[English] 日本語
Yorodumi
- PDB-2n8j: Structure and 15N relaxation data of Calmodulin bound to the endo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n8j
TitleStructure and 15N relaxation data of Calmodulin bound to the endothelial Nitric Oxide Synthase Calmodulin Binding Domain Peptide at Physiological Calcium Concentration
Components
  • Calmodulin
  • Nitric oxide synthase, endothelial
KeywordsPROTEIN BINDING / Calmodulin / Nitric Oxide Synthase / eNOS / Dynamics / Order parameters
Function / homology
Function and homology information


NOSIP mediated eNOS trafficking / negative regulation of muscle hyperplasia / NOSTRIN mediated eNOS trafficking / tetrahydrobiopterin metabolic process / smooth muscle hyperplasia / regulation of systemic arterial blood pressure by endothelin / regulation of nervous system process / : / : / : ...NOSIP mediated eNOS trafficking / negative regulation of muscle hyperplasia / NOSTRIN mediated eNOS trafficking / tetrahydrobiopterin metabolic process / smooth muscle hyperplasia / regulation of systemic arterial blood pressure by endothelin / regulation of nervous system process / : / : / : / : / superoxide-generating NAD(P)H oxidase activity / : / positive regulation of protein autophosphorylation / pulmonary valve morphogenesis / negative regulation of peptidyl-threonine phosphorylation / response to fluid shear stress / negative regulation of biomineral tissue development / Nitric oxide stimulates guanylate cyclase / : / type 3 metabotropic glutamate receptor binding / endocardial cushion morphogenesis / ROS and RNS production in phagocytes / homeostasis of number of cells within a tissue / tetrahydrobiopterin binding / arginine binding / aortic valve morphogenesis / positive regulation of peptidyl-threonine phosphorylation / positive regulation of DNA binding / CaM pathway / Cam-PDE 1 activation / positive regulation of protein serine/threonine kinase activity / Sodium/Calcium exchangers / Calmodulin induced events / ventricular septum morphogenesis / blood vessel remodeling / 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 / CaMK IV-mediated phosphorylation of CREB / positive regulation of Notch signaling pathway / CASP4 inflammasome assembly / Glycogen breakdown (glycogenolysis) / response to corticosterone / negative regulation of ryanodine-sensitive calcium-release channel activity / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / : / negative regulation of high voltage-gated calcium channel activity / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / cadmium ion binding / regulation of synaptic vesicle exocytosis / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / calcineurin-mediated signaling / RHO GTPases activate PAKs / nitric-oxide synthase binding / negative regulation of platelet activation / regulation of cell communication by electrical coupling involved in cardiac conduction / adenylate cyclase binding / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / nitric-oxide synthase (NADPH) / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / actin monomer binding / regulation of calcium-mediated signaling / catalytic complex / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / : / positive regulation of blood vessel endothelial cell migration / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / nitric-oxide synthase activity / endothelial cell migration / regulation of synaptic vesicle endocytosis / L-arginine catabolic process / detection of calcium ion / regulation of cardiac muscle contraction / cellular response to interferon-beta / negative regulation of blood pressure / RHO GTPases activate IQGAPs / activation of adenylate cyclase activity / calcium channel inhibitor activity / phosphatidylinositol 3-kinase binding / nitric oxide metabolic process / positive regulation of nitric-oxide synthase activity / nitric oxide biosynthetic process
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding ...Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / : / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like 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 / Nitric oxide synthase 3 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsPiazza, M. / Guillemette, G. / Dieckmann, T.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Studies of a Complex Between Endothelial Nitric Oxide Synthase and Calmodulin at Physiological Calcium Concentration.
Authors: Piazza, M. / Dieckmann, T. / Guillemette, J.G.
History
DepositionOct 16, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calmodulin
B: Nitric oxide synthase, endothelial


Theoretical massNumber of molelcules
Total (without water)19,1072
Polymers19,1072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-16 kcal/mol
Surface area10420 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1minimized average structure

-
Components

#1: Protein Calmodulin / CaM


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, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Nitric oxide synthase, endothelial / Constitutive NOS / cNOS / EC-NOS / Endothelial NOS / eNOS / NOS type III / NOSIII


Mass: 2385.844 Da / Num. of mol.: 1 / Fragment: UNP residues 491-512 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P29474

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCA
1413D (H)CCH-TOCSY
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliphatic
1712D 1H-1H edited filtered NOESY

-
Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] CaM, 1 mM eNOS, 100 mM potassium chloride, 30 mM MOPS, 4 mM EGTA, 6 mM CaEGTA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCaM-1[U-99% 13C; U-99% 15N]1
1 mMeNOS-21
100 mMpotassium chloride-31
30 mMMOPS-41
4 mMEGTA-51
6 mMCaEGTA-61
Sample conditionsIonic strength: 0.15 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2959
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

+
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