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- PDB-2lnh: Enterohaemorrhagic E. coli (EHEC) exploits a tryptophan switch to... -

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Basic information

Entry
Database: PDB / ID: 2lnh
TitleEnterohaemorrhagic E. coli (EHEC) exploits a tryptophan switch to hijack host F-actin assembly
Components
  • Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1
  • Neural Wiskott-Aldrich syndrome protein
  • Secreted effector protein EspF(U)
KeywordsSignaling Protein/Protein Binding / Protein complex / Signaling Protein-Protein Binding complex
Function / homology
Function and homology information


negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / NOSTRIN mediated eNOS trafficking / GTPase regulator activity / plasma membrane organization / actin cap / actin crosslink formation / vesicle organization ...negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / NOSTRIN mediated eNOS trafficking / GTPase regulator activity / plasma membrane organization / actin cap / actin crosslink formation / vesicle organization / cadherin binding involved in cell-cell adhesion / vesicle budding from membrane / vesicle transport along actin filament / actin polymerization or depolymerization / dendritic spine morphogenesis / protein-containing complex localization / RHOF GTPase cycle / proline-rich region binding / DCC mediated attractive signaling / Nephrin family interactions / regulation of postsynapse organization / positive regulation of filopodium assembly / RHOV GTPase cycle / positive regulation of actin filament polymerization / RHOJ GTPase cycle / RHOQ GTPase cycle / actin filament bundle assembly / CDC42 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / regulation of actin cytoskeleton organization / response to bacterium / FCGR3A-mediated phagocytosis / adherens junction / Regulation of actin dynamics for phagocytic cup formation / endocytic vesicle membrane / regulation of protein localization / actin cytoskeleton / lamellipodium / Clathrin-mediated endocytosis / actin binding / cytoplasmic vesicle / microtubule binding / protein-containing complex assembly / host cell cytoplasm / cytoskeleton / cell division / glutamatergic synapse / endoplasmic reticulum membrane / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
TccP2/EspF(U)-like / Type III secretion protein EspF / I-BAR domain containing protein IRTKS / IRTKS, SH3 domain / TccP2/EspF(U)-like superfamily / EspF protein repeat / SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / Actin nucleation-promoting factor WAS, C-terminal ...TccP2/EspF(U)-like / Type III secretion protein EspF / I-BAR domain containing protein IRTKS / IRTKS, SH3 domain / TccP2/EspF(U)-like superfamily / EspF protein repeat / SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / Actin nucleation-promoting factor WAS, C-terminal / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / WASP family, EVH1 domain / WH2 motif / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Actin nucleation-promoting factor WASL / 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 O157:H7 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailsfewest violations, model 1
AuthorsAitio, O. / Hellman, M. / Skehan, B. / Kesti, T. / Leong, J.M. / Saksela, K. / Permi, P.
CitationJournal: Structure / Year: 2012
Title: Enterohaemorrhagic Escherichia coli exploits a tryptophan switch to hijack host f-actin assembly.
Authors: Aitio, O. / Hellman, M. / Skehan, B. / Kesti, T. / Leong, J.M. / Saksela, K. / Permi, P.
History
DepositionDec 28, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Oct 31, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neural Wiskott-Aldrich syndrome protein
B: Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1
C: Secreted effector protein EspF(U)


Theoretical massNumber of molelcules
Total (without water)20,1243
Polymers20,1243
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 #1fewest violations

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Components

#1: Protein Neural Wiskott-Aldrich syndrome protein / N-WASP


Mass: 7262.023 Da / Num. of mol.: 1 / Fragment: UNP residues 207-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WASL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00401
#2: 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: SH3 domain 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
#3: Protein/peptide Secreted effector protein EspF(U) / EspF-like protein encoded on prophage U / Tir-cytoskeleton coupling protein TccP


Mass: 5301.970 Da / Num. of mol.: 1 / Fragment: UNP residues 221-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: O157:H7 / Gene: espF(U), tccP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0DJ89

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1412D 1H-13C HSQC
1522D 1H-13C HSQC
1632D 1H-13C HSQC
1713D HN(CA)CB
1823D HN(CA)CB
1933D HN(CA)CB
11013D CBCA(CO)NH
11123D CBCA(CO)NH
11233D CBCA(CO)NH
11313D HBHA(CO)NH
11423D HBHA(CO)NH
11533D HBHA(CO)NH
11613D C(CO)NH
11723D C(CO)NH
11833D C(CO)NH
11913D H(CCO)NH
12023D H(CCO)NH
12133D H(CCO)NH
12213D (H)CCH-COSY
12323D (H)CCH-COSY
12433D (H)CCH-COSY
12513D 1H-15N NOESY
12623D 1H-15N NOESY
12733D 1H-15N NOESY
12813D 1H-13C NOESY
12923D 1H-13C NOESY
13033D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-98% 13C; U-98% 15N] protein_1, 0.3 mM protein_2, 0.3 mM protein_3, 93% H2O/7% D2O93% H2O/7% D2O
20.5 mM protein_1, 0.5 mM [U-98% 13C; U-98% 15N] protein_2, 0.5 mM protein_3, 93% H2O/7% D2O93% H2O/7% D2O
30.5 mM protein_1, 0.5 mM protein_2, 0.5 mM [U-98% 13C; U-98% 15N] protein_3, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMentity_1-1[U-98% 13C; U-98% 15N]1
0.3 mMentity_2-21
0.3 mMentity_3-31
0.5 mMentity_1-42
0.5 mMentity_2-5[U-98% 13C; U-98% 15N]2
0.5 mMentity_3-62
0.5 mMentity_1-73
0.5 mMentity_2-83
0.5 mMentity_3-9[U-98% 13C; U-98% 15N]3
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
SPARKY3.11Goddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AMBER8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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