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- PDB-6o5g: Calmodulin in complex with isomalbrancheamide D -

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Basic information

Entry
Database: PDB / ID: 6o5g
TitleCalmodulin in complex with isomalbrancheamide D
ComponentsCalmodulin-1
KeywordsMETAL BINDING PROTEIN / EF hand
Function / homology
Function and homology information


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 ...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 / 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 / positive regulation of ryanodine-sensitive calcium-release channel activity / 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 / 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 / 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 / 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
Chem-LMJ / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsBeyett, T.S. / Fraley, A.E. / Tesmer, J.J.G.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL122416 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA70375 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118101 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Perturbation of the interactions of calmodulin with GRK5 using a natural product chemical probe.
Authors: Beyett, T.S. / Fraley, A.E. / Labudde, E. / Patra, D. / Coleman, R.C. / Eguchi, A. / Glukhova, A. / Chen, Q. / Williams, R.M. / Koch, W.J. / Sherman, D.H. / Tesmer, J.J.G.
History
DepositionMar 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)17,7997
Polymers17,1251
Non-polymers6756
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.858, 56.754, 117.168
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Calmodulin-1


Mass: 17124.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0DP23
#2: Chemical ChemComp-LMJ / (5aS,12aS,13aS)-9-bromo-8-chloro-12,12-dimethyl-2,3,11,12,12a,13-hexahydro-1H,5H,6H-5a,13a-(epiminomethano)indolizino[7 ,6-b]carbazol-14-one / isomalbrancheamide D


Mass: 448.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23BrClN3O
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.47 Å3/Da / Density % sol: 50.17 % / Mosaicity: 0.13 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 0.2 M MgCl2, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9839 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 20, 2018
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9839 Å / Relative weight: 1
ReflectionResolution: 1.89→39.06 Å / Num. obs: 13939 / % possible obs: 99.8 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.3 / Num. measured all: 181550 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.89-1.9313.60.559117378660.9635.2100
9.07-39.0610.30.05516111570.99638.699.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HEX

4hex


Resolution: 1.89→37.876 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2255 1391 10.01 %
Rwork0.1873 --
obs0.1912 13896 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.06 Å2 / Biso mean: 37.7201 Å2 / Biso min: 14.34 Å2
Refinement stepCycle: final / Resolution: 1.89→37.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 32 96 1257
Biso mean--49.6 41.4 -
Num. residues----143
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8903-1.95780.32961360.23661220100
1.9578-2.03620.26811370.20711234100
2.0362-2.12890.22931380.18771245100
2.1289-2.24110.22631380.1761122999
2.2411-2.38150.24771360.1861232100
2.3815-2.56530.25331390.20921239100
2.5653-2.82340.27911380.21061247100
2.8234-3.23170.25591390.2091260100
3.2317-4.07090.20471420.16641276100
4.0709-37.8760.17711480.1705132399
Refinement TLS params.Method: refined / Origin x: 13.2816 Å / Origin y: 63.8655 Å / Origin z: 125.3486 Å
111213212223313233
T0.1595 Å20.009 Å2-0.0236 Å2-0.1578 Å2-0.0028 Å2--0.2151 Å2
L0.2111 °2-0.1714 °20.0798 °2-0.8779 °21.5781 °2--5.1254 °2
S0.0046 Å °0.0275 Å °-0.004 Å °-0.1536 Å °-0.0858 Å °0.1076 Å °-0.4412 Å °-0.3092 Å °0.0468 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 5 through 147 or resid 176 or resid 201:205)

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