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- PDB-3ucy: Structure of Mg2+ bound N-terminal domain of calmodulin in the pr... -

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Basic information

Entry
Database: PDB / ID: 3ucy
TitleStructure of Mg2+ bound N-terminal domain of calmodulin in the presence of Zn2+
ComponentsCalmodulin
KeywordsCALCIUM-BINDING PROTEIN / EF-HAND / METAL BINDING / CALCIUM REGULATION
Function / homology
Function and homology information


: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / response to corticosterone / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor ...: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / response to corticosterone / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / regulation of synaptic vesicle endocytosis / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / PKA activation / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / Unblocking of NMDA receptors, glutamate binding and activation / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / Long-term potentiation / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / detection of calcium ion / DARPP-32 events / Smooth Muscle Contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of DNA binding / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / phosphatidylinositol 3-kinase binding / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to amphetamine / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / protein serine/threonine kinase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / regulation of cytokinesis / VEGFR2 mediated cell proliferation / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / mitochondrial membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / synaptic vesicle membrane / cellular response to type II interferon / Stimuli-sensing channels / spindle pole / response to calcium ion
Similarity search - Function
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 / EF-hand domain pair
Similarity search - Domain/homology
CACODYLATE ION / Calmodulin-1 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSenguen, F.T. / Grabarek, Z.
CitationJournal: Biochemistry / Year: 2012
Title: X-ray Structures of Magnesium and Manganese Complexes with the N-Terminal Domain of Calmodulin: Insights into the Mechanism and Specificity of Metal Ion Binding to an EF-Hand.
Authors: Senguen, F.T. / Grabarek, Z.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Feb 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_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.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.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.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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1156
Polymers8,8001
Non-polymers3155
Water1,22568
1
A: Calmodulin
hetero molecules

A: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,23012
Polymers17,5992
Non-polymers63010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1950 Å2
ΔGint-159 kcal/mol
Surface area8850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.298, 35.298, 142.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Calmodulin / / CaM


Mass: 8799.724 Da / Num. of mol.: 1 / Fragment: N-terminal domain residues 2-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM, CALM1, CALM2, CALM3, CALML2, CAM, CAM1, CAM2, CAM3, CAMB, CAMC, CAMIII
Plasmid: PAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62158, UniProt: P0DP23*PLUS

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Non-polymers , 5 types, 73 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100MM TRIS CACODYLATE, 25MM ZNCL2, 16% PEG8000, 100MM MGCL2, 20% ETHYLENE GLYCOL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2011 / Details: NINE QUADRANT
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionRedundancy: 27.4 % / Av σ(I) over netI: 18.29 / Number: 251118 / Rmerge(I) obs: 0.157 / Χ2: 1.33 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 9179 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.885099.910.1451.24828.1
3.083.8810010.1421.08632.7
2.693.0899.810.151.18626.4
2.442.6910010.1751.4125.9
2.272.4410010.2061.56426.4
2.132.2710010.2491.57726.7
2.032.1310010.3071.50226.7
1.942.0310010.371.40327
1.861.9410010.4631.24826.7
1.81.8610010.5921.11926.4
ReflectionResolution: 1.8→50 Å / Num. obs: 9179 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 27.4 % / Biso Wilson estimate: 31.869 Å2 / Rmerge(I) obs: 0.157 / Χ2: 1.325 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.8626.40.5928911.1191100
1.86-1.9426.70.4638731.2481100
1.94-2.03270.378761.4031100
2.03-2.1326.70.3078951.5021100
2.13-2.2726.70.2499051.5771100
2.27-2.4426.40.2068851.5641100
2.44-2.6925.90.1759151.411100
2.69-3.0826.40.159251.186199.8
3.08-3.8832.70.1429581.0861100
3.88-5028.10.14510561.248199.9

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→35.73 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 3.259 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 433 4.8 %RANDOM
Rwork0.201 ---
obs0.2023 9098 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.96 Å2 / Biso mean: 38.4893 Å2 / Biso min: 23.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---0.74 Å2-0 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms575 0 9 68 652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02620
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.985838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.417583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86626.56332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86115125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.745153
X-RAY DIFFRACTIONr_chiral_restr0.0960.293
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021466
LS refinement shellResolution: 1.8→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 29 -
Rwork0.243 517 -
all-546 -
obs--99.27 %

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