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- PDB-6mba: Crystal Structure of Human Nav1.4 CTerminal Domain in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 6mba
TitleCrystal Structure of Human Nav1.4 CTerminal Domain in Complex with apo Calmodulin
Components
  • Calmodulin-1
  • Sodium channel protein type 4 subunit alpha
KeywordsCALMODULIN-BINDING PROTEIN / SCN4A / voltage gated sodium channel / calmodulin / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of skeletal muscle contraction by action potential / establishment of protein localization to mitochondrial membrane / cardiac muscle cell action potential involved in contraction / type 3 metabotropic glutamate receptor binding / 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 / organelle localization by membrane tethering ...regulation of skeletal muscle contraction by action potential / establishment of protein localization to mitochondrial membrane / cardiac muscle cell action potential involved in contraction / type 3 metabotropic glutamate receptor binding / 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 / organelle localization by membrane tethering / sodium ion transport / 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 / Phase 0 - rapid depolarisation / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / adenylate cyclase binding / catalytic complex / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / postsynaptic cytosol / cellular response to interferon-beta / calcium channel inhibitor activity / phosphatidylinositol 3-kinase binding / 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 / adenylate cyclase activator activity / response to amphetamine / sarcomere / regulation of cytokinesis / protein serine/threonine kinase activator activity / nitric-oxide synthase regulator activity / spindle microtubule / calcium channel regulator activity / positive regulation of receptor signaling pathway via JAK-STAT / 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 / cytosol / cytoplasm
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
CARBONATE ION / 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: 1.799 Å
AuthorsYoder, J. / 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 29, 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)36,8469
Polymers36,4602
Non-polymers3867
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-46 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.720, 29.041, 94.991
Angle α, β, γ (deg.)90.00, 123.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-331-

HOH

21B-333-

HOH

31B-364-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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: 19607.188 Da / Num. of mol.: 1 / Fragment: cytoplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN4A / Plasmid: pGEX-6P / 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: pET-24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P0DP29

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Non-polymers , 5 types, 127 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CO3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.77 Å3/Da / Density % sol: 30.7 %
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-1 / Wavelength: 0.918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 2, 2017
RadiationMonochromator: VDCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.799→44.875 Å / Num. obs: 42682 / % possible obs: 91.4 % / Redundancy: 1.605 % / Biso Wilson estimate: 39.247 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.084 / Χ2: 1.189 / Net I/σ(I): 6.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.851.5810.4291.5331010.8250.59190.6
1.85-1.91.6190.3671.9331840.8240.50795.4
1.9-1.951.6160.2642.5131870.9130.36594.5
1.95-2.011.5850.2322.9829090.9170.32392.6
2.01-2.081.5820.1753.7427820.950.24289
2.08-2.151.4980.1374.4226610.9650.1991
2.15-2.231.5790.1275.6226450.9650.17790.1
2.23-2.321.6410.1146.2725600.9670.15994.7
2.32-2.431.6450.0877.3425430.980.12294
2.43-2.541.6270.0867.8123340.9760.11993.3
2.54-2.681.6320.0728.5922590.9820.193.5
2.68-2.841.610.0639.4420500.9850.08990.8
2.84-3.041.6240.06110.4119390.9830.08590.9
3.04-3.281.60.05711.0418310.9870.0890.7
3.28-3.61.6020.0511.8616180.9890.0787.6
3.6-4.021.4540.05411.7713730.9820.07782.9
4.02-4.651.6090.05312.6312540.9830.07586.8
4.65-5.691.7610.0513.2211250.9850.07189.5
5.69-8.051.7520.04213.248750.990.05991.2
8.05-44.51.7120.04613.374520.9870.06585.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OVN

4ovn


Resolution: 1.799→44.875 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 25.23
RfactorNum. reflection% reflection
Rfree0.2335 2120 4.97 %
Rwork0.2028 --
obs0.2043 42664 91.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.799→44.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 20 120 2352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162264
X-RAY DIFFRACTIONf_angle_d1.3843039
X-RAY DIFFRACTIONf_dihedral_angle_d26.329875
X-RAY DIFFRACTIONf_chiral_restr0.091334
X-RAY DIFFRACTIONf_plane_restr0.01400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7987-1.84050.31521360.30812659X-RAY DIFFRACTION89
1.8405-1.88650.33461480.30022820X-RAY DIFFRACTION95
1.8865-1.93760.29241460.26912827X-RAY DIFFRACTION95
1.9376-1.99460.28581470.27232677X-RAY DIFFRACTION93
1.9946-2.0590.27341400.25922689X-RAY DIFFRACTION91
2.059-2.13250.3441360.2442614X-RAY DIFFRACTION89
2.1325-2.21790.25041460.22532715X-RAY DIFFRACTION90
2.2179-2.31890.23691440.21822782X-RAY DIFFRACTION95
2.3189-2.44110.28751480.21292812X-RAY DIFFRACTION95
2.4411-2.5940.27051410.22682706X-RAY DIFFRACTION93
2.594-2.79430.27061450.22352723X-RAY DIFFRACTION93
2.7943-3.07540.2611410.2092714X-RAY DIFFRACTION91
3.0754-3.52030.22251380.192624X-RAY DIFFRACTION90
3.5203-4.43460.18721330.16112504X-RAY DIFFRACTION85
4.4346-44.88870.1791310.18012678X-RAY DIFFRACTION90
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)
13.7136-0.67941.47184.31580.61944.6018-0.14550.10020.259-0.33150.0462-0.4121-0.28780.17160.10050.2649-0.01640.05220.16420.00030.207940.47915.981733.8728
24.06850.6665-0.12074.51830.4764.577-0.12710.5042-0.268-0.47770.01340.63510.1775-0.70490.09140.3151-0.035-0.05240.3546-0.05450.295112.5189-5.414519.6744
39.9745-0.1254-5.884.0996-1.67994.22360.10591.50591.4721-0.41430.35760.8461-1.1542-3.0353-0.53560.95350.3331-0.35531.45490.20361.17463.1525.905813.9972
40.68860.78791.07523.13090.34386.45150.01670.39850.0311-0.3432-0.1358-0.194-0.06660.28110.10310.3141-0.00050.07740.15010.01420.222437.34990.258528.2335
57.7811-0.2439-0.06397.55324.01878.4329-0.11520.9001-0.1847-0.9476-0.0032-0.97490.08550.43660.09710.7978-0.01510.09920.5545-0.01220.423137.2835-4.28826.2505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 80 through 147 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1612 through 1688 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1691 through 1706 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1714 through 1748 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 75 )

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