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- PDB-7bf2: Ca2+-Calmodulin in complex with human muscle form creatine kinase... -

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Basic information

Entry
Database: PDB / ID: 7bf2
TitleCa2+-Calmodulin in complex with human muscle form creatine kinase peptide in extended 1:2 binding mode
Components
  • Calmodulin-1
  • Creatine kinase M-type
KeywordsCYTOSOLIC PROTEIN / Calmodulin / Calmodulin-peptide complex / Creatine kinase / calcium signaling / energy metabolism
Function / homology
Function and homology information


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 / Activation of Ca-permeable Kainate Receptor ...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 / 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 / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / negative regulation of peptidyl-threonine phosphorylation / calcineurin-mediated signaling / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of ryanodine-sensitive calcium-release channel activity / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / protein phosphatase activator activity / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / regulation of cardiac muscle contraction / detection of calcium ion / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / positive regulation of protein autophosphorylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / eNOS activation / regulation of calcium-mediated signaling / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / substantia nigra development / positive regulation of peptidyl-threonine phosphorylation / calyx of Held / FCERI mediated Ca+2 mobilization / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / regulation of cytokinesis / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of protein serine/threonine kinase activity / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / cellular response to type II interferon / spindle pole / response to calcium ion / calcium-dependent protein binding / RAS processing / 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 / 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
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
Creatine kinase M-type / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 M-type
DDD: Creatine kinase M-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5167
Polymers21,3563
Non-polymers1604
Water1,56787
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 area2820 Å2
ΔGint-74 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.695, 24.530, 60.349
Angle α, β, γ (deg.)90.000, 104.838, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains C D)

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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 M-type / Creatine kinase M chain / Creatine phosphokinase M-type / CPK-M / M-CK


Mass: 2251.672 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P06732, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 30.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
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: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.43→34.346 Å / Num. obs: 27542 / % possible obs: 97.13 % / Redundancy: 7 % / Biso Wilson estimate: 23.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05134 / Net I/σ(I): 14.6
Reflection shellResolution: 1.43→1.481 Å / Rmerge(I) obs: 1.506 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 2526 / CC1/2: 0.515 / % possible all: 91.07

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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: 1.43→34.346 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.201 / Average fsc free: 0.8945 / Average fsc work: 0.9076 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2281 1334 4.844 %
Rwork0.2006 26207 -
all0.202 --
obs-27541 97.459 %
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: 35.196 Å2
Baniso -1Baniso -2Baniso -3
1-1.079 Å2-0 Å2-0.155 Å2
2--0.142 Å20 Å2
3----0.999 Å2
Refinement stepCycle: LAST / Resolution: 1.43→34.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 4 87 1471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121454
X-RAY DIFFRACTIONr_bond_other_d0.0070.0171348
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.6521958
X-RAY DIFFRACTIONr_angle_other_deg0.7021.573145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1745181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.67923.8289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56915285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5291510
X-RAY DIFFRACTIONr_chiral_restr0.090.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021659
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02291
X-RAY DIFFRACTIONr_nbd_refined0.2530.2375
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.21303
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2739
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.2696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.050.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.232
X-RAY DIFFRACTIONr_nbd_other0.280.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.217
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0960.21
X-RAY DIFFRACTIONr_mcbond_it2.7563.098712
X-RAY DIFFRACTIONr_mcbond_other2.7533.093711
X-RAY DIFFRACTIONr_mcangle_it3.7794.611894
X-RAY DIFFRACTIONr_mcangle_other3.7814.617895
X-RAY DIFFRACTIONr_scbond_it4.423.792742
X-RAY DIFFRACTIONr_scbond_other4.4223.783739
X-RAY DIFFRACTIONr_scangle_it6.6735.4731063
X-RAY DIFFRACTIONr_scangle_other6.6735.4691062
X-RAY DIFFRACTIONr_lrange_it7.79538.2741716
X-RAY DIFFRACTIONr_lrange_other7.78538.1241701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.4670.352900.3311779X-RAY DIFFRACTION90.4647
1.467-1.5070.335860.3031825X-RAY DIFFRACTION96.1751
1.507-1.5510.303890.2721841X-RAY DIFFRACTION97.3273
1.551-1.5990.283860.2591754X-RAY DIFFRACTION97.2002
1.599-1.6510.277840.2531719X-RAY DIFFRACTION97.2492
1.651-1.7090.263760.2381650X-RAY DIFFRACTION97.6797
1.709-1.7730.263740.2271632X-RAY DIFFRACTION98.2153
1.773-1.8460.255780.2211552X-RAY DIFFRACTION98.1337
1.846-1.9280.259850.2091479X-RAY DIFFRACTION97.9336
1.928-2.0220.285790.2121434X-RAY DIFFRACTION97.9922
2.022-2.1310.273580.2061357X-RAY DIFFRACTION98.3322
2.131-2.260.229780.1841304X-RAY DIFFRACTION98.433
2.26-2.4160.221630.1891212X-RAY DIFFRACTION99.0676
2.416-2.6090.227510.1891159X-RAY DIFFRACTION99.0991
2.609-2.8570.221610.1911043X-RAY DIFFRACTION99.1914
2.857-3.1940.232560.205973X-RAY DIFFRACTION99.0375
3.194-3.6860.325320.186861X-RAY DIFFRACTION99.4432
3.686-4.510.175510.172722X-RAY DIFFRACTION99.1026
4.51-6.3590.24330.215578X-RAY DIFFRACTION98.2315

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