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- PDB-8rsw: Solution NMR structure of Pacsin 2 SH3 domain -

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Basic information

Entry
Database: PDB / ID: 8rsw
TitleSolution NMR structure of Pacsin 2 SH3 domain
ComponentsProtein kinase C and casein kinase substrate in neurons protein 2
KeywordsPEPTIDE BINDING PROTEIN / pacsin / FAP52 / SH3 domain
Function / homology
Function and homology information


caveola assembly / plasma membrane tubulation / phosphatidic acid binding / negative regulation of endocytosis / regulation of endocytosis / cytoskeletal protein binding / cytoskeleton organization / phospholipid binding / caveola / ruffle membrane ...caveola assembly / plasma membrane tubulation / phosphatidic acid binding / negative regulation of endocytosis / regulation of endocytosis / cytoskeletal protein binding / cytoskeleton organization / phospholipid binding / caveola / ruffle membrane / endocytosis / recycling endosome membrane / actin cytoskeleton organization / cytoskeleton / early endosome / endosome / focal adhesion / cytosol / cytoplasm
Similarity search - Function
PACSIN2, F-BAR domain / PACSIN1/PACSIN2, SH3 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain / Src homology 3 domains ...PACSIN2, F-BAR domain / PACSIN1/PACSIN2, SH3 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / 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
Protein kinase C and casein kinase substrate in neurons protein 2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / torsion angle dynamics / molecular dynamics
AuthorsTossavainen, H. / Permi, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Solution NMR structure of Pacsin 2 SH3 domain
Authors: Tossavainen, H. / Permi, P.
History
DepositionJan 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C and casein kinase substrate in neurons protein 2


Theoretical massNumber of molelcules
Total (without water)7,5621
Polymers7,5621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein kinase C and casein kinase substrate in neurons protein 2 / Focal adhesion protein of 52 kDa / FAP52


Mass: 7562.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: PACSIN2 / Production host: Escherichia coli (E. coli) / References: UniProt: O13154
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
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic13D HNCA
141isotropic13D HN(CO)CA
151isotropic13D iHNCA
161isotropic13D iHNCACB
171isotropic13D CBCA(CO)NH
181isotropic13D HNCO
191isotropic13D C(CO)NH
1101isotropic13D H(CCO)NH
1111isotropic23D (H)CCH-COSY
1121isotropic23D 1H-13C NOESY
1131isotropic23D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1.2 mM [U-13C; U-15N] Pacsin 2 SH3 domain, 20 mM bis-TRIS, 93% H2O/7% D2O
Label: sample 1 / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMPacsin 2 SH3 domain[U-13C; U-15N]1
20 mMbis-TRISnatural abundance1
Sample conditionsIonic strength units: M / Label: conditions 1 / pH: 6.8 / Pressure: ambient atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
VNMRVarianprocessing
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
torsion angle dynamics4
molecular dynamics5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 300 / Conformers submitted total number: 20

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