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- PDB-2k2o: Solution Structure of the inner DysF domain of human myoferlin -

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Basic information

Entry
Database: PDB / ID: 2k2o
TitleSolution Structure of the inner DysF domain of human myoferlin
ComponentsMyoferlin
KeywordsMEMBRANE PROTEIN / Myoferlin / Muscular Dystrophy / DysF / Dysferlin / Limb-girdle / Alternative splicing / Membrane / Nucleus / Phosphoprotein / Polymorphism / Transmembrane
Function / homology
Function and homology information


regulation of neurotransmitter secretion / plasma membrane repair / blood circulation / centriolar satellite / muscle contraction / caveola / phospholipid binding / synaptic vesicle membrane / nuclear envelope / cytoplasmic vesicle ...regulation of neurotransmitter secretion / plasma membrane repair / blood circulation / centriolar satellite / muscle contraction / caveola / phospholipid binding / synaptic vesicle membrane / nuclear envelope / cytoplasmic vesicle / nuclear membrane / intracellular membrane-bounded organelle / 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 / molecular dynamics
AuthorsPatel, P. / Harris, R. / Keep, N. / Driscoll, P.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Solution structure of the inner DysF domain of myoferlin and implications for limb girdle muscular dystrophy type 2b.
Authors: Patel, P. / Harris, R. / Geddes, S.M. / Strehle, E.M. / Watson, J.D. / Bashir, R. / Bushby, K. / Driscoll, P.C. / Keep, N.H.
History
DepositionApr 7, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myoferlin


Theoretical massNumber of molelcules
Total (without water)14,1951
Polymers14,1951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
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 Myoferlin / Fer-1-like protein 3


Mass: 14195.440 Da / Num. of mol.: 1 / Fragment: inner DysF domain (UNP residues 923-1040)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FER1L3, KIAA1207, MYOF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NZM1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1413D 1H-15N NOESY
1513D 1H-15N TOCSY
1623D HNCA
1723D HN(CO)CA
1823D HN(CA)CB
1923D CBCA(CO)NH
11023D HNCO
11123D HN(CA)CO
11223D HA(CA)NH
11323D HA(CACO)NH
11432D 1H-13C HSQC
1153aro-HSQC
1163aro-TOCSY-HSQC
1173aro-NOESY-HSQC
11833D (H)CCH-TOCSY
11933D 1H-13C NOESY
1201IPAP
1211IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM [U-100% 15N] DysF, 20 mM MES, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21.3 mM [U-100% 13C; U-100% 15N] DysF, 20 mM MES, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
31.3 mM [U-100% 13C; U-100% 15N] DysF, 20 mM MES, 100 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMDysF[U-100% 15N]1
20 mMMES1
100 mMsodium chloride1
1.3 mMDysF[U-100% 13C; U-100% 15N]2
20 mMMES2
100 mMsodium chloride2
1.3 mMDysF[U-100% 13C; U-100% 15N]3
20 mMMES3
100 mMsodium chloride3
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityPlusVarianUNITYPLUS5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
CCPN_AnalysisCCPNchemical shift assignment
CCPN_AnalysisCCPNpeak picking
CCPN_AnalysisCCPNdata analysis
TALOSCornilescu, Delaglio and Baxprotein dihedral angle backbone prediction
ProcheckNMRLaskowski and MacArthurdata analysis
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: Refinement in water
NMR constraintsNOE constraints total: 2810 / NOE intraresidue total count: 606 / NOE long range total count: 921 / NOE medium range total count: 316 / NOE sequential total count: 762
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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