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- PDB-9r3y: Solution NMR structure of N-WASP GBD in complex with EspFu R5 -

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Basic information

Entry
Database: PDB / ID: 9r3y
TitleSolution NMR structure of N-WASP GBD in complex with EspFu R5
Components
  • Actin nucleation-promoting factor WASL
  • Secreted effector protein EspF(U)
KeywordsSIGNALING PROTEIN / 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 / vesicle transport along actin filament / GTPase regulator activity / actin cap / NOSTRIN mediated eNOS trafficking / vesicle organization / vesicle budding from membrane ...negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / vesicle transport along actin filament / GTPase regulator activity / actin cap / NOSTRIN mediated eNOS trafficking / vesicle organization / vesicle budding from membrane / dendritic spine morphogenesis / actin polymerization or depolymerization / protein-containing complex localization / Nephrin family interactions / DCC mediated attractive signaling / regulation of postsynapse organization / positive regulation of filopodium assembly / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / actin filament polymerization / RAC1 GTPase cycle / EPHB-mediated forward signaling / FCGR3A-mediated phagocytosis / response to bacterium / Regulation of actin dynamics for phagocytic cup formation / endocytic vesicle membrane / lamellipodium / actin cytoskeleton / regulation of protein localization / Clathrin-mediated endocytosis / actin binding / actin cytoskeleton organization / protein-containing complex assembly / cytoplasmic vesicle / host cell cytoplasm / cell division / endoplasmic reticulum membrane / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
TccP2/EspF(U)-like superfamily / Type III secretion protein EspF / EspF protein repeat / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. ...TccP2/EspF(U)-like superfamily / Type III secretion protein EspF / EspF protein repeat / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain profile. / WH2 domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / PH-like domain superfamily
Similarity search - Domain/homology
Actin nucleation-promoting factor WASL / Secreted effector protein EspF(U)
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodSOLUTION NMR / restrained molecular dynamics
AuthorsTossavainen, H. / Permi, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland323435 Finland
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Intrinsically disordered enteropathogenic E. coli EspF exploits motif mimicry in high-affinity binding to neural Wiskott-Aldrich syndrome protein and sorting nexin 9.
Authors: Tossavainen, H. / Karjalainen, M. / Antenucci, L. / Hellman, M. / Permi, P.
History
DepositionMay 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin nucleation-promoting factor WASL
B: Secreted effector protein EspF(U)


Theoretical massNumber of molelcules
Total (without water)13,6052
Polymers13,6052
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Actin nucleation-promoting factor WASL / Neural Wiskott-Aldrich syndrome protein / N-WASP


Mass: 8303.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WASL / Production host: Escherichia coli (E. coli) / References: UniProt: O00401
#2: 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: espF(U), tccP, Z3072 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8X482
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HN(CA)CB
151isotropic13D HN(COCA)CB
161isotropic13D H(CCO)NH
171isotropic13D C(CO)NH
181isotropic13D HBHA(CO)NH
191isotropic13D (H)CCH-COSY
1101isotropic13D HCCmHm-TOCSY
1111isotropic12D (HB)CB(CGCD)HD
1121isotropic12D (HB)CB(CGCDCE)HE
1131isotropic13D 1H-15N NOESY
1141isotropic13D 1H-13C NOESY aliphatic
1151isotropic13D 1H-13C NOESY aliphatic
1161isotropic12D 15N, 13C filtered 1H-1H TOCSY
1171isotropic12D 15N, 13C filtered 1H-1H NOESY
1182isotropic12D 1H-15N HSQC
1192isotropic12D 1H-13C HSQC aliphatic
1202isotropic12D 1H-13C HSQC aromatic
1212isotropic13D 1H-13C NOESY aliphatic
1222isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-13C; U-15N] N-WASP GBD, 0.6 mM EspFu R5, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2Osample_195% H2O/5% D2O
solution20.4 mM N-WASP GBD, 0.3 mM [U-13C; U-15N] EspFu R5, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2Osample_295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMN-WASP GBD[U-13C; U-15N]1
0.6 mMEspFu R5natural abundance1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.4 mMN-WASP GBDnatural abundance2
0.3 mMEspFu R5[U-13C; U-15N]2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 0.11 M / Label: conditions_1 / pH: 6.5 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 20

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