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- PDB-6b8m: Crystal Structure of the Ca2+/CaM:Kv7.4 (KCNQ4) AB Domain Complex... -

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Basic information

Entry
Database: PDB / ID: 6b8m
TitleCrystal Structure of the Ca2+/CaM:Kv7.4 (KCNQ4) AB Domain Complex, 1 mM CaCl2 soak
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 / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / voltage-gated potassium channel activity / catalytic complex / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / potassium channel activity / 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 / Activation of AMPK downstream of NMDARs / presynaptic cytosol / 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 / FCERI mediated Ca+2 mobilization / substantia nigra development / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / basal plasma membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / spindle microtubule / calcium channel regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / sensory perception of sound / RAF activation / Transcriptional activation of mitochondrial biogenesis / response to calcium ion / potassium ion transport / cellular response to type II interferon / Stimuli-sensing channels / G2/M transition of mitotic cell cycle / long-term synaptic potentiation / spindle pole / RAS processing / Signaling by RAF1 mutants / calcium-dependent protein binding / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / 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: 2.3 Å
AuthorsChang, A. / Minor, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)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 1.1Jul 21, 2021Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value ..._pdbx_audit_support.funding_organization / _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
Revision 1.2Apr 27, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)107,78619
Polymers107,0658
Non-polymers72111
Water4,017223
1
A: Potassium voltage-gated channel subfamily KQT member 4
B: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8063
Polymers26,7662
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-57 kcal/mol
Surface area12850 Å2
MethodPISA
2
C: Potassium voltage-gated channel subfamily KQT member 4
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9985
Polymers26,7662
Non-polymers2323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-63 kcal/mol
Surface area13070 Å2
MethodPISA
3
E: Potassium voltage-gated channel subfamily KQT member 4
F: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9425
Polymers26,7662
Non-polymers1763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-68 kcal/mol
Surface area11990 Å2
MethodPISA
4
G: Potassium voltage-gated channel subfamily KQT member 4
H: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0396
Polymers26,7662
Non-polymers2724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-66 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.243, 143.853, 164.272
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#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.: 223 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M ammonium sulfate, 0.1M BisTris pH 6.5, 1mM CaCl2

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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: 2.3→14.942 Å / Num. obs: 109615 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.512 % / Biso Wilson estimate: 39.97 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.195 / Rrim(I) all: 0.215 / Χ2: 1.138 / Net I/σ(I): 7.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.445.2742.2340.74173520.4982.48299.9
2.44-2.65.4571.5471.14163460.6431.712100
2.6-2.85.7091.0961.71152790.8031.206100
2.8-3.065.620.6053.03141530.9160.667100
3.06-3.45.3350.2995.6127860.9760.331100
3.4-3.895.5080.13911.72113630.9930.153100
3.89-4.695.7920.07920.897310.9970.087100
4.69-6.335.4680.07221.2877010.9970.08100
6.33-14.9425.5960.03439.1649040.9990.03792.4

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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: 2.3→14.942 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.31
RfactorNum. reflection% reflection
Rfree0.2621 1999 3.52 %
Rwork0.2282 --
obs0.2294 56744 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 173.97 Å2 / Biso mean: 61.398 Å2 / Biso min: 28.83 Å2
Refinement stepCycle: final / Resolution: 2.3→14.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7120 0 31 223 7374
Biso mean--83.41 49.64 -
Num. residues----881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037266
X-RAY DIFFRACTIONf_angle_d0.5049756
X-RAY DIFFRACTIONf_chiral_restr0.0391065
X-RAY DIFFRACTIONf_plane_restr0.0031275
X-RAY DIFFRACTIONf_dihedral_angle_d24.4052790
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 (%)
2.3-2.35730.40511400.38593817395799
2.3573-2.42070.42721400.371238583998100
2.4207-2.49170.40141420.352438624004100
2.4917-2.57170.35511420.324638844026100
2.5717-2.66310.35021420.298738724014100
2.6631-2.76910.34591420.289638994041100
2.7691-2.89430.29141410.25963864400599
2.8943-3.04560.29891420.253539104052100
3.0456-3.23470.2911420.243638944036100
3.2347-3.48150.29471440.224239304074100
3.4815-3.82650.21441440.202239314075100
3.8265-4.36810.22121430.177439494092100
4.3681-5.45830.2141450.188239794124100
5.4583-14.94250.19851500.183540964246100

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