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

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Basic information

Entry
Database: PDB / ID: 3ewt
TitleCrystal Structure of calmodulin complexed with a peptide
Components
  • Calmodulin
  • Tumor necrosis factor receptor superfamily member 6
KeywordsCALCIUM BINDING PROTEIN / Calmodulin-peptide complex / Fas / death domain
Function / homology
Function and homology information


Fas signaling pathway / cellular response to hyperoxia / tumor necrosis factor receptor activity / FasL/ CD95L signaling / CD95 death-inducing signaling complex / : / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand ...Fas signaling pathway / cellular response to hyperoxia / tumor necrosis factor receptor activity / FasL/ CD95L signaling / CD95 death-inducing signaling complex / : / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / : / necroptotic signaling pathway / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / death-inducing signaling complex / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / motor neuron apoptotic process / Calmodulin induced events / TP53 Regulates Transcription of Death Receptors and Ligands / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / RIPK1-mediated regulated necrosis / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / regulation of synaptic vesicle exocytosis / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / response to corticosterone / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / regulation of stress-activated MAPK cascade / mitochondrion-endoplasmic reticulum membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / activation-induced cell death of T cells / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / : / Uptake and function of anthrax toxins / Long-term potentiation / adenylate cyclase binding / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / extrinsic apoptotic signaling pathway via death domain receptors / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / eNOS activation / Protein methylation / voltage-gated potassium channel complex / activation of adenylate cyclase activity / enzyme regulator activity / Activation of AMPK downstream of NMDARs / extrinsic apoptotic signaling pathway in absence of ligand / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / extrinsic apoptotic signaling pathway / calcium channel complex / nitric-oxide synthase regulator activity / substantia nigra development / adenylate cyclase activator activity / response to amphetamine / cellular response to amino acid starvation / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere
Similarity search - Function
Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / 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). ...Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / 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
Calmodulin-1 / Tumor necrosis factor receptor superfamily member 6 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4136
Polymers20,2522
Non-polymers1604
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-78 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.062, 40.062, 174.431
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-626-

HOH

21A-627-

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 6 / FASLG receptor / Apoptosis-mediating surface antigen FAS / Apo-1 antigen


Mass: 2702.220 Da / Num. of mol.: 1 / Fragment: Helix(1+2) of death domain / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) synthetic construct (others) / References: UniProt: P25445
#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.: 44 / 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 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 25%(w/v) PEG8000, 0.2M Sodium Acetate, 0.1M Sodium cacodylate, pH 5.5, 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: Sep 22, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 6946 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Rmerge(I) obs: 0.042 / Rsym value: 0.041
Reflection shellResolution: 2.4→2.46 Å / % possible all: 97.3

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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: 1L7Z

1l7z


Resolution: 2.4→19.9 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.491 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25916 312 4.5 %RANDOM
Rwork0.21664 ---
all0.21859 6575 --
obs0.21859 6575 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.709 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 4 44 1275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221239
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9631667
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2935157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66126.30865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.23815224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.376156
X-RAY DIFFRACTIONr_chiral_restr0.110.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02940
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.2682
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2880
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0970.221
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9161.5783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49921252
X-RAY DIFFRACTIONr_scbond_it1.73456
X-RAY DIFFRACTIONr_scangle_it3.0234.5415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 18 -
Rwork0.249 475 -
obs--99.6 %

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