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- PDB-3ewv: Crystal Structure of calmodulin complexed with a peptide -

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Basic information

Entry
Database: PDB / ID: 3ewv
TitleCrystal Structure of calmodulin complexed with a peptide
Components
  • Calmodulin
  • Tumor necrosis factor receptor superfamily member 16
KeywordsCALCIUM BINDING PROTEIN / Calmodulin-peptide complex / p75 / death domain
Function / homology
Function and homology information


NFG and proNGF binds to p75NTR / death receptor activity / detection of temperature stimulus / dorsal aorta development / Ceramide signalling / positive regulation of odontogenesis of dentin-containing tooth / negative regulation of hair follicle development / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / p75NTR negatively regulates cell cycle via SC1 ...NFG and proNGF binds to p75NTR / death receptor activity / detection of temperature stimulus / dorsal aorta development / Ceramide signalling / positive regulation of odontogenesis of dentin-containing tooth / negative regulation of hair follicle development / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / p75NTR negatively regulates cell cycle via SC1 / neurotrophin binding / nerve growth factor binding / nerve development / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / : / positive regulation of protein autophosphorylation / NADE modulates death signalling / negative regulation of peptidyl-threonine phosphorylation / Regulated proteolysis of p75NTR / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of peptidyl-threonine phosphorylation / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / positive regulation of DNA binding / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / hair follicle morphogenesis / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / response to corticosterone / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / NRAGE signals death through JNK / mitochondrion-endoplasmic reticulum membrane tethering / 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 / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / regulation of synaptic vesicle exocytosis / intracellular glucose homeostasis / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / odontogenesis of dentin-containing tooth / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / adenylate cyclase binding / Regulation of MECP2 expression and activity / DARPP-32 events / positive regulation of endothelial cell apoptotic process / catalytic complex / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / fibroblast growth factor receptor signaling pathway / detection of calcium ion / regulation of cardiac muscle contraction / Rho protein signal transduction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / p75NTR recruits signalling complexes / cellular response to interferon-beta / activation of adenylate cyclase activity / Protein methylation / NF-kB is activated and signals survival / calcium channel inhibitor activity / presynaptic cytosol / NRIF signals cell death from the nucleus / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / coreceptor activity / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / positive regulation of nitric-oxide synthase activity / titin binding
Similarity search - Function
Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / : / Tumor necrosis factor receptor member 16 trans-membrane domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region ...Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / : / Tumor necrosis factor receptor member 16 trans-membrane domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / 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
Tumor necrosis factor receptor superfamily member 16 / Calmodulin-1 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJiang, T. / Cao, P. / Gong, Y. / Yu, H.J. / Gui, W.J. / Zhang, W.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural insights into the mechanism of calmodulin binding to death receptors.
Authors: Cao, P. / Zhang, W. / Gui, W. / Dong, Y. / Jiang, T. / Gong, Y.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Jan 1, 2020Group: Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / pdbx_entity_src_syn / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
E: Tumor necrosis factor receptor superfamily member 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5816
Polymers19,4202
Non-polymers1604
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-72 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.936, 39.936, 181.993
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-192-

HOH

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Components

#1: Protein Calmodulin / CaM


Mass: 17550.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Tumor necrosis factor receptor superfamily member 16 / Low-affinity nerve growth factor receptor / NGF receptor / Gp80-LNGFR / p75 ICD / Low affinity ...Low-affinity nerve growth factor receptor / NGF receptor / Gp80-LNGFR / p75 ICD / Low affinity neurotrophin receptor p75NTR / CD271 antigen


Mass: 1870.183 Da / Num. of mol.: 1 / Fragment: Helix5 of death domain / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) synthetic construct (others) / References: UniProt: P08138
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.7
Details: 27%(w/v) PEG8000, 0.1M Magnesium acetate, 0.1M Ammonium acetate, 0.05M Sodium cacodylate, pH 4.7, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 2, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. obs: 5611 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.052 / Rsym value: 0.049
Reflection shellResolution: 2.6→2.66 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LIN

1lin


Resolution: 2.6→14.92 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.846 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28177 254 4.5 %RANDOM
Rwork0.22813 ---
all0.23061 5369 --
obs0.23061 5369 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.353 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.35 Å20 Å2
2--0.71 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.6→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 4 90 1346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221263
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9711701
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56326.02968
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.0315227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.855158
X-RAY DIFFRACTIONr_chiral_restr0.1030.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02970
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2570.2705
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2873
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1620.217
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7311.5801
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34921275
X-RAY DIFFRACTIONr_scbond_it1.6693462
X-RAY DIFFRACTIONr_scangle_it2.8464.5426
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 17 -
Rwork0.245 420 -
obs--99.77 %

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