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- PDB-9r4w: Solution NMR structure of SNX9 SH3 in complex with EspF -

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Basic information

Entry
Database: PDB / ID: 9r4w
TitleSolution NMR structure of SNX9 SH3 in complex with EspF
Components
  • LEE-encoded effector EspF
  • Sorting nexin-9
KeywordsCELL INVASION / complex
Function / homology
Function and homology information


lipid tube assembly / plasma membrane tubulation / 1-phosphatidylinositol binding / cuticular plate / Arp2/3 complex binding / cleavage furrow formation / positive regulation of membrane protein ectodomain proteolysis / clathrin-coated vesicle / endosomal transport / Golgi Associated Vesicle Biogenesis ...lipid tube assembly / plasma membrane tubulation / 1-phosphatidylinositol binding / cuticular plate / Arp2/3 complex binding / cleavage furrow formation / positive regulation of membrane protein ectodomain proteolysis / clathrin-coated vesicle / endosomal transport / Golgi Associated Vesicle Biogenesis / positive regulation of actin filament polymerization / positive regulation of protein kinase activity / mitotic cytokinesis / positive regulation of GTPase activity / regulation of synaptic vesicle endocytosis / ruffle / clathrin-coated pit / phosphatidylinositol binding / receptor-mediated endocytosis / cytoplasmic vesicle membrane / intracellular protein transport / trans-Golgi network / endocytosis / presynapse / Clathrin-mediated endocytosis / protein-containing complex assembly / cytoplasmic vesicle / cadherin binding / ubiquitin protein ligase binding / protein homodimerization activity / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Type III secretion protein EspF / EspF protein repeat / SNX9, SH3 domain / Sorting nexin-9, BAR domain / Sorting nexin-9, PX domain / Sorting nexin 9 family / Sorting nexin protein, WASP-binding domain / WASP-binding domain of Sorting nexin protein / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. ...Type III secretion protein EspF / EspF protein repeat / SNX9, SH3 domain / Sorting nexin-9, BAR domain / Sorting nexin-9, PX domain / Sorting nexin 9 family / Sorting nexin protein, WASP-binding domain / WASP-binding domain of Sorting nexin protein / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
LEE-encoded effector EspF / Sorting nexin-9
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
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
B: LEE-encoded effector EspF
A: Sorting nexin-9


Theoretical massNumber of molelcules
Total (without water)12,1092
Polymers12,1092
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/peptide LEE-encoded effector EspF


Mass: 4929.542 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
#2: Protein Sorting nexin-9 / SH3 and PX domain-containing protein 1 / Protein SDP1 / SH3 and PX domain-containing protein 3A


Mass: 7179.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX9, SH3PX1, SH3PXD3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5X1
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

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.3 mM [U-13C; U-15N] SNX9 SH3, 1.5 mM EspF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2Osample 193% H2O/7% D2O
solution21.9 mM SNX9 SH3, 1.5 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
1.3 mMSNX9 SH3[U-13C; U-15N]1
1.5 mMEspFnatural abundance1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
1.9 mMSNX9 SH3natural abundance2
1.5 mMEspF[U-13C; U-15N]2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 150 mM / 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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