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- PDB-2m5e: Structure of the C-domain of Calcium-saturated Calmodulin bound t... -

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Basic information

Entry
Database: PDB / ID: 2m5e
TitleStructure of the C-domain of Calcium-saturated Calmodulin bound to the IQ motif of NaV1.2
Components
  • Calmodulin
  • Sodium channel protein type 2 subunit alpha
KeywordsCALCIUM-BINDING PROTEIN/METAL TRANSPORT / Calcium Binding Protein / NaV1.2 / Ion Channel Gating / IQ Motif / Metal Binding / Sodium Channels / Metal Transport / Voltage Dependent / Voltage Gated / Calcium Binding Protein-Metal Transport Complex / Neuronal Peptides / EF-Hand / CALCIUM-BINDING PROTEIN-METAL TRANSPORT complex
Function / homology
Function and homology information


leucine zipper domain binding / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / corpus callosum development / paranode region of axon / membrane depolarization during action potential / dentate gyrus development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / axon initial segment / node of Ranvier ...leucine zipper domain binding / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / corpus callosum development / paranode region of axon / membrane depolarization during action potential / dentate gyrus development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / axon initial segment / node of Ranvier / voltage-gated sodium channel complex / voltage-gated sodium channel activity / optic nerve development / sodium ion transport / axon development / intercalated disc / neuronal action potential / enzyme regulator activity / T-tubule / myelination / sodium ion transmembrane transport / determination of adult lifespan / cerebral cortex development / memory / nervous system development / presynaptic membrane / neuron apoptotic process / cellular response to hypoxia / calmodulin binding / axon / calcium ion binding / glutamatergic synapse / membrane / plasma membrane / cytoplasm
Similarity search - Function
Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / SCN5A-like, C-terminal IQ motif / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site ...Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / SCN5A-like, C-terminal IQ motif / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / Voltage-dependent channel domain superfamily / : / 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
Similarity search - Domain/homology
Sodium channel protein type 2 subunit alpha / Calmodulin
Similarity search - Component
Biological speciesParamecium tetraurelia (eukaryote)
Rattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsFowler, C.A. / Feldkamp, M.D. / Yu, L. / Shea, M.A.
Citation
Journal: Biophys. Chem. / Year: 2017
Title: Calcium triggers reversal of calmodulin on nested anti-parallel sites in the IQ motif of the neuronal voltage-dependent sodium channel NaV1.2.
Authors: Hovey, L. / Fowler, C.A. / Mahling, R. / Lin, Z. / Miller, M.S. / Marx, D.C. / Yoder, J.B. / Kim, E.H. / Tefft, K.M. / Waite, B.C. / Feldkamp, M.D. / Yu, L. / Shea, M.A.
#1: Journal: Structure / Year: 2011
Title: Structural and Energetic Determinants of Apo Calmodulin Binding to the IQ Motif of the NaV1.2 Voltage-Dependent Sodium Channel
Authors: Feldkamp, M.D. / Yu, L. / Shea, M.A.
History
DepositionFeb 21, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Sodium channel protein type 2 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8674
Polymers11,7862
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 300structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Calmodulin / CaM


Mass: 8416.313 Da / Num. of mol.: 1 / Fragment: UNP residues 77-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium tetraurelia (eukaryote) / Strain: d4-2 / Gene: CAM, GSPATT00015825001 / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07463
#2: Protein/peptide Sodium channel protein type 2 subunit alpha / Sodium channel protein brain II subunit alpha / Sodium channel protein type II subunit alpha / ...Sodium channel protein brain II subunit alpha / Sodium channel protein type II subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.2


Mass: 3370.088 Da / Num. of mol.: 1 / Fragment: UNP residues 1901-1927
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Scn2a, Scn2a1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04775
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HMQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D HN(COCA)CB
1713D HNCO
1813D HN(CA)CO
1913D C(CO)NH
11013D H(CCO)NH
11113D 1H-15N NOESY
11223D 1H-13C NOESY
11323D (H)CCH-TOCSY
11412D 1H-15N HSQC
11522D 1H-13C HMQC
11623D 1H-13C edited, 12C filtered NOESY
11712D 1H-1H doubly 12C,14N filtered NOESY
11812D 1H-1H 12C,14N filtered TOCSY
11922D 1H-1H 12C filtered NOESY
12022D 1H-1H 12C,14N filtered TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-100% 13C; U-100% 15N] C-domain of Calmodulin, 1.5 mM IQ motif peptide of NaV1.2, 3.3 mM CALCIUM ION, 10 mM [U-2H] imidazole, 100 mM potassium chloride, 0.01 % sodium azide, 50 uM [U-2H] EDTA, 95% H2O/5% D2O95% H2O/5% D2O
21.5 mM [U-100% 13C; U-100% 15N] C-domain of Calmodulin, 1.5 mM IQ motif peptide of NaV1.2, 3.3 mM CALCIUM ION, 10 mM [U-2H] imidazole, 100 mM potassium chloride, 0.01 % sodium azide, 50 uM [U-2H] EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMC-domain of Calmodulin-1[U-100% 13C; U-100% 15N]1
1.5 mMIQ motif peptide of NaV1.2-21
3.3 mMCALCIUM ION-31
10 mMimidazole-4[U-2H]1
100 mMpotassium chloride-51
0.01 %sodium azide-61
50 uMEDTA-7[U-2H]1
1.5 mMC-domain of Calmodulin-8[U-100% 13C; U-100% 15N]2
1.5 mMIQ motif peptide of NaV1.2-92
3.3 mMCALCIUM ION-102
10 mMimidazole-11[U-2H]2
100 mMpotassium chloride-122
0.01 %sodium azide-132
50 uMEDTA-14[U-2H]2
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIBrukerAVANCE II5001
Bruker Avance IIBrukerAVANCE II8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
Sparky3.115Goddardchemical shift assignment
Sparky3.115Goddardpeak picking
Sparky3.115Goddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
Analysis2.1.5CCPNpeak picking
Analysis2.1.5CCPNchemical shift assignment
Analysis2.1.5CCPNdata analysis
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesdata analysis
CNSSOLVE1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVE1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSSOLVE1.21Brunger, Adams, Clore, Gros, Nilges and Readdata analysis
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Cloredata analysis
ProcheckNMR3.5.4Laskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: RESIDUES 1901-1903 AND 1925-1927 IN THE PEPTIDE ARE COMPLETELY UNRESTRAINED
NMR constraintsNOE constraints total: 2721 / NOE intraresidue total count: 492 / NOE long range total count: 399 / NOE medium range total count: 415 / NOE sequential total count: 393
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 21
NMR ensemble rmsDistance rms dev: 0.0039 Å / Distance rms dev error: 0.0001 Å

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