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- PDB-6b8p: Crystal Structure of the Mg2+/CaM:Kv7.4 (KCNQ4) AB domain complex -

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Basic information

Entry
Database: PDB / ID: 6b8p
TitleCrystal Structure of the Mg2+/CaM:Kv7.4 (KCNQ4) AB domain complex
Components
  • Calmodulin-1
  • Potassium voltage-gated channel subfamily KQT member 4
KeywordsMETAL TRANSPORT / ion channel / complex
Function / homology
Function and homology information


Voltage gated Potassium channels / CaM pathway / Sensory processing of sound by outer hair cells of the cochlea / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Sensory processing of sound by inner hair cells of the cochlea / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...Voltage gated Potassium channels / CaM pathway / Sensory processing of sound by outer hair cells of the cochlea / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Sensory processing of sound by inner hair cells of the cochlea / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / inner ear morphogenesis / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / voltage-gated potassium channel activity / Smooth Muscle Contraction / catalytic complex / potassium channel activity / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / voltage-gated potassium channel complex / potassium ion transmembrane transport / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / basal plasma membrane / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / sensory perception of sound / RAF activation / Transcriptional activation of mitochondrial biogenesis / potassium ion transport / Stimuli-sensing channels / cellular response to type II interferon / long-term synaptic potentiation / response to calcium ion / RAS processing / spindle pole / 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 / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Inactivation, recovery and regulation of the phototransduction cascade
Similarity search - Function
Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / EF-hand / : / Recoverin; domain 1 / 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 / Ion transport domain / Ion transport protein / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Potassium voltage-gated channel subfamily KQT member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChang, A. / Minor, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01 DC007664 United States
CitationJournal: Neuron / Year: 2018
Title: A Calmodulin C-Lobe Ca
Authors: Chang, A. / Abderemane-Ali, F. / Hura, G.L. / Rossen, N.D. / Gate, R.E. / Minor, D.L.
History
DepositionOct 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily KQT member 4
B: Calmodulin-1
C: Potassium voltage-gated channel subfamily KQT member 4
D: Calmodulin-1
E: Potassium voltage-gated channel subfamily KQT member 4
F: Calmodulin-1
G: Potassium voltage-gated channel subfamily KQT member 4
H: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,64317
Polymers107,0658
Non-polymers5789
Water5,386299
1
A: Potassium voltage-gated channel subfamily KQT member 4
B: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7913
Polymers26,7662
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-53 kcal/mol
Surface area12660 Å2
MethodPISA
2
C: Potassium voltage-gated channel subfamily KQT member 4
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8874
Polymers26,7662
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-50 kcal/mol
Surface area12920 Å2
MethodPISA
3
E: Potassium voltage-gated channel subfamily KQT member 4
F: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9835
Polymers26,7662
Non-polymers2163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-61 kcal/mol
Surface area11830 Å2
MethodPISA
4
G: Potassium voltage-gated channel subfamily KQT member 4
H: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9835
Polymers26,7662
Non-polymers2163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-55 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.141, 142.875, 164.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Potassium voltage-gated channel subfamily KQT member 4 / KQT-like 4 / Potassium channel subunit alpha KvLQT4 / Voltage-gated potassium channel subunit Kv7.4


Mass: 9913.735 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ4 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P56696
#2: Protein
Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Plasmid: pEGST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P0DP23
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M ammonium sulfate, 0.1M BisTris pH 6.5, 1mM MgCl2

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2016
RadiationMonochromator: Si(111) double crystal Khozu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→14.959 Å / Num. obs: 124600 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.734 % / Biso Wilson estimate: 41.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.102 / Χ2: 1.085 / Net I/σ(I): 12.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.334.6541.2341.4197370.6931.39299.6
2.33-2.484.5850.7672.2186670.8610.867100
2.48-2.684.7840.4893.48173770.9270.54999.9
2.68-2.924.880.2885.76160430.9710.323100
2.92-3.254.7230.14810.18145780.9890.166100
3.25-3.734.570.07119.21129150.9970.0899.9
3.73-4.494.9990.04133.43110530.9990.04699.9
4.49-6.094.7660.03835.4887450.9990.043100
6.09-14.9594.7860.02252.36548510.02593.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B8L

6b8l


Resolution: 2.2→14.959 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.27
RfactorNum. reflection% reflection
Rfree0.2404 1998 3.1 %
Rwork0.2071 --
obs0.2082 64486 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.34 Å2 / Biso mean: 60.5718 Å2 / Biso min: 24.92 Å2
Refinement stepCycle: final / Resolution: 2.2→14.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7053 0 29 299 7381
Biso mean--84.53 49.38 -
Num. residues----873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027210
X-RAY DIFFRACTIONf_angle_d0.4479684
X-RAY DIFFRACTIONf_chiral_restr0.0361058
X-RAY DIFFRACTIONf_plane_restr0.0031266
X-RAY DIFFRACTIONf_dihedral_angle_d22.8152768
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1975-2.25230.36081410.30234385452699
2.2523-2.31290.31861410.282344044545100
2.3129-2.38070.34651400.269844304570100
2.3807-2.45730.31391410.27443974538100
2.4573-2.54470.32221420.259844094551100
2.5447-2.6460.29181440.246244774621100
2.646-2.76570.30991400.253944064546100
2.7657-2.91050.26141420.232844654607100
2.9105-3.09140.29851430.235244594602100
3.0914-3.32770.24231410.222644494590100
3.3277-3.65810.21861450.201944924637100
3.6581-4.17730.19441440.177145164660100
4.1773-5.22540.20991440.169945254669100
5.2254-14.95930.20321500.174446744824100

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