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- PDB-6mc9: Crystal Structure of Human Nav1.4 C-Terminal (1599-1754) domain i... -

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Basic information

Entry
Database: PDB / ID: 6mc9
TitleCrystal Structure of Human Nav1.4 C-Terminal (1599-1754) domain in complex with calcium-bound calmodulin
Components
  • Calmodulin-1
  • Sodium channel protein type 4 subunit alpha
KeywordsPROTEIN BINDING / SCN4A / voltage gated sodium channel / calmodulin / calmodulin-binding protein
Function / homology
Function and homology information


regulation of skeletal muscle contraction by action potential / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / establishment of protein localization to membrane / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / sodium ion transport ...regulation of skeletal muscle contraction by action potential / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / establishment of protein localization to membrane / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / sodium ion transport / 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 / nitric-oxide synthase binding / regulation of synaptic vesicle exocytosis / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / detection of calcium ion / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / catalytic complex / postsynaptic cytosol / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / presynaptic cytosol / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / sodium ion transmembrane transport / regulation of heart rate / muscle contraction / calyx of Held / response to amphetamine / adenylate cyclase activator activity / sarcomere / protein serine/threonine kinase activator activity / nitric-oxide synthase regulator activity / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / calcium channel regulator activity / response to calcium ion / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Schaffer collateral - CA1 synapse / spindle pole / calcium-dependent protein binding / myelin sheath / growth cone / vesicle / transmembrane transporter binding / protein domain specific binding / calcium ion binding / centrosome / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Voltage gated sodium channel, alpha-4 subunit, mammalian / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / IQ motif profile. / Voltage-dependent channel domain superfamily / EF-hand ...Voltage gated sodium channel, alpha-4 subunit, mammalian / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / IQ motif profile. / Voltage-dependent channel domain superfamily / 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 / Sodium channel protein type 4 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsYoder, J.B. / Gabelli, S.B. / Amzel, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5R01HL128743 United States
CitationJournal: Nat Commun / Year: 2019
Title: Ca2+-dependent regulation of sodium channels NaV1.4 and NaV1.5 is controlled by the post-IQ motif.
Authors: Yoder, J.B. / Ben-Johny, M. / Farinelli, F. / Srinivasan, L. / Shoemaker, S.R. / Tomaselli, G.F. / Gabelli, S.B. / Amzel, L.M.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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: Sodium channel protein type 4 subunit alpha
B: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2256
Polymers36,0642
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-69 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.615, 72.615, 134.661
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Sodium channel protein type 4 subunit alpha / SkM1 / Sodium channel protein skeletal muscle subunit alpha / Sodium channel protein type IV ...SkM1 / Sodium channel protein skeletal muscle subunit alpha / Sodium channel protein type IV subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.4


Mass: 19211.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN4A / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P35499
#2: Protein Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calm1, Calm, Cam, Cam1, CaMI / Plasmid: pET24 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0DP29
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 0.1M MES pH 6.0, 20% PEG 6000, 1.0M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2017
RadiationMonochromator: VDCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→40.829 Å / Num. obs: 5845 / % possible obs: 99.9 % / Redundancy: 24.829 % / Biso Wilson estimate: 128.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.121 / Χ2: 1.008 / Net I/σ(I): 18.11 / Num. measured all: 145128 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.3824.8651.8412.084060.6831.879100
3.38-3.4823.541.2183.154130.831.245100
3.48-3.5826.4471.1223.733890.8711.143100
3.58-3.6925.8370.8814.933990.9420.899100
3.69-3.8125.1020.6346.973720.9580.647100
3.81-3.9423.7930.439.813670.9770.44100
3.94-4.0926.2540.35912.723500.9890.366100
4.09-4.2626.4290.26915.883450.9940.274100
4.26-4.4526.6190.22918.673230.9970.234100
4.45-4.6726.1390.18223.053160.9960.185100
4.67-4.9226.3620.16924.493090.9980.172100
4.92-5.2225.5750.16724.112850.9980.17100
5.22-5.5825.3170.16324.42710.9980.166100
5.58-6.0223.8520.14825.282560.9980.151100
6.02-6.622.0970.11130.492370.9980.114100
6.6-7.3824.2480.09235.992220.9990.094100
7.38-8.5221.2620.06842.781910.9990.07100
8.52-10.4322.8080.0649.981720.9990.061100
10.43-14.7522.1290.05454.031390.9990.055100
14.75-40.82916.8310.04846.54830.9970.04996.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G43

3g43


Resolution: 3.3→40.829 Å / SU ML: 0.71 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 34.28
RfactorNum. reflection% reflection
Rfree0.2853 513 4.96 %
Rwork0.24 --
obs0.2421 10333 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 275.41 Å2 / Biso mean: 145.5062 Å2 / Biso min: 73.78 Å2
Refinement stepCycle: final / Resolution: 3.3→40.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 4 0 2330
Biso mean--92.33 --
Num. residues----291
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3001-3.6320.43961290.326124492578
3.632-4.15710.2671300.264224512581
4.1571-5.23570.26831270.232224642591
5.2357-40.8320.27571270.222624562583
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)
15.4977-1.73030.53084.60362.82694.49910.4280.52830.88710.5850.5021-1.5969-0.37110.7409-1.0230.8311-0.01960.08791.1891-0.23211.424624.5695-4.007425.0058
25.9821.90773.58486.7526-0.85484.3850.0185-0.06941.1013-0.2226-0.5220.8696-0.0131-0.25250.42591.10370.15280.0510.9669-0.19951.0876-1.5679-8.738918.232
34.4138-2.9263-4.32123.31692.21696.0719-0.97461.19461.4111-1.88620.19220.9377-0.5831-0.73830.73482.1244-0.2482-0.77450.98240.01861.574612.467422.945824.3404
47.13952.87650.49912.77231.46366.0291-0.2511.0797-1.18180.544-0.142-0.14240.7138-0.3430.3691.2355-0.1047-0.04361.1257-0.2980.82094.8344-12.11378.2506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 7 through 75 )B7 - 75
2X-RAY DIFFRACTION2chain 'B' and (resid 80 through 147 )B80 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 1611 through 1711)A1611 - 1711
4X-RAY DIFFRACTION4chain 'A' and (resid 1717 through 1760)A1717 - 1760

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