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- PDB-9r4v: Solution structure of N-WASP GBD in complex with EspF -

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Basic information

Entry
Database: PDB / ID: 9r4v
TitleSolution structure of N-WASP GBD in complex with EspF
Components
  • Actin nucleation-promoting factor WASL
  • LEE-encoded effector EspF
KeywordsCELL INVASION / 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 / actin cytoskeleton / lamellipodium / regulation of protein localization / Clathrin-mediated endocytosis / actin binding / actin cytoskeleton organization / protein-containing complex assembly / cytoplasmic vesicle / cell division / endoplasmic reticulum membrane / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleus / plasma membrane / cytosol
Similarity search - Function
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 ...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
LEE-encoded effector EspF / Actin nucleation-promoting factor WASL
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 Finland288235 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 8, 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: LEE-encoded effector EspF


Theoretical massNumber of molelcules
Total (without water)13,2192
Polymers13,2192
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 LEE-encoded effector EspF


Mass: 4915.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: espF, NCTC8621_00139 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A376PNR8
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 HNCO
171isotropic13D iHNCO
181isotropic13D H(CCO)NH
191isotropic13D C(CO)NH
1101isotropic13D HBHA(CO)NH
1111isotropic13D (H)CCH-COSY
1121isotropic13D HCCmHm-TOCSY
1131isotropic12D (HB)CB(CGCD)HD
1141isotropic12D (HB)CB(CGCDCE)HE
1151isotropic13D 1H-15N NOESY
1161isotropic13D 1H-13C NOESY aliphatic
1171isotropic13D 1H-13C NOESY aromatic
1182isotropic12D 1H-15N HSQC
1192isotropic12D 1H-13C HSQC aliphatic
1202isotropic12D 1H-13C HSQC aromatic
1212isotropic13D HN(CA)CB
1222isotropic13D HN(COCA)CB
1232isotropic13D HNCO
1242isotropic13D iHNCO
1252isotropic13D H(CCO)NH
1262isotropic13D C(CO)NH
1272isotropic13D HBHA(CO)NH
1282isotropic13D (H)CCH-COSY
1292isotropic13D HCCmHm-TOCSY
1302isotropic12D (HB)CB(CGCD)HD
1312isotropic12D (HB)CB(CGCDCE)HE
1322isotropic13D 1H-15N NOESY
1332isotropic13D 1H-13C NOESY aliphatic
1342isotropic13D 1H-13C NOESY aromatic
1352isotropic14D HACACON
1362isotropic13D HA(CA)CON
1372isotropic13D HA(CA)NCO

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-13C; U-15N] N-WASP GBD, 0.6 mM EspF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2Osample 193% H2O/7% D2O
solution20.7 mM GBD, 0.5 mM [U-13C; U-15N] EspF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2Osample 293% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMN-WASP GBD[U-13C; U-15N]1
0.6 mMEspFnatural abundance1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.7 mMGBDnatural abundance2
0.5 mMEspF[U-13C; U-15N]2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 0.1 M / Label: conditions / 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
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 5
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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