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- PDB-4qnh: Calcium-calmodulin (T79D) complexed with the calmodulin binding d... -

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Basic information

Entry
Database: PDB / ID: 4qnh
TitleCalcium-calmodulin (T79D) complexed with the calmodulin binding domain from a small conductance potassium channel SK2-a
Components
  • Calmodulin
  • Small conductance calcium-activated potassium channel protein 2
Keywordsion transport/protein binding / ion channel / ion transport-protein binding complex
Function / homology
Function and homology information


Cam-PDE 1 activation / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Glycogen breakdown (glycogenolysis) / CaMK IV-mediated phosphorylation of CREB / Calcineurin activates NFAT / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CLEC7A (Dectin-1) induces NFAT activation / VEGFR2 mediated vascular permeability / RHO GTPases activate IQGAPs ...Cam-PDE 1 activation / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Glycogen breakdown (glycogenolysis) / CaMK IV-mediated phosphorylation of CREB / Calcineurin activates NFAT / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CLEC7A (Dectin-1) induces NFAT activation / VEGFR2 mediated vascular permeability / RHO GTPases activate IQGAPs / RHO GTPases activate PAKs / Activation of RAC1 downstream of NMDARs / Protein methylation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Calmodulin induced events / Stimuli-sensing channels / FCERI mediated Ca+2 mobilization / Smooth Muscle Contraction / Platelet degranulation / RAF activation / Ca2+ activated K+ channels / PKA activation / regulation of store-operated calcium channel activity / Ion transport by P-type ATPases / Synthesis of IP3 and IP4 in the cytosol / small conductance calcium-activated potassium channel activity / : / regulation of high voltage-gated calcium channel activity / Inactivation, recovery and regulation of the phototransduction cascade / membrane repolarization during atrial cardiac muscle cell action potential / Extra-nuclear estrogen signaling / RAS processing / calcium-activated potassium channel activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / Activation of Ca-permeable Kainate Receptor / type 3 metabotropic glutamate receptor binding / positive regulation of potassium ion transport / inward rectifier potassium channel activity / Ca2+ pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / establishment of protein localization to membrane / regulation of potassium ion transmembrane transport / RAF/MAP kinase cascade / positive regulation of DNA binding / negative regulation of high voltage-gated calcium channel activity / Ion homeostasis / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / alpha-actinin binding / regulation of synaptic vesicle endocytosis / regulation of neuronal synaptic plasticity / protein phosphatase activator activity / postsynaptic cytosol / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / Unblocking of NMDA receptors, glutamate binding and activation / detection of calcium ion / regulation of cardiac muscle contraction / phosphatidylinositol 3-kinase binding / smooth endoplasmic reticulum / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding / voltage-gated potassium channel complex / calcium channel regulator activity / potassium ion transmembrane transport / T-tubule / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / response to amphetamine / positive regulation of nitric-oxide synthase activity / adenylate cyclase activator activity / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / positive regulation of receptor signaling pathway via JAK-STAT
Similarity search - Function
Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / : ...Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-3 / Calmodulin-1 / Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsZhang, M. / Pascal, J.M. / Logothetis, D.E. / Zhang, J.F.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Selective phosphorylation modulates the PIP2 sensitivity of the CaM-SK channel complex.
Authors: Zhang, M. / Meng, X.Y. / Cui, M. / Pascal, J.M. / Logothetis, D.E. / Zhang, J.F.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
B: Small conductance calcium-activated potassium channel protein 2
R: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2865
Polymers29,1102
Non-polymers1763
Water3,369187
1
B: Small conductance calcium-activated potassium channel protein 2
R: Calmodulin
hetero molecules

B: Small conductance calcium-activated potassium channel protein 2
R: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,57210
Polymers58,2204
Non-polymers3526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area13490 Å2
ΔGint-158 kcal/mol
Surface area22080 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-51 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 65.960, 64.680
Angle α, β, γ (deg.)90.00, 93.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-619-

HOH

21B-643-

HOH

31B-653-

HOH

41R-1171-

HOH

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Components

#1: Protein Small conductance calcium-activated potassium channel protein 2 / SK2 / SKCa 2 / SKCa2 / KCa2.2


Mass: 12243.395 Da / Num. of mol.: 1 / Fragment: Calmodulin binding domain (UNP residues 396-487)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnn2 / Production host: Escherichia coli (E. coli) / References: UniProt: P70604
#2: Protein Calmodulin / CaM


Mass: 16866.529 Da / Num. of mol.: 1 / Mutation: T79D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Gene: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc
Production host: Escherichia coli (E. coli) / References: UniProt: P62161, UniProt: P0DP31*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 5.6
Details: 1.5 M Li2SO4, 0.5 M (NH4)2SO4, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 28, 2013
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.02→26.65 Å / Num. all: 21057 / Num. obs: 21057 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7
Reflection shellResolution: 2.02→2.07 Å / % possible all: 90.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→26.648 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1014 4.82 %Random
Rwork0.1818 ---
obs0.1843 21055 98.61 %-
all-21055 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→26.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 7 187 2054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141915
X-RAY DIFFRACTIONf_angle_d1.2872572
X-RAY DIFFRACTIONf_dihedral_angle_d14.677753
X-RAY DIFFRACTIONf_chiral_restr0.074289
X-RAY DIFFRACTIONf_plane_restr0.007339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.12650.2741110.22452769X-RAY DIFFRACTION95
2.1265-2.25960.27411670.19952839X-RAY DIFFRACTION100
2.2596-2.4340.27891570.1942849X-RAY DIFFRACTION99
2.434-2.67870.23041460.18972883X-RAY DIFFRACTION99
2.6787-3.06590.26261190.17992896X-RAY DIFFRACTION100
3.0659-3.86080.23191570.172888X-RAY DIFFRACTION99
3.8608-26.650.20581570.17472917X-RAY DIFFRACTION99

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