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- PDB-6os4: Calmodulin in complex with farnesyl cysteine methyl ester -

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Basic information

Entry
Database: PDB / ID: 6os4
TitleCalmodulin in complex with farnesyl cysteine methyl ester
ComponentsCalmodulin-1
KeywordsMETAL BINDING PROTEIN / Complex / lipid / translocation
Function / homology
Function and homology information


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 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation ...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 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / 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 / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Platelet degranulation / myelin sheath / Ca2+ pathway / RAF/MAP kinase cascade / vesicle / transmembrane transporter binding / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway
Similarity search - Function
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
s-farnesyl-l-cysteine methyl ester / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsGrant, B.M.M. / Enomoto, M. / Lee, K.Y. / Back, S.I. / Gebregiworgis, T. / Ishiyama, N. / Ikura, M. / Marshall, C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-154284 Canada
CitationJournal: Sci.Signal. / Year: 2020
Title: Calmodulin disrupts plasma membrane localization of farnesylated KRAS4b by sequestering its lipid moiety.
Authors: Grant, B.M.M. / Enomoto, M. / Back, S.I. / Lee, K.Y. / Gebregiworgis, T. / Ishiyama, N. / Ikura, M. / Marshall, C.B.
History
DepositionMay 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2216
Polymers16,7211
Non-polymers5005
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR PRE experiment: TEMPO, a PRE-active probe, was amine coupled to the exposed N-terminus of FCME. Upon addition to 15N CaM, areas of significant PRE-induced broadening, compared to ...Evidence: NMR PRE experiment: TEMPO, a PRE-active probe, was amine coupled to the exposed N-terminus of FCME. Upon addition to 15N CaM, areas of significant PRE-induced broadening, compared to unmodified FCME, where apparent at the position predicted by this crystal structure., fluorescence resonance energy transfer, In vivo FRET produced by a mTq2-CaM-SYFP2-KRAS4b-FMe chimeric construct in response to Ca2+ influx, and subsequent internalization, is consistent with our model of CaM sequestration of the KRAS4b membrane anchor
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Calmodulin-1
hetero molecules

A: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,44212
Polymers33,4432
Non-polymers1,00010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area1870 Å2
ΔGint-113 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.379, 40.379, 338.137
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

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Components

#1: Protein Calmodulin-1 /


Mass: 16721.350 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0DP23
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-5U0 / s-farnesyl-l-cysteine methyl ester


Mass: 339.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H33NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.2mM sodium acetate, 0.1mM cacodylate, 28% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1, 1.77
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationMonochromator: ACCEL/BRUKER DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.771
ReflectionResolution: 1.8→50 Å / Num. obs: 16439 / % possible obs: 99.6 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.013 / Rrim(I) all: 0.051 / Χ2: 0.998 / Net I/σ(I): 8.9 / Num. measured all: 226154
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.83130.487890.9690.1270.4980.4894.4
1.83-1.8614.10.4147500.9510.1090.4290.49899.7
1.86-1.913.50.3477890.9710.0930.3610.514100
1.9-1.9413.50.2677960.9880.0710.2770.53699.1
1.94-1.9813.10.2237620.9880.0610.2320.577100
1.98-2.0312.90.2058090.9890.0560.2130.60599.6
2.03-2.08130.1637810.990.0440.170.715100
2.08-2.1312.70.1417980.9940.0380.1470.774100
2.13-2.213.20.1198050.9940.0320.1230.838100
2.2-2.27130.1128030.9940.0310.1170.90799.9
2.27-2.3512.70.0918110.9970.0250.0950.972100
2.35-2.4412.50.0917850.9970.0250.0951.05399.9
2.44-2.5512.40.0818280.9980.0230.0841.092100
2.55-2.6913.30.0738420.9980.020.0761.161100
2.69-2.8614.10.0658050.9990.0170.0671.248100
2.86-3.0814.40.0618360.9990.0160.0641.41100
3.08-3.3915.60.0548520.9990.0140.0561.544100
3.39-3.8817.20.0478600.9990.0110.0481.63100
3.88-4.8816.20.0398910.9990.010.041.494100
4.88-5014.10.03510470.9990.010.0371.12100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→34.969 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.3
RfactorNum. reflection% reflection
Rfree0.2249 1951 10.1 %
Rwork0.1912 --
obs0.1945 19316 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.81 Å2 / Biso mean: 47.733 Å2 / Biso min: 21.44 Å2
Refinement stepCycle: final / Resolution: 2.05→34.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 27 60 1180
Biso mean--78.13 44.21 -
Num. residues----144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10130.24481430.23061206134998
2.1013-2.15810.23041370.201512111348100
2.1581-2.22160.19881410.195512601401100
2.2216-2.29330.20331420.186612181360100
2.2933-2.37520.20611490.185313011450100
2.3752-2.47030.27441330.197812031336100
2.4703-2.58270.2761370.211512491386100
2.5827-2.71880.22661350.18912561391100
2.7188-2.88910.23131420.209512631405100
2.8891-3.1120.23641300.199112381368100
3.112-3.42490.23421350.200412241359100
3.4249-3.91990.2091400.191512441384100
3.9199-4.93650.17841460.159212431389100
4.9365-34.97430.26961410.200412491390100

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