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- PDB-2k7m: Structure of the Connexin40 Carboxyl terminal Domain -

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Basic information

Entry
Database: PDB / ID: 2k7m
TitleStructure of the Connexin40 Carboxyl terminal Domain
ComponentsGap junction alpha-5 protein
KeywordsMEMBRANE PROTEIN / Protein / Gap Junction / Cell junction / Cell membrane / Membrane / Transmembrane
Function / homology
Function and homology information


renal system process involved in regulation of systemic arterial blood pressure / mitral valve development / pulmonary valve formation / septum primum development / foramen ovale closure / atrial cardiac muscle cell to AV node cell communication by electrical coupling / gap junction channel activity involved in atrial cardiac muscle cell-AV node cell electrical coupling / gap junction channel activity involved in bundle of His cell-Purkinje myocyte electrical coupling / regulation of Purkinje myocyte action potential / regulation of renin secretion into blood stream ...renal system process involved in regulation of systemic arterial blood pressure / mitral valve development / pulmonary valve formation / septum primum development / foramen ovale closure / atrial cardiac muscle cell to AV node cell communication by electrical coupling / gap junction channel activity involved in atrial cardiac muscle cell-AV node cell electrical coupling / gap junction channel activity involved in bundle of His cell-Purkinje myocyte electrical coupling / regulation of Purkinje myocyte action potential / regulation of renin secretion into blood stream / vasomotion / AV node cell to bundle of His cell communication by electrical coupling / cell communication involved in cardiac conduction / gap junction channel activity involved in AV node cell-bundle of His cell electrical coupling / regulation of bundle of His cell action potential / : / positive regulation of cell communication by chemical coupling / Gap junction assembly / bundle of His cell to Purkinje myocyte communication by electrical coupling / regulation of membrane depolarization during cardiac muscle cell action potential / negative regulation of glomerular filtration / gap junction channel activity involved in cardiac conduction electrical coupling / atrial ventricular junction remodeling / cell communication by chemical coupling / cell communication by electrical coupling / gap junction hemi-channel activity / SA node cell action potential / regulation of cell communication by electrical coupling / AV node cell to bundle of His cell communication / atrial septum morphogenesis / regulation of ventricular cardiac muscle cell membrane depolarization / regulation of atrial cardiac muscle cell action potential / gap junction assembly / endothelium development / regulation of AV node cell action potential / cardiac conduction system development / connexin complex / regulation of atrial cardiac muscle cell membrane depolarization / cardiac conduction / regulation of systemic arterial blood pressure / atrial septum development / gap junction channel activity / gap junction / ventricular cardiac muscle cell action potential / connexin binding / embryonic heart tube development / regulation of ventricular cardiac muscle cell membrane repolarization / embryonic limb morphogenesis / cell communication by electrical coupling involved in cardiac conduction / artery morphogenesis / ventricular septum development / ventricular septum morphogenesis / blood vessel development / outflow tract morphogenesis / regulation of heart rate by cardiac conduction / plasma membrane => GO:0005886 / intercalated disc / regulation of cardiac muscle contraction / positive regulation of vasoconstriction / negative regulation of blood pressure / blood vessel diameter maintenance / skeletal system development / cell projection / potassium ion transport / disordered domain specific binding / cell-cell signaling / heart development / angiogenesis
Similarity search - Function
Gap junction alpha-5 protein (Cx40) / Gap junction alpha-5 protein (Cx40), C-terminal / Connexin 40 C-terminal domain / Connexin, C-terminal / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin ...Gap junction alpha-5 protein (Cx40) / Gap junction alpha-5 protein (Cx40), C-terminal / Connexin 40 C-terminal domain / Connexin, C-terminal / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin / Connexins signature 1. / Connexins signature 2. / Connexin homologues / Gap junction channel protein cysteine-rich domain
Similarity search - Domain/homology
Gap junction alpha-5 protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsBouvier, D. / Spagnol, G. / Kieken, F. / Vitrac, H. / Kellezi, A. / Forge, V.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Characterization of the structure and intermolecular interactions between the connexin40 and connexin43 carboxyl-terminal and cytoplasmic loop domains.
Authors: Bouvier, D. / Spagnol, G. / Chenavas, S. / Kieken, F. / Vitrac, H. / Brownell, S. / Kellezi, A. / Forge, V. / Sorgen, P.L.
History
DepositionAug 14, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gap junction alpha-5 protein


Theoretical massNumber of molelcules
Total (without water)11,9591
Polymers11,9591
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Gap junction alpha-5 protein / Connexin-40 / Cx40


Mass: 11959.017 Da / Num. of mol.: 1 / Fragment: UNP residues 252-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gja5, Cxn-40 / Production host: Escherichia coli (E. coli) / References: UniProt: P28234

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Gap Junction Protein Connexin40
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 10 mM [U-95% 13C; U-95% 15N] potassium chloride, 150 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMpotassium chloride[U-95% 13C; U-95% 15N]1
150 mMsodium chloride1
Sample conditionsIonic strength: 150 / pH: 6.0 / Pressure: ambient / Temperature: 280 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificprocessing
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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