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- PDB-2l1a: Solution NMR structure of the N-terminal GTPase-like domain of di... -

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Basic information

Entry
Database: PDB / ID: 2l1a
TitleSolution NMR structure of the N-terminal GTPase-like domain of dictyostelium discoideum Fomin C
ComponentsFormin-C
Keywordsactin binding protein / fruiting body formation
Function / homology
Function and homology information


sorocarp spore cell differentiation / macropinosome / actin filament network formation / culmination involved in sorocarp development / cortical actin cytoskeleton organization / actin filament bundle assembly / actin filament binding / cell-cell junction / gene expression / cytoskeleton ...sorocarp spore cell differentiation / macropinosome / actin filament network formation / culmination involved in sorocarp development / cortical actin cytoskeleton organization / actin filament bundle assembly / actin filament binding / cell-cell junction / gene expression / cytoskeleton / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like (UB roll) - #530 / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain ...Ubiquitin-like (UB roll) - #530 / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Ubiquitin-like (UB roll) / Armadillo-like helical / Armadillo-type fold / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesDictyostelium discoideum (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, final refinement in water-shell
Model detailslowest energy, model 1
AuthorsDames, S.A. / Schoenichen, A. / Stephan, G. / Geyer, M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure, dynamics, lipid binding, and physiological relevance of the putative GTPase-binding domain of Dictyostelium formin C.
Authors: Dames, S.A. / Junemann, A. / Sass, H.J. / Schonichen, A. / Stopschinski, B.E. / Grzesiek, S. / Faix, J. / Geyer, M.
History
DepositionJul 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2May 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: Formin-C


Theoretical massNumber of molelcules
Total (without water)12,0761
Polymers12,0761
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Formin-C / @


Mass: 12075.733 Da / Num. of mol.: 1
Fragment: N-terminal potential GTPase-binding domain, residues 1-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: forC, DDB_G0287295 / Plasmid: pGEX-4T1 tev / Production host: Escherichia coli (E. coli) / References: UniProt: Q54KF1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCA
1423D C(CO)NH-TOCSY
1523D CBCANH
1613D HNHA
1723D (H)CCH-TOCSY
1813D HNHB
1923D HACAHB-COSY
11023D HNCO
11122D 13C-{13CO}-1H-13C HSQC
11222D 13C-{15N}-1H-13C HSQC
11323D 1H-15N NOESY
11423D 1H-13C NOESY aliphatic
11523D 1H-13C NOESY aromatic
11633D 1H-13C NOESY aliphatic
11742D 1H-15N HSQC-IPAP
11843D HN(CO)CA Jcaha
11943D HN(CO)CA Jcacb
1201{1H}-15N-NOE
121115N-T1
122115N-T2
12312D 1H-15N HSQC
12422D 1H-13C HSQC
12522D 1H-15N HSQC
12632D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.03 mM [U-100% 15N] forC/ A, 50 mM potassium phosphate, 50 mM sodium chloride, 0.2 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21.03 mM [U-100% 13C; U-100% 15N] forC/ A, 50 mM potassium phosphate, 50 mM sodium chloride, 0.2% sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
31.03 mM [U-100% 13C; U-100% 15N] forC/ A, 50 mM potassium phosphate, 50 mM sodium chloride, 0.2% sodium azide, 100% D2O100% D2O
41.03 mM [U-100% 13C; U-100% 15N] forC/ A, 50 mM potassium phosphate, 50 mM sodium chloride, 0.2 v/v sodium azide, 8.6 w/v C12E5, 2 v/v hexanol, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.03 mMforC/ A-1[U-100% 15N]1
50 mMpotassium phosphate-21
50 mMsodium chloride-31
0.2 %sodium azide-41
1.03 mMforC/ A-5[U-100% 13C; U-100% 15N]2
50 mMpotassium phosphate-62
50 mMsodium chloride-72
0.2 %sodium azide-82
1.03 mMforC/ A-9[U-100% 13C; U-100% 15N]3
50 mMpotassium phosphate-103
50 mMsodium chloride-113
0.2 %sodium azide-123
1.03 mMforC/ A-13[U-100% 13C; U-100% 15N]4
50 mMpotassium phosphate-144
50 mMsodium chloride-154
0.2 v/vsodium azide-164
8.6 w/vC12E5-174
2 v/vhexanol-184
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
X-PLORrefinement
RefinementMethod: torsion angle dynamics, simulated annealing, final refinement in water-shell
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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