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- PDB-2kxc: 1H, 13C, and 15N Chemical Shift Assignments for IRTKS-SH3 and Esp... -

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Basic information

Entry
Database: PDB / ID: 2kxc
Title1H, 13C, and 15N Chemical Shift Assignments for IRTKS-SH3 and EspFu-R47 complex
Components
  • Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1
  • EspF-like protein
KeywordsPROTEIN BINDING / IRTKS-SH3 / EspFu / Complex Structure
Function / homology
Function and homology information


plasma membrane organization / actin crosslink formation / cadherin binding involved in cell-cell adhesion / RHOF GTPase cycle / proline-rich region binding / positive regulation of actin filament polymerization / actin filament bundle assembly / RAC3 GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle ...plasma membrane organization / actin crosslink formation / cadherin binding involved in cell-cell adhesion / RHOF GTPase cycle / proline-rich region binding / positive regulation of actin filament polymerization / actin filament bundle assembly / RAC3 GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle / regulation of actin cytoskeleton organization / adherens junction / actin binding / host cell cytoplasm / cytoskeleton / extracellular exosome / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Type III secretion protein EspF / I-BAR domain containing protein IRTKS / IRTKS, SH3 domain / TccP2/EspF(U)-like superfamily / EspF protein repeat / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / AH/BAR domain superfamily ...Type III secretion protein EspF / I-BAR domain containing protein IRTKS / IRTKS, SH3 domain / TccP2/EspF(U)-like superfamily / EspF protein repeat / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Secreted effector protein EspF(U) / Secreted effector protein EspF(U) / Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics, TORSION ANGLE DYNAMICS
Model detailslowest energy, model 1
AuthorsAitio, O. / Hellman, M. / Kazlauskas, A. / Vingadassalom, D.F. / Leong, J.M. / Saksela, K. / Permi, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Recognition of tandem PxxP motifs as a unique Src homology 3-binding mode triggers pathogen-driven actin assembly
Authors: Aitio, O. / Hellman, M. / Kazlauskas, A. / Vingadassalom, D.F. / Leong, J.M. / Saksela, K. / Permi, P.
History
DepositionApr 30, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1
B: EspF-like protein


Theoretical massNumber of molelcules
Total (without water)12,8622
Polymers12,8622
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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 / BAI1-associated protein 2-like protein 1 / Insulin receptor tyrosine kinase substrate


Mass: 7559.607 Da / Num. of mol.: 1 / Fragment: IRTKS-SH3 domain, UNP residues 339-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAIAP2L1, IRTKS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UHR4
#2: Protein/peptide EspF-like protein / Tir-cytoskeleton coupling protein


Mass: 5301.970 Da / Num. of mol.: 1 / Fragment: EspFu-R47 domain, UNP residues 268-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8X2D5, UniProt: P0DJ89*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D (H)CCH-COSY
1423D 1H-15N NOESY
1523D 1H-13C NOESY
1623D (H)CCH-COSY
1712D 1H-15N HSQC
1822D 1H-15N HSQC
1912D 1H-13C HSQC
11022D 1H-13C HSQC
11113D HN(CA)CB
11223D HN(CA)CB
11313D CBCA(CO)NH
11423D CBCA(CO)NH
11513D HBHA(CO)NH
11623D HBHA(CO)NH
11713D C(CO)NH
11823D C(CO)NH
11913D H(CCO)NH
12023D H(CCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.48 mM [U-98% 13C; U-98% 15N] IRTKS-SH3-1, 0.48 mM EspFu-R47-2, 93% H2O/7% D2O93% H2O/7% D2O
20.9 mM [U-98% 13C; U-98% 15N] EspFu-R47-3, 0.9 mM IRTKS-SH3-4, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.48 mMIRTKS-SH3-1[U-98% 13C; U-98% 15N]1
0.48 mMEspFu-R47-21
0.9 mMEspFu-R47-3[U-98% 13C; U-98% 15N]2
0.9 mMIRTKS-SH3-42
Sample conditionsIonic strength: 50 / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.11Goddardchemical shift assignment
CYANA_2.12.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: molecular dynamics, TORSION ANGLE DYNAMICS / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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