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- PDB-2k3b: Seeing the Invisible: Structures of Excited Protein States by Rel... -

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Basic information

Entry
Database: PDB / ID: 2k3b
TitleSeeing the Invisible: Structures of Excited Protein States by Relaxation Dispersion NMR
ComponentsActin-binding protein
KeywordsSTRUCTURAL PROTEIN / CPMG / Abp1p / Ark1p / Invisible State / Acetylation / Actin-binding / Cytoplasm / Cytoskeleton / Phosphoprotein / SH3 domain
Function / homology
Function and homology information


protein localization to actin cortical patch / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch assembly / site of polarized growth / actin cortical patch / regulation of actin filament polymerization / mating projection tip / barbed-end actin filament capping / cortical actin cytoskeleton / actin filament binding ...protein localization to actin cortical patch / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch assembly / site of polarized growth / actin cortical patch / regulation of actin filament polymerization / mating projection tip / barbed-end actin filament capping / cortical actin cytoskeleton / actin filament binding / cell cortex / cytoplasm
Similarity search - Function
Fungal actin-binding protein 1, second SH3 domain / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains ...Fungal actin-binding protein 1, second SH3 domain / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Actin-binding protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsVallurupalli, P. / Hansen, F.D. / Kay, L.E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy
Authors: Vallurupalli, P. / Hansen, D.F. / Kay, L.E.
History
DepositionApr 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: Actin-binding protein


Theoretical massNumber of molelcules
Total (without water)6,9931
Polymers6,9931
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 / 960structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Actin-binding protein


Mass: 6993.485 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ABP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15891

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N CT-CW,TROSY,anti-TROSY CPMG
12215N CT-CW,TROSY,anti-TROSY CPMG
13313CO CT-inphase,TROSY,anti-TROSY CPMG
14413CA CT-CW,TROSY,anti-TROSY CPMG

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Sample preparation

Details
Solution-IDContentsSolvent system
1~1.5 mM [90 % U 2H; ~100% U 15N] Abp1p, ~0.105 mM [90% U 2H; ~100% U 15N] Ark1p, 90% H2O/10% D2O90% H2O/10% D2O
2~1.5 mM [90 % U 2H; ~100% U 15N] Abp1p, ~0.105 mM Ark1p, 90% H2O/10% D2O90% H2O/10% D2O
3~1.5 mM [90 % U 2H; ~100% U 15N; 13CO labeled] Abp1p, ~0.105 mM Ark1p, 90% H2O/10% D2O90% H2O/10% D2O
4~1.5 mM [90 % U 2H; ~100% U 15N; 13Ca labeled] Abp1p, ~0.105 mM Ark1p, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMAbp1p[90 % U 2H; ~100% U 15N]1
0.105 mMArk1p[90% U 2H; ~100% U 15N]1
1.5 mMAbp1p[90 % U 2H; ~100% U 15N]2
0.105 mMArk1p2
1.5 mMAbp1p[90 % U 2H; ~100% U 15N; 13CO labeled]3
0.105 mMArk1p3
1.5 mMAbp1p[90 % U 2H; ~100% U 15N; 13Ca labeled]4
0.105 mMArk1p4
Sample conditionsIonic strength: ~0.150 / pH: 7.0 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 960 / Conformers submitted total number: 10

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