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- PDB-4e53: Calmodulin and Nm peptide complex -

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Basic information

Entry
Database: PDB / ID: 4.0E+53
TitleCalmodulin and Nm peptide complex
ComponentsCalmodulin, Linker, IQ motif of Neuromodulin
KeywordsPROTEIN BINDING / Calmodulin (CaM) / Intrinsically unstructured proteins / Protein kinase C (PKC) / Neuromodulin / Growth associated protein -43 (GAP-43) / Long Term Potentiation (LTP) / Long Term Depression (LTD) / IQ motif
Function / homology
Function and homology information


L1CAM interactions / axon choice point recognition / negative regulation of calcium ion transmembrane transporter activity / 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 / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor ...L1CAM interactions / axon choice point recognition / negative regulation of calcium ion transmembrane transporter activity / 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 / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / radial glial cell differentiation / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Calcineurin activates NFAT / Reduction of cytosolic Ca++ levels / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / Ion transport by P-type ATPases / RAF activation / VEGFR2 mediated vascular permeability / lysophosphatidic acid binding / RAS processing / phosphatidylinositol phosphate binding / FCERI mediated Ca+2 mobilization / Ca2+ pathway / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / RAF/MAP kinase cascade / PKA activation / growth cone membrane / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / regulation of postsynaptic specialization assembly / response to auditory stimulus / Smooth Muscle Contraction / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / Platelet degranulation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / : / regulation of filopodium assembly / tissue regeneration / Stimuli-sensing channels / establishment of protein localization to mitochondrial membrane / Ion homeostasis / astrocyte differentiation / type 3 metabotropic glutamate receptor binding / filopodium membrane / regulation of growth / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / phosphatidylserine binding / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / adenylate cyclase binding / catalytic complex / cell fate commitment / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / postsynaptic cytosol / cellular response to interferon-beta / activation of adenylate cyclase activity / calcium channel inhibitor activity / presynaptic cytosol / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of nitric-oxide synthase activity / titin binding / enzyme regulator activity / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / response to amphetamine / regulation of heart rate / calyx of Held / axon guidance / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / sarcomere
Similarity search - Function
Neuromodulin (GAP-43) / Neuromodulin (GAP-43), C-terminal / Neuromodulin, palmitoylation site / Neuromodulin gap junction N-terminal / Neuromodulin, phosphorylation site / Neuromodulin / Gap junction protein N-terminal region / Neuromodulin (GAP-43) signature 1. / Neuromodulin (GAP-43) signature 2. / IQ calmodulin-binding motif ...Neuromodulin (GAP-43) / Neuromodulin (GAP-43), C-terminal / Neuromodulin, palmitoylation site / Neuromodulin gap junction N-terminal / Neuromodulin, phosphorylation site / Neuromodulin / Gap junction protein N-terminal region / Neuromodulin (GAP-43) signature 1. / Neuromodulin (GAP-43) signature 2. / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / 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 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Neuromodulin / Calmodulin-1 / Calmodulin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69 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:
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Assembly

Deposited unit
A: Calmodulin, Linker, IQ motif of Neuromodulin
B: Calmodulin, Linker, IQ motif of Neuromodulin


Theoretical massNumber of molelcules
Total (without water)41,4862
Polymers41,4862
Non-polymers00
Water1,24369
1
A: Calmodulin, Linker, IQ motif of Neuromodulin


Theoretical massNumber of molelcules
Total (without water)20,7431
Polymers20,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calmodulin, Linker, IQ motif of Neuromodulin


Theoretical massNumber of molelcules
Total (without water)20,7431
Polymers20,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.386, 79.285, 136.064
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calmodulin, Linker, IQ motif of Neuromodulin


Mass: 20743.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chimera of Calmodulin, Linker, IQ motif of Neuromodulin
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGS21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P62204, UniProt: P06837, UniProt: P0DP26*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2

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Sample preparation

CrystalDensity Matthews: 5.16 Å3/Da / Density % sol: 76.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.12mM MgAcO, 8% PEG 3350, 10% EtOH, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSRRC BL13B110.978
ROTATING ANODEBRUKER AXS MICROSTAR21.541
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 15, 2011
Bruker Platinum 1352CCDJun 7, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
21.5411
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.255
11-K, -H, -L20.247
11K, H, -L30.241
11-h,-k,l40.257
ReflectionResolution: 2.69→50 Å / Num. all: 23563 / Num. obs: 23563 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.69→2.74 Å / % possible all: 85.5

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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: 2.69→30 Å / Cor.coef. Fo:Fc: 0.787 / Cor.coef. Fo:Fc free: 0.664 / SU B: 7.702 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31817 1278 5.7 %RANDOM
Rwork0.27604 ---
obs0.2785 21094 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.101 Å2
Baniso -1Baniso -2Baniso -3
1-12.47 Å20 Å2-0.51 Å2
2--23.17 Å20 Å2
3----35.64 Å2
Refinement stepCycle: LAST / Resolution: 2.69→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2646 0 0 69 2715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222672
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9623576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.99426.027146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.01815516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9811516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022022
X-RAY DIFFRACTIONr_mcbond_it0.2231.51654
X-RAY DIFFRACTIONr_mcangle_it0.41422646
X-RAY DIFFRACTIONr_scbond_it0.64231018
X-RAY DIFFRACTIONr_scangle_it1.0624.5930
LS refinement shellResolution: 2.69→2.759 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 75 -
Rwork0.176 1191 -
obs--73.65 %

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