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- PDB-7uiq: Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain a... -

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Basic information

Entry
Database: PDB / ID: 7uiq
TitleCocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and Tiam1
Components
  • Calcium/calmodulin-dependent protein kinase type II subunit alpha
  • T-lymphoma invasion and metastasis-inducing protein 1
KeywordsTRANSFERASE / CaMKII / Kinase / Human / CAMK2A
Function / homology
Function and homology information


brain-derived neurotrophic factor receptor signaling pathway / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / RAC3 GTPase cycle / CDC42 GTPase cycle / RAC2 GTPase cycle / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / peptidyl-threonine autophosphorylation / NRAGE signals death through JNK ...brain-derived neurotrophic factor receptor signaling pathway / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / RAC3 GTPase cycle / CDC42 GTPase cycle / RAC2 GTPase cycle / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / peptidyl-threonine autophosphorylation / NRAGE signals death through JNK / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / RAC1 GTPase cycle / G alpha (12/13) signalling events / RHOA GTPase cycle / Ca2+/calmodulin-dependent protein kinase / kinocilium / dendritic spine development / negative regulation of hydrolase activity / regulation of neurotransmitter secretion / cell-cell contact zone / activation of GTPase activity / Trafficking of AMPA receptors / regulation of neuron migration / positive regulation of calcium ion transport / calcium/calmodulin-dependent protein kinase activity / positive regulation of axonogenesis / Assembly and cell surface presentation of NMDA receptors / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of GTPase activity / CaMK IV-mediated phosphorylation of CREB / small GTPase-mediated signal transduction / Phase 0 - rapid depolarisation / Rac protein signal transduction / pericentriolar material / 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 / ephrin receptor signaling pathway / positive regulation of cardiac muscle cell apoptotic process / regulation of protein localization to plasma membrane / cellular response to interferon-beta / ephrin receptor binding / Ion homeostasis / Ras activation upon Ca2+ influx through NMDA receptor / guanyl-nucleotide exchange factor activity / response to ischemia / cell-matrix adhesion / angiotensin-activated signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / G1/S transition of mitotic cell cycle / positive regulation of NF-kappaB transcription factor activity / positive regulation of neuron projection development / receptor tyrosine kinase binding / phospholipid binding / cellular response to type II interferon / 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 / cell-cell junction / calcium ion transport / Signaling by BRAF and RAF1 fusions / kinase activity / cell migration / RAF/MAP kinase cascade / Ca2+ pathway / microtubule binding / dendritic spine / calmodulin binding / protein phosphorylation / neuron projection / postsynaptic density / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / : / T-lymphoma invasion and metastasis CC-Ex domain / Tiam1 second PH domain-like / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Raf-like Ras-binding domain ...TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / : / T-lymphoma invasion and metastasis CC-Ex domain / Tiam1 second PH domain-like / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / NTF2-like domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / PDZ domain / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-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
Rho guanine nucleotide exchange factor TIAM1 / Calcium/calmodulin-dependent protein kinase type II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.11 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
DepositionMar 29, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionApr 6, 2022ID: 6X8V
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 subunit alpha
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: T-lymphoma invasion and metastasis-inducing protein 1
D: T-lymphoma invasion and metastasis-inducing protein 1


Theoretical massNumber of molelcules
Total (without water)65,4174
Polymers65,4174
Non-polymers00
Water00
1
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: T-lymphoma invasion and metastasis-inducing protein 1


Theoretical massNumber of molelcules
Total (without water)32,7092
Polymers32,7092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: T-lymphoma invasion and metastasis-inducing protein 1


Theoretical massNumber of molelcules
Total (without water)32,7092
Polymers32,7092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.433, 137.416, 156.473
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGHISHISAA8 - 2732 - 267
21ARGARGHISHISBB8 - 2732 - 267
12SERSERALAALACC1545 - 15585 - 18
22SERSERALAALADD1545 - 15585 - 18

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.847187, 0.014563, -0.531095), (-0.531177, -0.002202, 0.847258), (0.011169, 0.999892, 0.009601)-17.52026, 18.57642, -18.804079
3given(1), (1), (1)
4given(-0.837121, -0.024778, -0.546456), (-0.546779, 0.008403, 0.837235), (-0.016153, 0.999658, -0.020582)-18.12244, 17.882339, -20.14686

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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.: 2 / 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 T-lymphoma invasion and metastasis-inducing protein 1 / TIAM-1


Mass: 2160.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q60610

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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: 3.57 Å3/Da / Density % sol: 65.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 16% PEG 6000, 0.1% v/v Triton X-114

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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: Apr 22, 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: 3.11→50 Å / Num. obs: 16346 / % possible obs: 93.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.266 / Rpim(I) all: 0.134 / Rrim(I) all: 0.3 / Χ2: 2.527 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.12-3.173.50.677470.5650.3950.7831.3891.9
3.17-3.233.60.6047770.550.3510.7041.39690.8
3.23-3.293.70.4897790.6830.2760.5651.47191
3.29-3.363.70.4317960.7520.2410.4971.50590.8
3.36-3.433.80.3557690.7750.1980.4091.36990.9
3.43-3.513.90.497850.8010.2480.5522.57992
3.51-3.640.317940.8440.1670.3541.51790.5
3.6-3.740.2957640.8560.1580.3371.56590.1
3.7-3.814.20.2657840.8960.1410.3021.68891.4
3.81-3.934.20.2758090.9080.1430.3111.93992.1
3.93-4.074.30.2627860.9190.1350.2971.77692.8
4.07-4.234.50.2378100.9270.1190.2671.95792.7
4.23-4.434.70.2158150.9490.1050.2412.1792.7
4.43-4.664.90.1948030.9550.0930.2162.03593.5
4.66-4.955.30.2118380.9610.0980.2332.45593.8
4.95-5.335.50.2658380.9420.1190.2911.97795.3
5.33-5.875.70.3078500.9070.1380.3382.34597.1
5.87-6.725.80.2918980.9210.1320.3212.92999.6
6.72-8.465.90.2119270.9660.0950.2324.371100
8.46-505.20.1349770.9750.0660.157.0997.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VZK

6vzk


Resolution: 3.11→31.54 Å / Cor.coef. Fo:Fc: 0.829 / Cor.coef. Fo:Fc free: 0.742 / SU B: 29.732 / SU ML: 0.488 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.535 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3092 782 4.8 %RANDOM
Rwork0.2585 ---
obs0.2609 15535 93.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.38 Å2 / Biso mean: 30.655 Å2 / Biso min: 6.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2--2.02 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: final / Resolution: 3.11→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 0 0 4430
Num. residues----563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134536
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174210
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.6366152
X-RAY DIFFRACTIONr_angle_other_deg1.1621.5729735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2015557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4122.035231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.33715752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1281527
X-RAY DIFFRACTIONr_chiral_restr0.0550.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02957
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A202716.2
2C10322.54
LS refinement shellResolution: 3.115→3.196 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.558 36 -
Rwork0.39 1042 -
all-1078 -
obs--85.15 %

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