[English] 日本語
Yorodumi
- PDB-8ahs: Crystal structure of human Ca2+/Calmodulin in complex with melittin -

+
Open data


ID or keywords:

Loading...

-
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 / 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 ...other organism cell membrane / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / 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 / porin activity / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / molecular function inhibitor activity / pore complex / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / protein kinase inhibitor activity / 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 / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / 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 / eNOS activation / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / monoatomic ion transport / 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 / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / cellular response to type II interferon / spindle pole / response to calcium ion / RAS processing / 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 / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Inactivation, recovery and regulation of the phototransduction cascade / Platelet degranulation / myelin sheath
Similarity search - Function
Melittin/ Api allergen / Melittin / : / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more