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- PDB-6b8l: Crystal Structure of the Apo/CaM:Kv7.4 (KCNQ4) AB Domain Complex -

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Basic information

Entry
Database: PDB / ID: 6b8l
TitleCrystal Structure of the Apo/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 / Sensory processing of sound by outer hair cells of the cochlea / CaM pathway / 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 / Sensory processing of sound by outer hair cells of the cochlea / CaM pathway / 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 / CaMK IV-mediated phosphorylation of CREB / PKA activation / 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 ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / voltage-gated potassium channel activity / detection of calcium ion / potassium channel activity / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / presynaptic cytosol / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / substantia nigra development / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / calyx of Held / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / basal plasma membrane / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / regulation of cytokinesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / spindle microtubule / calcium channel regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / Stimuli-sensing channels / RAF activation / sensory perception of sound / Transcriptional activation of mitochondrial biogenesis / potassium ion transport / RAS processing / cellular response to type II interferon / long-term synaptic potentiation / response to calcium ion / 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 / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / 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 / Resolution: 2.3 Å
AuthorsChang, A. / Abderemane-Ali, F. / Minor, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)DC007664 United States
CitationJournal: Neuron / Year: 2018
Title: A Calmodulin C-Lobe Ca2+-Dependent Switch Governs Kv7 Channel Function
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 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.2Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)107,54513
Polymers107,0658
Non-polymers4805
Water5,116284
1
A: Potassium voltage-gated channel subfamily KQT member 4
B: Calmodulin-1


Theoretical massNumber of molelcules
Total (without water)26,7662
Polymers26,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-31 kcal/mol
Surface area11890 Å2
MethodPISA
2
C: Potassium voltage-gated channel subfamily KQT member 4
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9584
Polymers26,7662
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-41 kcal/mol
Surface area12220 Å2
MethodPISA
3
E: Potassium voltage-gated channel subfamily KQT member 4
F: Calmodulin-1


Theoretical massNumber of molelcules
Total (without water)26,7662
Polymers26,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-42 kcal/mol
Surface area11700 Å2
MethodPISA
4
G: Potassium voltage-gated channel subfamily KQT member 4
H: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0545
Polymers26,7662
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-64 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.435, 142.453, 164.313
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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 284 / 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: 58.49 % / Mosaicity: 0.514 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2M ammonium sulfate, 0.1M BisTris pH 6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1801
2801
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.9797
SYNCHROTRONAPS 23-ID-B21.072
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMar 27, 2015
DECTRIS PILATUS 6M2PIXELAug 20, 2016
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double flat crystal, Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111) double crystal KhozuSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
21.0721
ReflectionResolution: 2.3→50 Å / Num. obs: 57501 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 31.47 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.047 / Rrim(I) all: 0.128 / Χ2: 1.254 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.347.40.92828330.9320.3660.9981.43100
2.34-2.387.40.62328450.9610.2460.671.408100
2.38-2.437.40.59328320.9590.2340.6381.406100
2.43-2.487.40.52828380.970.2080.5671.422100
2.48-2.537.40.4428620.9740.1730.4731.409100
2.53-2.597.40.39228360.9730.1540.4211.41100
2.59-2.667.40.32528900.9820.1280.3491.438100
2.66-2.737.40.29928240.9840.1180.3221.476100
2.73-2.817.40.24528660.9880.0970.2641.456100
2.81-2.97.40.19328440.9910.0760.2071.486100
2.9-37.40.16128710.9920.0630.1731.36100
3-3.127.40.13728640.9930.0540.1481.276100
3.12-3.267.40.12228390.9930.0480.1311.141100
3.26-3.447.40.11228890.9940.0440.1211.147100
3.44-3.657.20.11228900.990.0450.121.027100
3.65-3.936.90.12728930.9870.0520.1371.179100
3.93-4.337.10.08728710.9940.0350.0941.00999.9
4.33-4.957.10.06829260.9960.0270.0730.859100
4.95-6.247.20.05829320.9970.0230.0630.868100
6.24-507.10.04630560.9990.0190.0490.84999.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.3→48.888 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.5
RfactorNum. reflection% reflection
Rfree0.2456 5475 9.96 %
Rwork0.1984 --
obs0.2031 54987 94.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.19 Å2 / Biso mean: 46.0271 Å2 / Biso min: 17.51 Å2
Refinement stepCycle: final / Resolution: 2.3→48.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6921 0 25 284 7230
Biso mean--74.68 38.05 -
Num. residues----858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077074
X-RAY DIFFRACTIONf_angle_d0.849505
X-RAY DIFFRACTIONf_chiral_restr0.0471042
X-RAY DIFFRACTIONf_plane_restr0.0051239
X-RAY DIFFRACTIONf_dihedral_angle_d21.6462713
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2825-2.30840.28421130.21081014112759
2.3084-2.33560.30581580.22861528168688
2.3356-2.36410.29391680.21091529169790
2.3641-2.3940.28431680.21311539170790
2.394-2.42550.28731720.23111585175791
2.4255-2.45870.32021670.22681554172190
2.4587-2.49380.28871750.2281585176092
2.4938-2.5310.31431780.21181635181394
2.531-2.57060.26891720.21941573174593
2.5706-2.61270.31781810.20151610179194
2.6127-2.65780.25791770.21431631180895
2.6578-2.70610.25651830.22311665184895
2.7061-2.75820.28641900.2331642183295
2.7582-2.81450.26121810.22231646182796
2.8145-2.87560.31541860.21511678186497
2.8756-2.94250.28991860.22271679186597
2.9425-3.01610.26341910.22591723191498
3.0161-3.09760.28181910.221715190699
3.0976-3.18880.26011900.2281720191099
3.1888-3.29170.26531930.21941722191599
3.2917-3.40930.26071900.21491708189899
3.4093-3.54580.26321930.19921728192199
3.5458-3.70710.26031890.21961709189898
3.7071-3.90250.22621960.181731192799
3.9025-4.14680.21871910.17011711190299
4.1468-4.46680.20391970.153117621959100
4.4668-4.91590.19061960.161817621958100
4.9159-5.62640.22851950.18417681963100
5.6264-7.08520.24112010.210918012002100
7.0852-48.89960.18462070.17081859206699

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