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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


lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube assembly / RNA polymerase II transcription repressor complex / regulation of cell cycle process / T-tubule organization / negative regulation of potassium ion transmembrane transport / host cell filopodium ...lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube assembly / RNA polymerase II transcription repressor complex / regulation of cell cycle process / T-tubule organization / negative regulation of potassium ion transmembrane transport / host cell filopodium / ADP-ribose 1''-phosphate phosphatase / varicosity / mRNA methyltransferase activity / extrinsic component of synaptic vesicle membrane / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / axon initial segment / poly(A) RNA polymerase activity / cerebellar mossy fiber / positive regulation of astrocyte differentiation / nucleus localization / node of Ranvier / aspartic-type endopeptidase inhibitor activity / I band / RNA polymerase binding / nucleus organization / regulation of neuron differentiation / regulation of cytoskeleton organization / clathrin binding / positive regulation of actin filament polymerization / endosome to lysosome transport / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / regulation of heart rate by cardiac conduction / positive regulation of endocytosis / negative regulation of amyloid-beta formation / synaptic vesicle endocytosis / axon terminus / cysteine-type peptidase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / cytoskeleton organization / T-tubule / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / phospholipid binding / tau protein binding / Z disc / endocytosis / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / actin filament binding / synaptic vesicle / actin cytoskeleton / nucleoside-triphosphate phosphatase / GTPase binding / Clathrin-mediated endocytosis / nuclear envelope / protein-folding chaperone binding / protease binding / vesicle / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / endosome / RNA helicase / positive regulation of apoptotic process / RNA-directed RNA polymerase / axon / viral RNA genome replication / RNA-dependent RNA polymerase activity / dendrite / DNA-templated transcription / glutamatergic synapse / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / GTP binding / host cell plasma membrane / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Amphiphysin 2 / Amphiphysin 2, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / : / : / : / Non-structural protein 3, zinc-binding domain ...Amphiphysin 2 / Amphiphysin 2, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / : / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / BAR 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 / Viral (Superfamily 1) RNA helicase / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / 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 / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / 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 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water0
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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