (resseq 6:6 or resseq 8:21 or resseq 25:46 or resseq 55:272 )E25 - 46
541chain E and (resseq 6:6 or resseq 8:21 or resseq 25:46 or resseq 55:272 )E55 - 272
112chain D and (resseq 282:295 )D282 - 295
212chain A and (resseq 281:298 )A281 - 298
312chain B and (resseq 281:296 )B281 - 296
412chain C and (resseq 281:297 )C281 - 297
512chain E and (resseq 282:298 )E282 - 298

NCS ensembles :
ID
1
2

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Components

#1: Protein
Calcium/calmodulin dependent protein kinase II


Mass: 30454.711 Da / Num. of mol.: 5 / Mutation: N130D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-43, K11E8.1, K11E8.1d / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6Q0, UniProt: O62305*PLUS
#2: Protein/peptide
Calcium/calmodulin-dependent protein kinase II inhibitor 1 / calcium/calmodulin-dependent protein kinase II inhibitor alpha / CaM-KIINalpha / CaMKIINalpha


Mass: 2009.489 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Camk2n1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JI15
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 20% 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.4→83.1 Å / Num. all: 21895 / Num. obs: 21523 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.4→3.6 Å / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
MOSFLM3.3.9data reduction
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.372→71.708 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.775 / SU ML: 2.46 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1809 8.4 %RANDOM
Rwork0.23 ---
obs0.234 21523 89.49 %-
all-21523 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.658 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 158.02 Å2 / Biso mean: 75.503 Å2 / Biso min: 18.97 Å2
Baniso -1Baniso -2Baniso -3
1-17.454 Å20 Å2-1.642 Å2
2---2.433 Å20 Å2
3----15.021 Å2
Refinement stepCycle: LAST / Resolution: 3.372→71.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10884 0 0 77 10961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811196
X-RAY DIFFRACTIONf_angle_d1.10115168
X-RAY DIFFRACTIONf_chiral_restr0.071668
X-RAY DIFFRACTIONf_plane_restr0.0041943
X-RAY DIFFRACTIONf_dihedral_angle_d16.5384088
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11D2005X-RAY DIFFRACTIONPOSITIONAL0.059
12A2005X-RAY DIFFRACTIONPOSITIONAL0.059
13B2017X-RAY DIFFRACTIONPOSITIONAL0.047
14C2026X-RAY DIFFRACTIONPOSITIONAL0.046
15E2005X-RAY DIFFRACTIONPOSITIONAL0.05
21D111X-RAY DIFFRACTIONPOSITIONAL0.043
22A111X-RAY DIFFRACTIONPOSITIONAL0.043
23B111X-RAY DIFFRACTIONPOSITIONAL0.048
24C111X-RAY DIFFRACTIONPOSITIONAL0.059
25E111X-RAY DIFFRACTIONPOSITIONAL0.048
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.372-3.4630.4371060.3331225133171
3.463-3.5650.4271170.3071274139178
3.565-3.680.3271230.2691348147180
3.68-3.8120.2731390.2391417155684
3.812-3.9640.3161280.2181438156686
3.964-4.1450.2741320.2251494162689
4.145-4.3630.2781450.2061562170793
4.363-4.6370.2311560.1961620177696
4.637-4.9950.261490.2021623177296
4.995-5.4970.2581530.2121644179797
5.497-6.2920.3191510.2341621177296
6.292-7.9260.241540.2161691184598
7.926-71.7240.2421560.21517571913100

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