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- PDB-4jpz: Voltage-gated sodium channel 1.2 C-terminal domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4jpz
TitleVoltage-gated sodium channel 1.2 C-terminal domain in complex with FGF13U and Ca2+/calmodulin
Components
  • Calmodulin
  • Fibroblast growth factor 13
  • Sodium channel protein type 2 subunit alpha
KeywordsTRANSPORT PROTEIN / EF hand and IQ motif / ion channel / membrane
Function / homology
Function and homology information


establishment of neuroblast polarity / regulation of cardiac muscle cell action potential involved in regulation of contraction / positive regulation of voltage-gated sodium channel activity / negative regulation of collateral sprouting / branching morphogenesis of a nerve / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity ...establishment of neuroblast polarity / regulation of cardiac muscle cell action potential involved in regulation of contraction / positive regulation of voltage-gated sodium channel activity / negative regulation of collateral sprouting / branching morphogenesis of a nerve / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / paranode region of axon / establishment of protein localization to mitochondrial membrane / dentate gyrus development / negative regulation of microtubule depolymerization / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding / cardiac muscle cell action potential involved in contraction / node of Ranvier / voltage-gated sodium channel complex / inhibitory synapse assembly / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Interaction between L1 and Ankyrins / Calmodulin induced events / 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 / voltage-gated sodium channel activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / positive regulation of DNA binding / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / positive regulation of peptidyl-threonine phosphorylation / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / sodium ion transport / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / beta-tubulin binding / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / cerebral cortex cell migration / microtubule polymerization / regulation of synaptic vesicle endocytosis / Ion transport by P-type ATPases / positive regulation of protein autophosphorylation / Uptake and function of anthrax toxins / Long-term potentiation / Calcineurin activates NFAT / protein phosphatase activator activity / Regulation of MECP2 expression and activity / regulation of ryanodine-sensitive calcium-release channel activity / adenylate cyclase binding / DARPP-32 events / intercalated disc / sodium channel regulator activity / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / lateral plasma membrane / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / neuronal action potential / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / enzyme regulator activity / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / neurogenesis / voltage-gated potassium channel complex
Similarity search - Function
iswi atpase / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / HBGF/FGF family signature. / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / Fibroblast growth factor family / Fibroblast growth factor ...iswi atpase / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / HBGF/FGF family signature. / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Cytokine IL1/FGF / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Voltage-dependent channel domain superfamily / EF-hand / : / Recoverin; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Fibroblast growth factor 13 / Sodium channel protein type 2 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.02 Å
AuthorsWang, C. / Chung, B.C. / Yan, H. / Wang, H.G. / Lee, S.Y. / Pitt, G.S.
CitationJournal: Nat Commun / Year: 2014
Title: Structural analyses of Ca(2+)/CaM interaction with NaV channel C-termini reveal mechanisms of calcium-dependent regulation.
Authors: Wang, C. / Chung, B.C. / Yan, H. / Wang, H.G. / Lee, S.Y. / Pitt, G.S.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor 13
B: Sodium channel protein type 2 subunit alpha
C: Calmodulin
E: Fibroblast growth factor 13
H: Sodium channel protein type 2 subunit alpha
I: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,31714
Polymers118,9966
Non-polymers3218
Water55831
1
A: Fibroblast growth factor 13
B: Sodium channel protein type 2 subunit alpha
C: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6587
Polymers59,4983
Non-polymers1604
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-81 kcal/mol
Surface area21560 Å2
MethodPISA
2
E: Fibroblast growth factor 13
H: Sodium channel protein type 2 subunit alpha
I: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6587
Polymers59,4983
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-80 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.133, 86.106, 109.399
Angle α, β, γ (deg.)90.00, 100.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fibroblast growth factor 13 / FGF-13 / Fibroblast growth factor homologous factor 2 / FHF-2


Mass: 21609.592 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF13, FHF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92913
#2: Protein Sodium channel protein type 2 subunit alpha / HBSC II / Sodium channel protein brain II subunit alpha / Sodium channel protein type II subunit ...HBSC II / Sodium channel protein brain II subunit alpha / Sodium channel protein type II subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.2


Mass: 21036.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN2A, NAC2, SCN2A1, SCN2A2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99250
#3: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUES RRRP AT POSITIONS 59-62 ARE ISOFORM 2 NATURAL VARIANTS, UNP CODE Q92913-2

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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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 7.5
Details: 14% pEG3350, 300 mM sodium acetate,50 mM Tris pH 7.5, and 2 mM CaCl2, EVAPORATION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2012
RadiationMonochromator: double crystal, Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.02→50 Å / Num. all: 53782 / Num. obs: 53782 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.02-3.17177.8
3.17-3.25179.4
3.25-3.35183.2
3.35-3.46187.4
3.46-3.58192.6
3.58-3.72193.8
3.72-3.89195.9
3.89-4.1198
4.1-4.35198.6
4.35-4.69198.8
4.69-5.16199.3
5.16-5.91199.5
5.91-7.44199.7
7.44-50199.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXmodel building
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.02→48.23 Å / SU ML: 0.44 / σ(F): 1.4 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 3581 7.24 %
Rwork0.212 --
obs0.2145 49449 91.8 %
all-49445 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.02→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6952 0 8 31 6991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117122
X-RAY DIFFRACTIONf_angle_d1.0419621
X-RAY DIFFRACTIONf_dihedral_angle_d14.9662708
X-RAY DIFFRACTIONf_chiral_restr0.0711036
X-RAY DIFFRACTIONf_plane_restr0.0041242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.12790.36682480.31913032X-RAY DIFFRACTION60
3.1279-3.25310.32522880.30373926X-RAY DIFFRACTION79
3.2531-3.40120.32823400.2914478X-RAY DIFFRACTION89
3.4012-3.58040.33563810.26814766X-RAY DIFFRACTION96
3.5804-3.80470.27323720.24154854X-RAY DIFFRACTION97
3.8047-4.09830.27663840.22744910X-RAY DIFFRACTION99
4.0983-4.51040.27253930.214978X-RAY DIFFRACTION99
4.5104-5.16250.21863900.18284995X-RAY DIFFRACTION100
5.1625-6.50160.22953910.18864937X-RAY DIFFRACTION100
6.5016-48.23650.18273940.17564992X-RAY DIFFRACTION100

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