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- PDB-2h2m: Solution Structure of the N-terminal domain of COMMD1 (Murr1) -

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Basic information

Entry
Database: PDB / ID: 2h2m
TitleSolution Structure of the N-terminal domain of COMMD1 (Murr1)
ComponentsCOMM domain-containing protein 1
KeywordsMETAL TRANSPORT / all alpha-helical
Function / homology
Function and homology information


negative regulation of sodium ion transmembrane transport / plasma membrane to endosome transport / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein localization to cell surface / copper ion homeostasis / Golgi to plasma membrane transport / phosphatidic acid binding / phosphatidylinositol-3,4-bisphosphate binding / sodium channel inhibitor activity / phosphatidylinositol-3,5-bisphosphate binding ...negative regulation of sodium ion transmembrane transport / plasma membrane to endosome transport / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein localization to cell surface / copper ion homeostasis / Golgi to plasma membrane transport / phosphatidic acid binding / phosphatidylinositol-3,4-bisphosphate binding / sodium channel inhibitor activity / phosphatidylinositol-3,5-bisphosphate binding / Cul2-RING ubiquitin ligase complex / negative regulation of NF-kappaB transcription factor activity / phosphatidylinositol-3,4,5-trisphosphate binding / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of protein ubiquitination / nucleotide-excision repair / recycling endosome / protein transport / Neddylation / early endosome / endosome membrane / endosome / copper ion binding / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
COMMD1 N-terminal domain / COMM domain-containing protein 1 / COMMD1 N-terminal domain / COMM domain / COMM domain / COMM domain profile.
Similarity search - Domain/homology
COMM domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsSommerhalter, M. / Zhang, Y. / Rosenzweig, A.C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Solution Structure of the COMMD1 N-terminal Domain.
Authors: Sommerhalter, M. / Zhang, Y. / Rosenzweig, A.C.
History
DepositionMay 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 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: COMM domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)11,9111
Polymers11,9111
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)20 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein COMM domain-containing protein 1 / Protein Murr1


Mass: 11910.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N668

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-edited NOESY
1223D 13C-edited NOESY
1322D aromatic NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM N-COMMD1, U-15N,13C 25mM phosphate buffer, 50mM NaCl, pH 6.1, 90% H2O, 10% D2O90% H2O/10% D2O
20.95mM N-COMMD1, U-15N,13C 25mM phosphate buffer, 50mM NaCl, pH 6.1, 100% D2O100% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 6.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDeLaglioprocessing
ARIA1.2Lingestructure solution
ARIA1.2Lingerefinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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