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- PDB-7bf1: Ca2+-Calmodulin in complex with peptide from brain-type creatine ... -

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Basic information

Entry
Database: PDB / ID: 7bf1
TitleCa2+-Calmodulin in complex with peptide from brain-type creatine kinase in extended 1:2 binding mode
Components
  • Calmodulin-1
  • Creatine kinase B-type
KeywordsCYTOSOLIC PROTEIN / Calmodulin / Calmodulin-peptide complex / Creatine kinase / calcium signaling / energy metabolism
Function / homology
Function and homology information


futile creatine cycle / creatine kinase / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels ...futile creatine cycle / creatine kinase / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / RND3 GTPase cycle / Activation of Ca-permeable Kainate Receptor / 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 / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / 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 / RHO GTPases activate PAKs / calcineurin-mediated signaling / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / 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 / RHO GTPases activate IQGAPs / 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 / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / RAF activation / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / cellular response to type II interferon / long-term synaptic potentiation / response to calcium ion / RAS processing / spindle pole / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Inactivation, recovery and regulation of the phototransduction cascade / Platelet degranulation / myelin sheath / Ca2+ pathway / RAF/MAP kinase cascade
Similarity search - Function
ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. ...ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / : / 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
ACETYL GROUP / Calmodulin-1 / Creatine kinase B-type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsSprenger, J. / Akerfeldt, K.S. / Bredfelt, J. / Patel, N. / Rowlett, R. / Trifan, A. / Vanderbeck, A. / Lo Leggio, L. / Snogerup Linse, S.
CitationJournal: Curr Res Struct Biol / Year: 2021
Title: Calmodulin complexes with brain and muscle creatine kinase peptides.
Authors: Sprenger, J. / Trifan, A. / Patel, N. / Vanderbeck, A. / Bredfelt, J. / Tajkhorshid, E. / Rowlett, R. / Lo Leggio, L. / Akerfeldt, K.S. / Linse, S.
History
DepositionDec 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Calmodulin-1
CCC: Creatine kinase B-type
DDD: Creatine kinase B-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4608
Polymers21,2563
Non-polymers2045
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, 2 peptides bind 1 CaM molecule
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-72 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.411, 59.534, 52.477
Angle α, β, γ (deg.)90.000, 98.343, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#2: Protein/peptide Creatine kinase B-type / Brain creatine kinase / B-CK / Creatine kinase B chain / Creatine phosphokinase B-type / CPK-B


Mass: 2201.614 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P12277, creatine kinase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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, hanging drop
Details: 25% PEG 1500, 0.1 M SPG buffer pH 4-5. CaM-CKBpeptide ratios of 1:4
PH range: 4-5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972424 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972424 Å / Relative weight: 1
ReflectionResolution: 1.24→39.161 Å / Num. obs: 41629 / % possible obs: 96.95 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08768 / Net I/σ(I): 9.76
Reflection shellResolution: 1.24→1.284 Å / Rmerge(I) obs: 1.608 / Num. unique obs: 4151 / CC1/2: 0.471

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2l7l

2l7l


Resolution: 1.24→39.161 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.136 / SU B: 2.434 / SU ML: 0.044 / Average fsc free: 0.8839 / Average fsc work: 0.8917 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1863 2091 5.027 %
Rwork0.1351 39502 -
all0.138 --
obs-41593 98.847 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.434 Å2
Baniso -1Baniso -2Baniso -3
1--0.444 Å20 Å2-0.933 Å2
2---1.256 Å20 Å2
3---1.892 Å2
Refinement stepCycle: LAST / Resolution: 1.24→39.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 7 148 1558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121509
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181394
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.652029
X-RAY DIFFRACTIONr_angle_other_deg0.6331.5733256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3695192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.57823.41898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70215303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7461512
X-RAY DIFFRACTIONr_chiral_restr0.0920.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
X-RAY DIFFRACTIONr_nbd_refined0.2540.2405
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21267
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2740
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.2741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.286
X-RAY DIFFRACTIONr_metal_ion_refined0.0730.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.231
X-RAY DIFFRACTIONr_nbd_other0.2210.298
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.229
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.10.21
X-RAY DIFFRACTIONr_mcbond_it2.8571.892740
X-RAY DIFFRACTIONr_mcbond_other2.7491.887739
X-RAY DIFFRACTIONr_mcangle_it3.1712.827933
X-RAY DIFFRACTIONr_mcangle_other3.1732.831934
X-RAY DIFFRACTIONr_scbond_it4.5612.463769
X-RAY DIFFRACTIONr_scbond_other4.5582.464770
X-RAY DIFFRACTIONr_scangle_it5.4123.4861093
X-RAY DIFFRACTIONr_scangle_other5.413.4881094
X-RAY DIFFRACTIONr_lrange_it5.48824.1571830
X-RAY DIFFRACTIONr_lrange_other5.29723.8731809
X-RAY DIFFRACTIONr_rigid_bond_restr3.66932903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.2720.2981520.2812906X-RAY DIFFRACTION98.7726
1.272-1.3070.2961400.2642820X-RAY DIFFRACTION98.8314
1.307-1.3450.2611400.2382787X-RAY DIFFRACTION98.6518
1.345-1.3860.2411400.2022647X-RAY DIFFRACTION98.2376
1.386-1.4320.211460.1662621X-RAY DIFFRACTION99.1046
1.432-1.4820.181260.142479X-RAY DIFFRACTION98.824
1.482-1.5380.1751440.1212441X-RAY DIFFRACTION98.9663
1.538-1.6010.1641350.1092309X-RAY DIFFRACTION98.5881
1.601-1.6720.1511250.0972230X-RAY DIFFRACTION99.2415
1.672-1.7530.1471100.082198X-RAY DIFFRACTION99.3971
1.753-1.8480.171040.0932031X-RAY DIFFRACTION99.0719
1.848-1.960.1931040.0971913X-RAY DIFFRACTION98.6308
1.96-2.0950.176860.0971841X-RAY DIFFRACTION99.0236
2.095-2.2620.131960.0921711X-RAY DIFFRACTION99.7241
2.262-2.4780.187880.111570X-RAY DIFFRACTION99.1627
2.478-2.770.197790.1351399X-RAY DIFFRACTION98.7308
2.77-3.1970.219630.1491226X-RAY DIFFRACTION97.7997
3.197-3.9110.192530.1511075X-RAY DIFFRACTION99.5587
3.911-5.5160.158410.147820X-RAY DIFFRACTION97.3982
5.516-39.1610.252190.2478X-RAY DIFFRACTION98.0276

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