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- PDB-6x5g: Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain a... -

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Basic information

Entry
Database: PDB / ID: 6x5g
TitleCocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and LRRC7 inhibitory domain
Components
  • Calcium/calmodulin-dependent protein kinase type II subunit alpha
  • Leucine-rich repeat-containing protein 7
KeywordsTRANSFERASE / CaMKII / Kinase / Human / CAMK2A
Function / homology
Function and homology information


peptidyl-threonine autophosphorylation / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / Ca2+/calmodulin-dependent protein kinase / neurotransmitter receptor transport, endosome to postsynaptic membrane / dendritic spine development / negative regulation of hydrolase activity / regulation of neurotransmitter secretion / establishment or maintenance of epithelial cell apical/basal polarity / axon initial segment ...peptidyl-threonine autophosphorylation / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / Ca2+/calmodulin-dependent protein kinase / neurotransmitter receptor transport, endosome to postsynaptic membrane / dendritic spine development / negative regulation of hydrolase activity / regulation of neurotransmitter secretion / establishment or maintenance of epithelial cell apical/basal polarity / axon initial segment / Trafficking of AMPA receptors / regulation of neuron migration / positive regulation of calcium ion transport / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / regulation of mitochondrial membrane permeability involved in apoptotic process / CaMK IV-mediated phosphorylation of CREB / receptor clustering / 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 / Long-term potentiation / Regulation of MECP2 expression and activity / regulation of neuronal synaptic plasticity / glutamate receptor binding / HSF1-dependent transactivation / positive regulation of cardiac muscle cell apoptotic process / regulation of protein localization to plasma membrane / cellular response to interferon-beta / Ion homeostasis / Ras activation upon Ca2+ influx through NMDA receptor / response to ischemia / angiotensin-activated signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / adherens junction / RAF activation / G1/S transition of mitotic cell cycle / positive regulation of NF-kappaB transcription factor activity / cell-cell adhesion / positive regulation of neuron projection development / cellular response to type II interferon / specific granule lumen / 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 / calcium ion transport / kinase activity / Signaling by BRAF and RAF1 fusions / RAF/MAP kinase cascade / Ca2+ pathway / basolateral plasma membrane / dendritic spine / calmodulin binding / protein phosphorylation / neuron projection / postsynaptic density / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / protein kinase binding / protein homodimerization activity / mitochondrion / extracellular region / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / : / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / NTF2-like domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / : / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / NTF2-like domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat 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
Leucine-rich repeat-containing protein 7 / Calcium/calmodulin-dependent protein kinase type II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsOzden, C. / Stratton, M.M. / Garman, S.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2022
Title: CaMKII binds both substrates and activators at the active site.
Authors: Ozden, C. / Sloutsky, R. / Mitsugi, T. / Santos, N. / Agnello, E. / Gaubitz, C. / Foster, J. / Lapinskas, E. / Esposito, E.A. / Saneyoshi, T. / Kelch, B.A. / Garman, S.C. / Hayashi, Y. / Stratton, M.M.
History
DepositionMay 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 2.0Apr 6, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.organism_common_name / _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_mon_prot_cis.pdbx_omega_angle
Description: Atoms with unrealistic or zero occupancies / Details: We have gotten rid of some water molecules. / Provider: author / Type: Coordinate replacement
Revision 2.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 alpha
B: Leucine-rich repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3965
Polymers33,0492
Non-polymers3473
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-7 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.290, 66.173, 61.706
Angle α, β, γ (deg.)90.000, 99.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30548.086 Da / Num. of mol.: 1 / Mutation: D135N, Q223K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2A, CAMKA, KIAA0968 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: Protein/peptide Leucine-rich repeat-containing protein 7 / Densin-180 / Densin / Protein LAP1


Mass: 2500.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96NW7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10% w/v PEG 20000, 2% v/v 1,4-Dioxane, 0.1 M Bicine

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K thorughout the collection / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Jul 24, 2019 / Details: Rigaku VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 23182 / % possible obs: 93.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.041 / Rrim(I) all: 0.077 / Χ2: 1.557 / Net I/σ(I): 9.6 / Num. measured all: 79898
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.883.30.32510670.8980.2030.3841.31986.5
1.88-1.923.30.28310670.9010.1760.3341.31886.9
1.92-1.953.40.23211030.9310.1430.2731.34590.7
1.95-1.993.40.19611230.9510.1210.231.30189.4
1.99-2.043.50.17710700.9590.1090.2081.30889.2
2.04-2.083.50.1611330.9660.0980.1881.45792.3
2.08-2.143.50.13911530.9720.0850.1631.36790.5
2.14-2.193.60.12211240.9770.0750.1431.38193.5
2.19-2.263.60.11811430.9810.0720.1391.51593.1
2.26-2.333.60.11411620.9830.0690.1341.57295.5
2.33-2.413.60.09511820.9870.0580.1111.55693.2
2.41-2.513.50.08911770.9880.0550.1051.43396.4
2.51-2.633.60.08711630.9850.0540.1031.62794.4
2.63-2.763.50.07811830.9880.0480.0921.66595.6
2.76-2.943.50.07412050.9860.0460.0871.78997.6
2.94-3.163.50.06112060.9920.0380.0721.73996.6
3.16-3.483.40.05112120.9930.0320.061.797.1
3.48-3.993.40.04612080.9940.0290.0551.88997.7
3.99-5.023.30.04512350.9930.0290.0541.98898.2
5.02-5030.04212660.9940.0280.051.77698.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VZK

6vzk


Resolution: 1.85→33.11 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.307 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 1122 4.8 %RANDOM
Rwork0.1871 ---
obs0.189 22043 93.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.5 Å2 / Biso mean: 22.461 Å2 / Biso min: 12.18 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.46 Å2
2--0.13 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.85→33.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 23 107 2372
Biso mean--53.79 25.19 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132337
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172165
X-RAY DIFFRACTIONr_angle_refined_deg1.631.6393167
X-RAY DIFFRACTIONr_angle_other_deg1.3771.5735004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8855284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44221.328128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4315384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5871518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02510
LS refinement shellResolution: 1.85→1.895 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.284 96 -
Rwork0.231 1457 -
obs--85.9 %

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