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- PDB-5i22: Amphiphysin SH3 in complex with Chikungunya virus nsP3 peptide -

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Basic information

Entry
Database: PDB / ID: 5i22
TitleAmphiphysin SH3 in complex with Chikungunya virus nsP3 peptide
Components
  • CHIKV nsP3 peptide
  • Myc box-dependent-interacting protein 1
KeywordsTRANSCRIPTION / SH3 domain / function: protein binding Chikungunya virus nsP3 peptide / function: viral replication
Function / homology
Function and homology information


negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / lipid tube assembly / nucleus localization / varicosity / T-tubule organization / regulation of cell cycle process / RNA polymerase II transcription repressor complex ...negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / lipid tube assembly / nucleus localization / varicosity / T-tubule organization / regulation of cell cycle process / RNA polymerase II transcription repressor complex / negative regulation of potassium ion transmembrane transport / extrinsic component of synaptic vesicle membrane / cerebellar mossy fiber / positive regulation of astrocyte differentiation / aspartic-type endopeptidase inhibitor activity / ADP-ribose 1''-phosphate phosphatase / host cell filopodium / axon initial segment / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / node of Ranvier / RNA polymerase binding / mRNA modification / I band / regulation of neuron differentiation / clathrin binding / positive regulation of actin filament polymerization / endosome to lysosome transport / nucleus organization / regulation of cytoskeleton organization / negative regulation of amyloid-beta formation / positive regulation of endocytosis / regulation of heart rate by cardiac conduction / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / synaptic vesicle endocytosis / 7-methylguanosine mRNA capping / signaling adaptor activity / axon terminus / cytoskeleton organization / T-tubule / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / cysteine-type peptidase activity / Transferases; Transferring one-carbon groups; Methyltransferases / phospholipid binding / host cell cytoplasmic vesicle membrane / tau protein binding / Z disc / endocytosis / actin filament binding / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / synaptic vesicle / nuclear envelope / actin cytoskeleton / Clathrin-mediated endocytosis / protein-folding chaperone binding / nucleoside-triphosphate phosphatase / GTPase binding / protease binding / methylation / vesicle / response to lipopolysaccharide / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / postsynapse / RNA helicase activity / endosome / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / positive regulation of apoptotic process / symbiont-mediated suppression of host gene expression / axon / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / dendrite / GTP binding / host cell nucleus / host cell plasma membrane / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Amphiphysin 2 / Amphiphysin 2, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / BAR domain / : / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily ...Amphiphysin 2 / Amphiphysin 2, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / BAR domain / : / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / AH/BAR domain superfamily / Variant SH3 domain / Viral (Superfamily 1) RNA helicase / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Roll / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Myc box-dependent-interacting protein 1 / Polyprotein P1234
Similarity search - Component
Biological speciesHomo sapiens (human)
Chikungunya virus
MethodSOLUTION NMR
AuthorsTossavainen, H. / Aitio, O. / Hellman, M. / Saksela, K. / Permi, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis of the High Affinity Interaction between the Alphavirus Nonstructural Protein-3 (nsP3) and the SH3 Domain of Amphiphysin-2.
Authors: Tossavainen, H. / Aitio, O. / Hellman, M. / Saksela, K. / Permi, P.
History
DepositionFeb 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Oct 23, 2019Group: Data collection / Experimental preparation / Category: pdbx_nmr_exptl_sample_conditions
Item: _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_exptl_sample_conditions.temperature_units
Revision 1.5Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myc box-dependent-interacting protein 1
B: CHIKV nsP3 peptide


Theoretical massNumber of molelcules
Total (without water)11,2952
Polymers11,2952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1070 Å2
ΔGint-2 kcal/mol
Surface area6640 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

#1: Protein Myc box-dependent-interacting protein 1 / Amphiphysin II / Amphiphysin-like protein / Box-dependent myc-interacting protein 1 / Bridging integrator 1


Mass: 9356.412 Da / Num. of mol.: 1 / Fragment: SH3 fragment, UNP residue 513-593
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIN1, AMPHL / Production host: Escherichia coli (E. coli) / References: UniProt: O00499
#2: Protein/peptide CHIKV nsP3 peptide


Mass: 1938.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q8JUX6*PLUS

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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
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D H(CCO)NH
151isotropic13D C(CCO)NH
161isotropic13D (H)CCH-COSY
1101isotropic12D (HB)CB(CGCD)HD
191isotropic12D (HB)CB(CGCDCE)HE
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] amphiphysin 2 SH3, 0.5 mM [U-13C; U-15N] CHIKV nsP3 peptide, 90% H2O/10% D2O
Label: sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMamphiphysin 2 SH3[U-13C; U-15N]1
0.5 mMCHIKV nsP3 peptide[U-13C; U-15N]1
Sample conditionsIonic strength units: Not defined / Label: conditions / pH: 6.5 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
VNMRVarianprocessing
NMR ensembleConformers submitted total number: 20

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