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- PDB-7oj9: NMR solution structure of SNX9 SH3 - EEEV nsP3 peptide complex -

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Basic information

Entry
Database: PDB / ID: 7oj9
TitleNMR solution structure of SNX9 SH3 - EEEV nsP3 peptide complex
Components
  • EEEV nsP3 peptide
  • Sorting nexin-9
KeywordsENDOCYTOSIS / 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 / regulation of synaptic vesicle endocytosis / endosomal transport ...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 / regulation of synaptic vesicle endocytosis / endosomal transport / positive regulation of actin filament polymerization / Golgi Associated Vesicle Biogenesis / mitotic cytokinesis / positive regulation of protein kinase activity / clathrin-coated pit / ruffle / receptor-mediated endocytosis / phosphatidylinositol binding / positive regulation of GTPase activity / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / endocytosis / Clathrin-mediated endocytosis / presynapse / cytoplasmic vesicle / protein-containing complex assembly / cadherin binding / ubiquitin protein ligase binding / protein homodimerization activity / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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
Biological speciesHomo sapiens (human)
Eastern equine encephalitis virus
MethodSOLUTION NMR / simulated annealing - molecular dynamics
AuthorsTossavainen, H. / Permi, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: Structure / Year: 2022
Title: Structure of SNX9 SH3 in complex with a viral ligand reveals the molecular basis of its unique specificity for alanine-containing class I SH3 motifs.
Authors: Tossavainen, H. / Ugurlu, H. / Karjalainen, M. / Hellman, M. / Antenucci, L. / Fagerlund, R. / Saksela, K. / Permi, P.
History
DepositionMay 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 15, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: EEEV nsP3 peptide
A: Sorting nexin-9


Theoretical massNumber of molelcules
Total (without water)9,7282
Polymers9,7282
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1320 Å2
ΔGint-9 kcal/mol
Surface area6550 Å2
MethodPISA
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 EEEV nsP3 peptide


Mass: 2548.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Eastern equine encephalitis virus
#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

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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 CBCA(CO)NH
161isotropic13D HNCO
171isotropic13D iHNCO
181isotropic13D H(CCO)NH
191isotropic13D (H)CC(CO)NH
1101isotropic13D HBHA(CO)NH
1111isotropic13D (H)CCH-COSY
1121isotropic13D HCCmHm-TOCSY
1131isotropic12D (HB)CB(CGCD)HD
1161isotropic12D (HB)CB(CGCDCE)HE
1151isotropic13D 1H-13C NOESY aliphatic
1141isotropic13D 1H-13C NOESY aromatic
1171isotropic13D 1H-15N NOESY
1181isotropic1X-filtered-, 13C-edited NOESY
1191isotropic1F1, F2, 15N, 13C-filtered NOESY
1201isotropic1X-filtered NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] SNX9 SH3, 1 mM EEEV nsP3 peptide, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O
Label: sample_1 / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSNX9 SH3[U-13C; U-15N]1
1 mMEEEV nsP3 peptidenatural abundance1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 0.15 M / Label: conditions_1 / pH: 6.5 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing - 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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