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- PDB-6cmy: Solution NMR Structure Determination of Mouse Melanoregulin -

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Basic information

Entry
Database: PDB / ID: 6cmy
TitleSolution NMR Structure Determination of Mouse Melanoregulin
ComponentsMelanoregulin
KeywordsLIPID BINDING PROTEIN / alpha helical / CRAC motif / melanosome transport / cellular pigementation / dilute suppressor locus
Function / homology
Function and homology information


: / minus-end-directed organelle transport along microtubule / melanosome localization / phagosome maturation / melanosome transport / developmental pigmentation / melanocyte differentiation / melanosome membrane / pigmentation / phosphatidylinositol binding ...: / minus-end-directed organelle transport along microtubule / melanosome localization / phagosome maturation / melanosome transport / developmental pigmentation / melanocyte differentiation / melanosome membrane / pigmentation / phosphatidylinositol binding / cytoplasmic vesicle membrane / melanosome / late endosome membrane / apical plasma membrane / lysosomal membrane / protein-containing complex
Similarity search - Function
Melanoregulin / Melanoregulin
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsRout, A.K. / Wu, X. / Strub, M.P. / Starich, M.R. / Hammer III, J.A. / Tjandra, N.
CitationJournal: Structure / Year: 2018
Title: The Structure of Melanoregulin Reveals a Role for Cholesterol Recognition in the Protein's Ability to Promote Dynein Function.
Authors: Rout, A.K. / Wu, X. / Starich, M.R. / Strub, M.P. / Hammer, J.A. / Tjandra, N.
History
DepositionMar 6, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionSep 19, 2018ID: 5KBO
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Melanoregulin


Theoretical massNumber of molelcules
Total (without water)21,3641
Polymers21,3641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 12520 structures with lowest energy
RepresentativeModel #1fewest outliers

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Components

#1: Protein Melanoregulin / Dilute suppressor protein / Whn-dependent transcript 2


Mass: 21364.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mreg, Dsu, Gm974, Wdt2 / Plasmid: pMAL2cx / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6NVG5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
323isotropic22D 1H-13C HSQC
232isotropic13D HNCO
242isotropic13D HNCA
252isotropic13D HN(COCA)CB
262isotropic13D HN(CA)CB
172isotropic13D HBHA(CO)NH
3103isotropic13D HMCMCBCA
3113isotropic23D ILV-CH3 NOESY
1121isotropic22D IPAP
1131isotropic21H T2

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1120 uM [U-99% 15N] Melanoregulin, 90% H2O/10% D2O15N sample90% H2O/10% D2O
solution2120 uM [U-99% 13C; U-99% 15N] Melanoregulin, 90% H2O/10% D2O15N13C90% H2O/10% D2O
solution3120 uM [U-99% 13C; U-99% 15N] Melanoregulin, 99.9% D2O15N13C99.9% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
120 uMMelanoregulin[U-99% 15N]1
120 uMMelanoregulin[U-99% 13C; U-99% 15N]2
120 uMMelanoregulin[U-99% 13C; U-99% 15N]3
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
150mM KPi 1mM EDTA 1mM DTT 0.02% (w/v) NaN3 The sample exhibits aggregation above concentrations of 150 uM. L-Arg and L-Gln were added at 1 mM or 5mM concentrations to improve sample stability.no NaCl Not definedbuffer_16.3ambient atm302 K
250mM KPi 1mM EDTA 1mM DTT 0.02% (w/v) NaN3 The sample exhibits aggregation above concentrations of 150 uM. L-Arg and L-Gln were added at 1 mM or 5mM concentrations to improve sample stability.no NaCl Not definedbuffer_26.3ambient atm302 K
350mM KPi 1mM EDTA 1mM DTT 0.02% (w/v) NaN3 The sample exhibits aggregation above concentrations of 150 uM. L-Arg and L-Gln were added at 1 mM or 5mM concentrations to improve sample stability.no NaCl Not definedbuffer_36.3ambient atm302 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker Avanace IIIBrukerAvanace III8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: fewest outliers
NMR ensembleConformer selection criteria: 20 structures with lowest energy
Conformers calculated total number: 125 / Conformers submitted total number: 20

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