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- PDB-2f3y: Calmodulin/IQ domain complex -

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Basic information

Entry
Database: PDB / ID: 2f3y
TitleCalmodulin/IQ domain complex
Components
  • Calmodulin
  • Voltage-dependent L-type calcium channel alpha-1C subunit
KeywordsMETAL BINDING PROTEIN / calmodulin / calmodulin complex / calcium channnel / Cav1.2 / IQ domain
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / immune system development / positive regulation of adenylate cyclase activity / membrane depolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of muscle contraction / membrane depolarization during AV node cell action potential / high voltage-gated calcium channel activity ...voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / immune system development / positive regulation of adenylate cyclase activity / membrane depolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of muscle contraction / membrane depolarization during AV node cell action potential / high voltage-gated calcium channel activity / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / cardiac conduction / L-type voltage-gated calcium channel complex / : / membrane depolarization during cardiac muscle cell action potential / establishment of protein localization to mitochondrial membrane / cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding / regulation of ventricular cardiac muscle cell action potential / NCAM1 interactions / camera-type eye development / cardiac muscle cell action potential involved in contraction / embryonic forelimb morphogenesis / calcium ion transport into cytosol / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / voltage-gated calcium channel complex / 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 / 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 / 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 / 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 / alpha-actinin binding / RHO GTPases activate PAKs / calcineurin-mediated signaling / regulation of heart rate by cardiac conduction / regulation of synaptic vesicle endocytosis / Ion transport by P-type ATPases / positive regulation of protein autophosphorylation / Uptake and function of anthrax toxins / calcium ion import across plasma membrane / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / voltage-gated calcium channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / 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 / voltage-gated potassium channel complex
Similarity search - Function
Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated ...Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / : / 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 / Calmodulin-3 / Voltage-dependent L-type calcium channel subunit alpha-1C / Voltage-dependent L-type calcium channel subunit alpha-1C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsFallon, J.L. / Quiocho, F.A.
Citation
Journal: Structure / Year: 2005
Title: Structure of Calmodulin Bound to the Hydrophobic IQ Domain of the Cardiac Ca(v)1.2 Calcium Channel.
Authors: Fallon, J.L. / Halling, D.B. / Hamilton, S.L. / Quiocho, F.A.
#1: Journal: Am.J.Physiol., Cell Physiol. / Year: 2005
Title: Calmodulin interactions with IQ peptides from voltage-dependent calcium channels
Authors: Black, D.J. / Halling, D.B. / Mandich, D.V. / Pedersen, S.E. / Altshuld, R.A. / Hamilton, S.L.
#2: Journal: Science / Year: 1992
Title: Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex
Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A.
#3: Journal: Structure / Year: 2003
Title: A closed compact structure of native Ca(2+)-calmodulin
Authors: Fallon, J.L. / Quiocho, F.A.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 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_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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Calmodulin
B: Voltage-dependent L-type calcium channel alpha-1C subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7378
Polymers19,5282
Non-polymers2096
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-82 kcal/mol
Surface area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.200, 30.960, 63.940
Angle α, β, γ (deg.)90.00, 114.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1372-

HOH

21A-1417-

HOH

31A-1418-

HOH

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: calm1, calm2, calm3 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Voltage-dependent L-type calcium channel alpha-1C subunit / Voltage- gated calcium channel alpha subunit Cav1.2 / Calcium channel / L type / alpha-1 ...Voltage- gated calcium channel alpha subunit Cav1.2 / Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle


Mass: 2806.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: the IQ domain of the cardiac Cav1.2 channel / References: UniProt: Q13933, UniProt: Q13936*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 32% PEG 4000, 50mM TRIS, 50 mM MgCl2, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.95144, 1.24242, 0.95056, 0.91838
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2005
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951441
21.242421
30.950561
40.918381
Reflection

D res high: 2 Å / D res low: 50 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2% possible obs
1.91195940.0610.97996.5
1.82186070.0640.94492
3.73199900.0691.17998.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.315099.410.0270.8921.9
3.424.3110010.0280.7631.9
2.993.4210010.0460.9211.9
2.712.9910010.0730.9681.9
2.522.7110010.0940.9871.9
2.372.5299.910.1381.1081.9
2.252.3799.810.1481.1081.9
2.152.2597.310.1741.0681.8
2.072.1590.210.2191.0081.7
22.0778.810.2561.0221.6
4.315099.620.0290.9111.9
3.424.3110020.0310.7692
2.993.4210020.0510.9441.9
2.712.9910020.0830.9411.9
2.522.7199.920.1081.0091.9
2.372.5298.920.160.9831.9
2.252.379720.1640.9821.8
2.152.2588.720.1911.0031.7
2.072.1574.720.2280.9741.5
22.0761.120.2951.0261.4
4.315099.830.0331.193.9
3.424.3110030.0340.9913.9
2.993.4210030.0491.0473.9
2.712.9910030.0781.1483.9
2.522.7110030.1011.2213.9
2.372.5210030.1391.2173.8
2.252.3710030.1511.2353.8
2.152.2599.830.1811.273.6
2.072.1596.930.2221.3213.3
22.0791.130.261.2142.9
ReflectionResolution: 1.42→50 Å / Num. all: 29439 / Num. obs: 28262 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.042 / Χ2: 1.241
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.233 / Num. unique all: 1848 / Χ2: 0.831 / % possible all: 64.1

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Phasing

PhasingMethod: MAD
Phasing dm shellResolution: 3→25 Å / Delta phi final: 0.148 / FOM : 0.153 / Reflection: 5945

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
MAR345data collection
RefinementMethod to determine structure: MAD / Resolution: 1.45→24.37 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 335913728 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2635 9.9 %RANDOM
Rwork0.189 ---
all0.189 27644 --
obs0.189 26483 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.43 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-1.29 Å2
2--2.81 Å20 Å2
3----2.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.45→24.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 6 331 1662
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it2.251.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 413 10.2 %
Rwork0.222 3624 -
obs-4037 88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2water.topwater_rep.param
X-RAY DIFFRACTION3ion.topion.param

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