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- PDB-2mp4: Solution Structure of ADF like UNC-60A Protein of Caenorhabditis ... -

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Basic information

Entry
Database: PDB / ID: 2mp4
TitleSolution Structure of ADF like UNC-60A Protein of Caenorhabditis elegans
ComponentsActin-depolymerizing factor 1, isoforms a/b
KeywordsPROTEIN BINDING / ADF/cofilin protein
Function / homology
Function and homology information


muscle thin filament assembly / actin filament fragmentation / actin filament severing / actin filament depolymerization / locomotion / embryo development ending in birth or egg hatching / cortical actin cytoskeleton / positive regulation of actin filament polymerization / skeletal muscle thin filament assembly / striated muscle thin filament ...muscle thin filament assembly / actin filament fragmentation / actin filament severing / actin filament depolymerization / locomotion / embryo development ending in birth or egg hatching / cortical actin cytoskeleton / positive regulation of actin filament polymerization / skeletal muscle thin filament assembly / striated muscle thin filament / cell motility / actin filament binding / actin cytoskeleton / ribonucleoprotein complex / cytoplasm
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Actin-depolymerizing factor 1, isoforms a/b
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsShukla, V. / Yadav, R. / Kabra, A. / Kumar, D. / Ono, S. / Arora, A.
CitationJournal: To be Published
Title: NMR Structure and Backbone dynamics of ADF like UNC-60A protein from Caenorhabditis elegans: its divergence from conventional ADF/cofilin
Authors: Shukla, V. / Yadav, R. / Jain, A. / Tripathi, S. / Kabra, A. / Kumar, D. / Ono, S. / Arora, A.
History
DepositionMay 11, 2014Deposition site: BMRB / Processing site: PDBJ
SupersessionJun 11, 2014ID: 2LRB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin-depolymerizing factor 1, isoforms a/b


Theoretical massNumber of molelcules
Total (without water)18,3921
Polymers18,3921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Actin-depolymerizing factor 1, isoforms a/b / Uncoordinated protein 60


Mass: 18391.828 Da / Num. of mol.: 1 / Fragment: UNP residues 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-60, C38C3.5 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): BL21(DE3) / References: UniProt: Q07750

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1423D HNCO
1523D HNCA
1623D C(CO)NH
1723D H(CCO)NH
1833D (H)CCH-TOCSY
1932D 1H-13C HSQC aliphatic
11032D 1H-13C HSQC aromatic
11113D 1H-15N NOESY
11233D 1H-13C NOESY aliphatic
11333D 1H-13C NOESY aromatic
11422D CB(CGCDCE)HE
11522D CB(CGCD)HD
11623D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.65 mM [U-99% 15N] UNC-60A-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 0.1 % sodium azide-4, 7 % [U-99% 2H] D2O-5, 93 % H2O-6, 93% H2O/7% D2O93% H2O/7% D2O
20.65 mM [U-99% 13C; U-99% 15N] UNC-60A-7, 20 mM sodium phosphate-8, 50 mM sodium chloride-9, 0.1 % sodium azide-10, 7 % [U-99% 2H] D2O-11, 93 % H2O-12, 93% H2O/7% D2O93% H2O/7% D2O
30.65 mM [U-99% 13C; U-99% 15N] UNC-60A-13, 20 mM sodium phosphate-14, 50 mM sodium chloride-15, 0.1 % sodium azide-16, 100 % D2O-17, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.65 mMUNC-60A-1[U-99% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
0.1 %sodium azide-41
7 %D2O-5[U-99% 2H]1
93 %H2O-61
0.65 mMUNC-60A-7[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate-82
50 mMsodium chloride-92
0.1 %sodium azide-102
7 %D2O-11[U-99% 2H]2
93 %H2O-122
0.65 mMUNC-60A-13[U-99% 13C; U-99% 15N]3
20 mMsodium phosphate-143
50 mMsodium chloride-153
0.1 %sodium azide-163
100 %D2O-173
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker Avance3BrukerAvance38002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichdata analysis
PSVS1.4Bhattacharya and Montelionevalidation of structural parameter
iCINGDoreleijersvalidation of structural parameter
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
CNSrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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