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- PDB-6g4a: FLN5 (full length) -

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Basic information

Entry
Database: PDB / ID: 6g4a
TitleFLN5 (full length)
ComponentsGelation factor
KeywordsSTRUCTURAL PROTEIN / FILAMIN / GELATION FACTOR
Function / homology
Function and homology information


regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex ...regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex / phototaxis / macropinocytic cup / RHO GTPases activate PAKs / protein kinase B binding / actin crosslink formation / thermotaxis / hyperosmotic response / mitogen-activated protein kinase binding / lamellipodium assembly / cortical actin cytoskeleton / cell leading edge / pseudopodium / phagocytic cup / phagocytosis / response to cAMP / extracellular matrix / cell motility / small GTPase binding / actin filament binding / cell migration / cell cortex / actin cytoskeleton organization / plasma membrane / cytoplasm
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDictyostelium discoideum (eukaryote)
MethodSOLUTION NMR / molecular dynamics
AuthorsWaudby, C.A. / Wlodarski, T. / Karyadi, M.-E. / Cassaignau, A.M.E. / Chan, S.H.S. / Wentink, A.S. / Schmidt-Engler, J.M. / Camilloni, C. / Vendruscolo, M. / Cabrita, L.D. / Christodoulou, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust097806/Z/11/Z United Kingdom
CitationJournal: To Be Published
Title: Mapping energy landscapes of a growing filamin domain reveals an intermediate associated with proline isomerization during biosynthesis
Authors: Waudby, C.A. / Wlodarski, T. / Karyadi, M.-E. / Cassaignau, A.M.E. / Chan, S.H.S. / Wentink, A.S. / Schmidt-Engler, J.M. / Camilloni, C. / Vendruscolo, M. / Cabrita, L.D. / Christodoulou, J.
History
DepositionMar 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gelation factor


Theoretical massNumber of molelcules
Total (without water)12,1671
Polymers12,1671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, NMR diffusion and linewidth
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6650 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 572structures with the least restraint violations
RepresentativeModel #1medoid

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Components

#1: Protein Gelation factor / Actin-binding protein 120 / ABP-120


Mass: 12167.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: abpC, DDB_G0269100 / Production host: Escherichia coli (E. coli) / References: UniProt: P13466

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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
121isotropic13D HNCO
131isotropic13D HNHA
141isotropic13D HN(COCA)CB

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Sample preparation

DetailsType: solution
Contents: 200 uM [U-13C; U-15N] FLN5, 10 mM HEPES, 30 mM ammonium chloride, 12 mM magnesium chloride, 2 mM beta-mercaptoethanol, 1 mM EDTA, 90% H2O/10% D2O
Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMFLN5[U-13C; U-15N]1
10 mMHEPESnatural abundance1
30 mMammonium chloridenatural abundance1
12 mMmagnesium chloridenatural abundance1
2 mMbeta-mercaptoethanolnatural abundance1
1 mMEDTAnatural abundance1
Sample conditionsIonic strength: 158 mM / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
GROMACS4.6.5http://www.gromacs.org/structure calculation
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 572 / Conformers submitted total number: 10

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