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- PDB-7mpa: Structure and topology of DWORF in bicelles by oriented solid-sta... -

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Basic information

Entry
Database: PDB / ID: 7mpa
TitleStructure and topology of DWORF in bicelles by oriented solid-state NMR
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase regulator DWORF
KeywordsMEMBRANE PROTEIN / Regulin / miniprotein / sarcoplasmic reticulum / oriented solid state NMR spectroscopy / chemical shift anisotropy / dipolar coupling / separated local field
Function / homologySarcoplasmic/endoplasmic reticulum calcium ATPase regulator DWORF / regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of slow-twitch skeletal muscle fiber contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / enzyme activator activity / sarcoplasmic reticulum membrane / membrane => GO:0016020 / Sarcoplasmic/endoplasmic reticulum calcium ATPase regulator DWORF
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / simulated annealing
AuthorsReddy, U.V. / Weber, D.K. / Veglia, G.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL143816 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM64742 United States
CitationJournal: Structure / Year: 2022
Title: A kink in DWORF helical structure controls the activation of the sarcoplasmic reticulum Ca 2+ -ATPase.
Authors: Reddy, U.V. / Weber, D.K. / Wang, S. / Larsen, E.K. / Gopinath, T. / De Simone, A. / Robia, S. / Veglia, G.
History
DepositionMay 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase regulator DWORF


Theoretical massNumber of molelcules
Total (without water)3,9091
Polymers3,9091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 5000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Sarcoplasmic/endoplasmic reticulum calcium ATPase regulator DWORF / SERCA regulator DWORF / Dwarf open reading frame / DWORF / Small transmembrane regulator of ion transport 1


Mass: 3908.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STRIT1, DWORF / Production host: Escherichia coli (E. coli) / References: UniProt: P0DN84

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experimentSample state: anisotropic / Type: 2D 1H-15N SE-SAMPI4

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Sample preparation

DetailsType: bicelle
Contents: 2.5 mM [U-15N] Dwarf Open Reading Frame (DWORF), 20 mM HEPES, 20 mM potassium chloride, 5 mM magnesium chloride, 5 mM ethylene glycol-bis(b-aminoethyl ether)-N,N,N',N'-tetraacetic acid ...Contents: 2.5 mM [U-15N] Dwarf Open Reading Frame (DWORF), 20 mM HEPES, 20 mM potassium chloride, 5 mM magnesium chloride, 5 mM ethylene glycol-bis(b-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA), 0.02 % sodium azide, 2.5 % glycerol, 5 mM DTT, 267 mM 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 67 mM 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC), 74 mM 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), 6 mM 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (14:0 PE-DTPA), 5 mM ytterbium chloride, 100% H20
Label: DWORF in bicelles / Solvent system: 100% H20
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMDwarf Open Reading Frame (DWORF)[U-15N]1
20 mMHEPESnatural abundance1
20 mMpotassium chloridenatural abundance1
5 mMmagnesium chloridenatural abundance1
5 mMethylene glycol-bis(b-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA)natural abundance1
0.02 %sodium azidenatural abundance1
2.5 %glycerolnatural abundance1
5 mMDTTnatural abundance1
267 mM1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)natural abundance1
67 mM1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC)natural abundance1
74 mM1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC)natural abundance1
6 mM1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (14:0 PE-DTPA)natural abundance1
5 mMytterbium chloridenatural abundance1
Sample conditionsIonic strength: 30 mM / Label: DWORF in bicelles / pH: 7.0 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKYLee, Tonelli and Markleypeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 5000 / Conformers submitted total number: 10

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