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- PDB-6n5w: Crystal structure of the Ca2+/CaM complex with independent peptid... -

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Basic information

Entry
Database: PDB / ID: 6n5w
TitleCrystal structure of the Ca2+/CaM complex with independent peptides of Kv7.4 (KCNQ4) A & B domains
Components
  • (Potassium voltage-gated channel subfamily KQT member 4) x 2
  • Calmodulin-1
KeywordsMETAL BINDING PROTEIN / ion channel / calmodulin / KCNQ4 peptides / 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 / positive regulation of ryanodine-sensitive calcium-release channel activity / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor ...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 / positive regulation of ryanodine-sensitive calcium-release channel activity / 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 / inner ear morphogenesis / CREB1 phosphorylation through the activation of Adenylate Cyclase / 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 / organelle localization by membrane tethering / negative regulation of ryanodine-sensitive calcium-release channel activity / 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 / voltage-gated potassium channel activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / 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 / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / 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 / voltage-gated potassium channel complex / regulation of calcium-mediated signaling / 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 / basal plasma membrane / calyx of Held / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / regulation of cytokinesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / 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: 2.15 Å
AuthorsTaylor, A.B. / Archer, C.R. / Shapiro, M.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS043394 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS094461 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32 HL007446 United States
CitationJournal: J. Biol. Chem. / Year: 2019
Title: A mutually induced conformational fit underlies Ca2+-directed interactions between calmodulin and the proximal C terminus of KCNQ4 K+channels.
Authors: Archer, C.R. / Enslow, B.T. / Taylor, A.B. / De la Rosa, V. / Bhattacharya, A. / Shapiro, M.S.
History
DepositionNov 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily KQT member 4
B: Potassium voltage-gated channel subfamily KQT member 4
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2165
Polymers23,1363
Non-polymers802
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-72 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.510, 130.570, 36.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 3217.747 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P56696
#2: Protein/peptide Potassium voltage-gated channel subfamily KQT member 4 / KQT-like 4 / Potassium channel subunit alpha KvLQT4 / Voltage-gated potassium channel subunit Kv7.4


Mass: 3065.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P56696
#3: Protein Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Plasmid: pETGQ.HCaM / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DP23
#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.: 23 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.3 M sodium citrate, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→43.52 Å / Num. obs: 11851 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 45.6 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.06 / Rsym value: 0.157 / Net I/σ(I): 8.1
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1702 / CC1/2: 0.535 / Rpim(I) all: 0.404 / Rsym value: 1.073 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UMO

4umo


Resolution: 2.15→41.278 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.3
RfactorNum. reflection% reflection
Rfree0.2739 1179 9.98 %
Rwork0.2325 --
obs0.2367 11810 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.9 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 2 23 1522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011514
X-RAY DIFFRACTIONf_angle_d1.1272032
X-RAY DIFFRACTIONf_dihedral_angle_d23.281581
X-RAY DIFFRACTIONf_chiral_restr0.077227
X-RAY DIFFRACTIONf_plane_restr0.005269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.24790.39211180.34251326X-RAY DIFFRACTION100
2.2479-2.36640.34331770.31811259X-RAY DIFFRACTION100
2.3664-2.51460.29851180.2991319X-RAY DIFFRACTION100
2.5146-2.70870.35131770.27961284X-RAY DIFFRACTION100
2.7087-2.98120.34111180.2711360X-RAY DIFFRACTION100
2.9812-3.41240.32741770.26121281X-RAY DIFFRACTION100
3.4124-4.29860.26941180.19431386X-RAY DIFFRACTION100
4.2986-41.28610.20351760.19651416X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.01060.8776-0.43191.3045-0.48320.4599-0.26580.0964-0.1637-0.39480.6325-0.0231-0.3436-0.56460.13660.50730.1133-0.01370.3210.09960.2434-18.605120.8231-5.8396
20.2397-0.1532-0.20430.15020.22420.33990.10140.05030.00950.5764-0.3538-0.4282-0.1181-0.054200.3744-0.03520.01230.37470.02930.305-14.042310.4558-9.6824
31.7814-0.1787-0.57661.02010.40420.7380.06310.2590.0710.1034-0.0651-0.2743-0.08820.003-00.2917-0.02690.03840.34910.05950.3907-9.14946.1267-15.8142
41.6641-0.2153-0.57710.58470.92964.57170.4137-0.18140.14460.2120.27250.1581-1.3472-0.25062.06270.66730.13210.16250.4170.23920.5055-19.698525.87061.7816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 338 through 356 )
2X-RAY DIFFRACTION2chain 'B' and (resid 525 through 549 )
3X-RAY DIFFRACTION3chain 'C' and (resid 4 through 78 )
4X-RAY DIFFRACTION4chain 'C' and (resid 79 through 147 )

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