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- PDB-8ahs: Crystal structure of human Ca2+/Calmodulin in complex with melittin -

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Basic information

Entry
Database: PDB / ID: 8ahs
TitleCrystal structure of human Ca2+/Calmodulin in complex with melittin
Components
  • Calmodulin-1
  • Melittin
KeywordsMETAL BINDING PROTEIN / hub protein / linear recognition motif
Function / homology
Function and homology information


other organism cell membrane / 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 / molecular function inhibitor activity ...other organism cell membrane / 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 / molecular function inhibitor activity / 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 / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / porin activity / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / pore complex / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / protein kinase inhibitor activity / Unblocking of NMDA receptors, glutamate binding and activation / 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 / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / catalytic complex / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / monoatomic ion transport / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / regulation of heart rate / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / calcium channel regulator activity / RAF activation / Transcriptional activation of mitochondrial biogenesis / response to calcium ion / cellular response to type II interferon / Stimuli-sensing channels / G2/M transition of mitotic cell cycle / long-term synaptic potentiation / spindle pole / RAS processing / calcium-dependent protein binding / 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 / Signaling by BRAF and RAF1 fusions / Platelet degranulation / Inactivation, recovery and regulation of the phototransduction cascade / myelin sheath / toxin activity / RAF/MAP kinase cascade
Similarity search - Function
Melittin/ Api allergen / Melittin / 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. ...Melittin/ Api allergen / Melittin / 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
Melittin / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Apis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsDurvanger, Z. / Harmat, V.
Funding support Hungary, European Union, 3items
OrganizationGrant numberCountry
Hungarian National Research, Development and Innovation Office2018-1.2.1-NKP-2018-00005 Hungary
European Regional Development FundVEKOP-2.3.2-16-2017-00014, VEKOP-2.3.3-15-2017-00018European Union
Hungarian National Research, Development and Innovation OfficeThematic Excellence Program Synth+ Hungary
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structures of calmodulin-melittin complexes show multiple binding modes lacking classical anchoring interactions.
Authors: Durvanger, Z. / Juhasz, T. / Liliom, K. / Harmat, V.
History
DepositionJul 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-1
C: Melittin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8656
Polymers19,7052
Non-polymers1604
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.770, 40.770, 350.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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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 Melittin / MEL / MLT / Allergen Api m 3 / Allergen Api m III


Mass: 2852.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Apis mellifera (honey bee) / References: UniProt: P01501
#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.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 0.2M NaCl, 22w/v% PEG3350, 0.1M Bis-Tris, pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.45→35.31 Å / Num. obs: 7039 / % possible obs: 98.4 % / Redundancy: 10.07 % / Biso Wilson estimate: 90.09 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.051 / Net I/σ(I): 19.46
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
2.45-2.551.146860.7131.586186.2
2.55-2.652.196250.9410.8731
2.65-2.753.695820.9560.5231

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3sui

3sui


Resolution: 2.48→35.31 Å / SU ML: 0.3647 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 41.5678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2696 310 4.66 %
Rwork0.267 6342 -
obs0.2673 6652 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.41 Å2
Refinement stepCycle: LAST / Resolution: 2.48→35.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 4 3 1148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341160
X-RAY DIFFRACTIONf_angle_d0.72341577
X-RAY DIFFRACTIONf_chiral_restr0.0455184
X-RAY DIFFRACTIONf_plane_restr0.006215
X-RAY DIFFRACTIONf_dihedral_angle_d14.5096383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-3.120.43341430.37392863X-RAY DIFFRACTION88.7
3.12-35.310.25151670.2553479X-RAY DIFFRACTION99.51
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)
18.57827045342-1.87091904042.466990046945.11212622541-0.04690762295596.938578277120.6460278629530.3894043598070.428019713491-0.201812553587-0.2150370929040.421414294586-0.60397474456-1.2129682222-0.3661254367810.9645520958090.285073626450.1781822779560.7516201126590.1491306650920.615525067033-2.3913096108-26.4918056781-17.7439690854
29.14478549487-6.23114140623-1.951818553184.83453980143-0.2350020641648.99198027277-0.332660370922-0.379917533633-0.3657922867340.9548456477920.178190355627-1.078819046260.1992331008560.375178575980.1287246177680.698316473474-0.1019573823020.03584659096690.370554220334-0.002474740662060.843058448291-6.82050820721-10.8473278839-5.78853541628
38.491484018920.52194104772-3.44942481491.10129034362-0.624209272488.413751126610.05784985066150.56883008747-0.243817008280.526734331019-1.009408791341.08261258691-0.358026209129-1.5594648080.2936888463490.8617592619690.0262220287646-0.03544086742020.2450731870820.009120185107270.704433339271-15.9294648575-6.98763438932-8.14112908721
49.62392266573-5.30324851184-0.5611417937673.707213977931.106299212953.911418207230.5010032069711.19581872339-1.69305359642-0.371573580423-0.6794872040070.8168895970260.0887511438315-0.8070204461481.905300814062.024412511220.6146586428811.105816795970.692449321322-0.2537337960361.26570696509-9.71860931051-20.9476660266-12.4888277418
54.072585638071.003385170772.475475134673.892433052870.5540726137221.52479759072-2.195200171322.53022938572.31745707058-1.047261236721.876417776741.04151699059-0.261577840878-0.4758785254210.05376744145362.436216176090.4278710773110.6440870146671.466284397240.7692505975761.26611828471-3.50178512489-7.44984510126-18.8374388289
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 75 )AA4 - 751 - 72
22chain 'A' and (resid 76 through 128 )AA76 - 12873 - 123
33chain 'A' and (resid 129 through 146 )AA129 - 146124 - 141
44chain 'C' and (resid 2 through 12 )CF2 - 121 - 11
55chain 'C' and (resid 13 through 24 )CF13 - 2412 - 23

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