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- PDB-4e50: Calmodulin and Ng peptide complex -

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Basic information

Entry
Database: PDB / ID: 4.0E+50
TitleCalmodulin and Ng peptide complex
ComponentsCalmodulin, Linker, IQ motif of Neurogranin
KeywordsPROTEIN BINDING / Calmodulin (CaM) / Intrinsically unstructured proteins / Protein kinase C (PKC) / Neurogranin / Long Term Potentiation (LTP) / Long Term Depression (LTD) / IQ motif
Function / homology
Function and homology information


trans-Golgi network transport vesicle membrane / CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / CLEC7A (Dectin-1) induces NFAT activation ...trans-Golgi network transport vesicle membrane / CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / CLEC7A (Dectin-1) induces NFAT activation / Synthesis of IP3 and IP4 in the cytosol / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Calcineurin activates NFAT / eNOS activation / Ion transport by P-type ATPases / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / RAF activation / VEGFR2 mediated vascular permeability / RAS processing / Smooth Muscle Contraction / Ca2+ pathway / negative regulation of calcium ion transmembrane transporter activity / FCERI mediated Ca+2 mobilization / RAF/MAP kinase cascade / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / PKA activation / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Platelet degranulation / telencephalon development / : / establishment of protein localization to mitochondrial membrane / Stimuli-sensing channels / phosphatidic acid binding / Ion homeostasis / type 3 metabotropic glutamate receptor binding / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / response to corticosterone / postsynaptic modulation of chemical synaptic transmission / dendritic spine head / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / protein phosphatase activator activity / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of cyclic-nucleotide phosphodiesterase activity / associative learning / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / calcium-mediated signaling / spindle microtubule / mitochondrial membrane / positive regulation of receptor signaling pathway via JAK-STAT / synaptic vesicle membrane / spindle pole / cellular response to type II interferon / response to calcium ion / calcium-dependent protein binding / disordered domain specific binding / G2/M transition of mitotic cell cycle / myelin sheath
Similarity search - Function
IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site / 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
Calmodulin-1 / Neurogranin / Calmodulin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsKumar, V. / Sivaraman, J.
CitationJournal: Sci Rep / Year: 2013
Title: Structural basis for the interaction of unstructured neuron specific substrates neuromodulin and neurogranin with calmodulin
Authors: Kumar, V. / Chichili, V.P.R. / Zhong, L. / Tang, X. / Velazquez-Campoy, A. / Sheu, F.-S. / Seetharaman, J. / Gerges, N.Z. / Sivaraman, J.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin, Linker, IQ motif of Neurogranin


Theoretical massNumber of molelcules
Total (without water)20,6581
Polymers20,6581
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.467, 76.467, 46.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Calmodulin, Linker, IQ motif of Neurogranin /


Mass: 20657.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of Calmodulin, Linker, IQ motif of Neurogranin
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGS21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P62204, UniProt: P60761, UniProt: P0DP26*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.32 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M imidazole, 1.2M sodium citrate tribasic dihydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.92
11K, H, -L20.08
ReflectionResolution: 2.6→30 Å / Num. all: 8503 / Num. obs: 8503 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.69 Å / % possible all: 92.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.928 / SU B: 48.697 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27529 359 4.7 %RANDOM
Rwork0.2408 ---
obs0.24229 7200 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.328 Å2
Baniso -1Baniso -2Baniso -3
1-9.16 Å20 Å20 Å2
2--9.16 Å20 Å2
3----18.31 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 0 22 1280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221270
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9611696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.17725.73568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.28115248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.972158
X-RAY DIFFRACTIONr_chiral_restr0.1130.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02955
X-RAY DIFFRACTIONr_mcbond_it0.611.5786
X-RAY DIFFRACTIONr_mcangle_it1.17921254
X-RAY DIFFRACTIONr_scbond_it1.463484
X-RAY DIFFRACTIONr_scangle_it2.624.5442
LS refinement shellResolution: 2.699→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 36 -
Rwork0.227 514 -
obs--98.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6377-0.25580.23522.43160.81350.48210.04680.00850.10040.0179-0.16180.1960.1637-0.02610.11490.418-0.00910.00970.29410.0040.305333.641610.3103-0.5169
213.3378-1.4557-11.55972.81127.815619.4760.03760.0411-0.28940.0416-0.35230.2375-0.0075-0.18920.31470.61250.04090.06690.26690.04990.098433.9387.3914.025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 176
2X-RAY DIFFRACTION2A201 - 222

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