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- PDB-1ksr: THE REPEATING SEGMENTS OF THE F-ACTIN CROSS-LINKING GELATION FACT... -

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Basic information

Entry
Database: PDB / ID: 1ksr
TitleTHE REPEATING SEGMENTS OF THE F-ACTIN CROSS-LINKING GELATION FACTOR (ABP-120) HAVE AN IMMUNOGLOBULIN FOLD, NMR, 20 STRUCTURES
ComponentsGELATION FACTOR
KeywordsACTIN BINDING PROTEIN / IMMUNOGLOBULIN / GELATION FACTOR / ABP-120
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 / DISTANCE GEOMETRY, SIMULATED ANNEALING, ENERGY MINIMIZATION.
AuthorsFucini, P. / Renner, C. / Herberhold, C. / Noegel, A.A. / Holak, T.A.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: The repeating segments of the F-actin cross-linking gelation factor (ABP-120) have an immunoglobulin-like fold.
Authors: Fucini, P. / Renner, C. / Herberhold, C. / Noegel, A.A. / Holak, T.A.
#1: Journal: J.Cell Biol. / Year: 1990
Title: Human Endothelial Actin-Binding Protein (Abp-280, Nonmuscle Filamin): A Molecular Leaf Spring
Authors: Gorlin, J.B. / Yamin, R. / Egan, S. / Stewart, M. / Stossel, T.P. / Kwiatkowski, D.J. / Hartwig, J.H.
#2: Journal: J.Cell Biol. / Year: 1989
Title: The Dictyostelium Gelation Factor Shares a Putative Actin Binding Site with Alpha-Actinins and Dystrophin and Also Has a Rod Domain Containing Six 100-Residue Motifs that Appear to Have a Cross-Beta Conformation
Authors: Noegel, A.A. / Rapp, S. / Lottspeich, F. / Schleicher, M. / Stewart, M.
#3: Journal: J.Cell Biol. / Year: 1985
Title: Ligand-Induced Changes in the Location of Actin, Myosin, 95K (Alpha-Actinin), and 120K Protein in Amebae of Dictyostelium Discoideum
Authors: Carboni, J.M. / Condeelis, J.S.
#4: Journal: J.Cell Biol. / Year: 1984
Title: Properties of the 120,000-and 95,000-Dalton Actin-Binding Proteins from Dictyostelium Discoideum and Their Possible Functions in Assembling the Cytoplasmic Matrix
Authors: Condeelis, J. / Vahey, M. / Carboni, J.M. / Demey, J. / Ogihara, S.
History
DepositionFeb 7, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GELATION FACTOR


Theoretical massNumber of molelcules
Total (without water)10,5161
Polymers10,5161
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)20 / 45NUMBER (0) OF RESIDUAL CONSTRAINS VIOLATION (THRESHOLDS: 0.45 A FOR NOES AND 10.0 DEGREE FOR ANGLES)
Representative

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Components

#1: Protein GELATION FACTOR / ABP-120


Mass: 10516.427 Da / Num. of mol.: 1 / Fragment: ROD 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Strain: AX3 / Cell line: BL21 / Cellular location: CYTOPLASM, CELL CORTEX / Gene: ABPC / Plasmid: PT7-7 / Cellular location (production host): CYTOPLASM / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE) / References: UniProt: P13466

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121CBCA(CO)NH
131HSQC
1412D NOESY
1513D NOESY
1613D TOCSY
1712D TOCSY.

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Sample preparation

Sample conditionspH: 7.0 / Temperature: 304 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AMXBrukerAMX7502

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
X-PLORBRUNGERrefinement
CCNMR (HOME MADE)MADE)structure solution
X-PLORstructure solution
UXNMR (BRUKER). UXNMR (BRUKER).(BRUKER).structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, ENERGY MINIMIZATION.
Software ordinal: 1
NMR ensembleConformer selection criteria: NUMBER (0) OF RESIDUAL CONSTRAINS VIOLATION (THRESHOLDS: 0.45 A FOR NOES AND 10.0 DEGREE FOR ANGLES)
Conformers calculated total number: 45 / Conformers submitted total number: 20

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