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- PDB-7k6b: Solution Structure of the Dysferlin C2A Domain in its Calcium-fre... -

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Basic information

Entry
Database: PDB / ID: 7k6b
TitleSolution Structure of the Dysferlin C2A Domain in its Calcium-free State
ComponentsIsoform 15 of Dysferlin
KeywordsMEMBRANE PROTEIN / membrane repair / calcium-binding / beta-sandwich
Function / homology
Function and homology information


monocyte activation involved in immune response / regulation of neurotransmitter secretion / macrophage activation involved in immune response / calcium-dependent phospholipid binding / negative regulation of phagocytosis / endocytic vesicle / centriolar satellite / Smooth Muscle Contraction / T-tubule / cytoplasmic vesicle membrane ...monocyte activation involved in immune response / regulation of neurotransmitter secretion / macrophage activation involved in immune response / calcium-dependent phospholipid binding / negative regulation of phagocytosis / endocytic vesicle / centriolar satellite / Smooth Muscle Contraction / T-tubule / cytoplasmic vesicle membrane / sarcolemma / phospholipid binding / synaptic vesicle membrane / late endosome / early endosome / endosome / calcium ion binding / extracellular exosome / plasma membrane
Similarity search - Function
Ferlin A-domain / FerA (NUC095) domain / FerA / Ferlin B-domain / FerIin domain / Ferlin, C-terminal domain / Ferlin, second C2 domain / Ferlin family / Ferlin, third C2 domain / Ferlin, fourth C2 domain ...Ferlin A-domain / FerA (NUC095) domain / FerA / Ferlin B-domain / FerIin domain / Ferlin, C-terminal domain / Ferlin, second C2 domain / Ferlin family / Ferlin, third C2 domain / Ferlin, fourth C2 domain / Ferlin, fifth C2 domain / Ferlin, sixth C2 domain / Ferlin, first C2 domain / FerB (NUC096) domain / FerI (NUC094) domain / Ferlin C-terminus / Ferlin dsRNA-binding domain-like domain / FerB / FerI / Peroxin/Ferlin domain / Dysferlin domain, N-terminal region. / Dysferlin domain, C-terminal region. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, Y. / Mercier, P. / Santamaria, L. / Shaw, G.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-14606 Canada
CitationJournal: Biochem.J. / Year: 2021
Title: Calcium binds and rigidifies the dysferlin C2A domain in a tightly coupled manner.
Authors: Wang, Y. / Tadayon, R. / Santamaria, L. / Mercier, P. / Forristal, C.J. / Shaw, G.S.
History
DepositionSep 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 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

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 15 of Dysferlin


Theoretical massNumber of molelcules
Total (without water)14,8231
Polymers14,8231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Isoform 15 of Dysferlin / Dystrophy-associated fer-1-like protein / Fer-1-like protein 1


Mass: 14822.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYSF, FER1L1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O75923

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC NH2 only
122isotropic12D 1H-13C HSQC
1121isotropic13D HNCA
141isotropic13D HN(CO)CA
131isotropic13D HNCO
151isotropic13D HN(CA)CB
161isotropic13D CBCA(CO)NH
171isotropic13D C(CO)NH
181isotropic13D H(CCO)NH
1112isotropic13D (H)CCH-TOCSY
191isotropic13D 1H-15N NOESY
1102isotropic13D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O15N,13C Sample90% H2O/10% D2O
solution21 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 100% D2O15N,13C Sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDSSnatural abundance1
25 mMMESnatural abundance1
150 mMNaClnatural abundance1
5 mMEDTAnatural abundance1
1 mMDTTnatural abundance1
0.3 mMProtein[U-13C; U-15N]1
1 mMDSSnatural abundance2
25 mMMESnatural abundance2
150 mMNaClnatural abundance2
5 mMEDTAnatural abundance2
1 mMDTTnatural abundance2
0.3 mMProtein[U-13C; U-15N]2
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz / Details: cold-probe

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIH2.37Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 6 / Details: refinement in explicit water solvent
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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