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- PDB-6f55: Complex structure of PACSIN SH3 domain and TRPV4 proline rich region -

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Basic information

Entry
Database: PDB / ID: 6f55
TitleComplex structure of PACSIN SH3 domain and TRPV4 proline rich region
Components
  • PACSIN 3
  • PRR
KeywordsPEPTIDE BINDING PROTEIN / PROTEIN
Function / homology
Function and homology information


plasma membrane tubulation / osmosensory signaling pathway / monoatomic cation channel activity / adherens junction / calcium channel activity / intracellular calcium ion homeostasis / calmodulin binding / apical plasma membrane / lipid binding / ATP binding ...plasma membrane tubulation / osmosensory signaling pathway / monoatomic cation channel activity / adherens junction / calcium channel activity / intracellular calcium ion homeostasis / calmodulin binding / apical plasma membrane / lipid binding / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Protein kinase C and casein kinase substrate in neurons protein 3 / Transient receptor potential cation channel subfamily V member 4 / 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 / Transient receptor potential cation channel subfamily V member 1-4 ...Protein kinase C and casein kinase substrate in neurons protein 3 / Transient receptor potential cation channel subfamily V member 4 / 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 / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / SH3 Domains / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ion transport domain / Ion transport protein / Roll / Mainly Beta
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily V member 4 / PACSIN 3
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGlogowski, N.A. / Goretzki, B. / Diehl, E. / Duchardt-Ferner, E. / Hacker, C. / Hellmich, U.A.
CitationJournal: Structure / Year: 2018
Title: Structural Basis of TRPV4 N Terminus Interaction with Syndapin/PACSIN1-3 and PIP2.
Authors: Goretzki, B. / Glogowski, N.A. / Diehl, E. / Duchardt-Ferner, E. / Hacker, C. / Gaudet, R. / Hellmich, U.A.
History
DepositionNov 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PACSIN 3
B: PRR


Theoretical massNumber of molelcules
Total (without water)9,0152
Polymers9,0152
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1010 Å2
ΔGint-7 kcal/mol
Surface area5930 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein PACSIN 3 / Protein kinase C and casein kinase substrate in neurons 3


Mass: 7398.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: PACSIN3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1G1I6
#2: Protein/peptide PRR / Transient receptor potential cation channel subfamily V member 4


Mass: 1616.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A0A1D5PXA5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
1157isotropic43D HNCO
1147isotropic43D HN(CA)CO
1137isotropic23D HNCA
1127isotropic43D HN(CO)CA
1167isotropic43D HN(CA)CB
1117isotropic43D HBHA(CO)NH
1106isotropic43D H(CCO)NH
196isotropic43D H(CCO)NH
1206isotropic12D 1H-15N HSQC
116isotropic13D 1H-15N NOESY-HSQC
1186isotropic22D 1H-13C HSQC aromatic
126isotropic23D 1H-13C NOESY aromatic
1196isotropic32D 1H-13C HSQC aliphatic
136isotropic33D 1H-13C NOESY aliphatic
1176isotropic22D 13C filtered and 13C edited NOESY-HSQC
1216isotropic33D 13C filtered and 13C edited NOESY-HSQC aromatic
1226isotropic23D 13C filtered and 13C edited NOESY-HSQC aliphatic
1241isotropic23D 13C filtered NOESY
1236isotropic42D 13C filtered TOCSY
1254isotropic22D 1H-13C HSQC aliphatic
1264isotropic22D 1H-13C NOESY-HSQC
1318isotropic22D 1H-13C HSQC aliphatic
1308isotropic22D 1H-13C NOESY-HSQC
1295isotropic32D 1H-13C HSQC aliphatic
1285isotropic32D 1H-13C NOESY-HSQC
1279isotropic22D 1H-13C HSQC aliphatic
1329isotropic22D 1H-13C NOESY-HSQC
13310isotropic22D 1H-13C HSQC aliphatic
13410isotropic22D 1H-13C NOESY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1250 uM [U-13C; U-15N] ggPacSH3, 1.25 mM unlabeled PRR, 90% H2O/10% D2OggPacSH3_PRR_250uM90% H2O/10% D2O
solution7250 uM [U-13C; U-15N] ggPacSH3, 90% H2O/10% D2OggPacSH390% H2O/10% D2O
solution6576 uM [U-13C; U-15N] ggPacSH3, 2.88 mM unlabeled PRR, 90% H2O/10% D2OggPacSH3_PRR_576uM90% H2O/10% D2O
solution4256.8 uM unlabeled ggPacSH3, 1.284 mM selectively 13C P124 and 15N A125 PRR, 90% H2O/10% D2OggPacSH3_PRR_13CP124_15NA12590% H2O/10% D2O
solution5256.8 uM [U-13C; U-15N] ggPacSH3, 1.284 mM selectively 13C P128 PRR, 90% H2O/10% D2OggPacSH3_PRR_13CP12890% H2O/10% D2O
solution8235 uM unlabeled ggPacSH3, 1.175 mM selectively 13C P126 PRR, 90% H2O/10% D2OggPacSH3_PRR_13CP12690% H2O/10% D2O
solution9235 uM unlabeled ggPacSH3, 1.175 mM selectively 13C K122 P130 PRR, 90% H2O/10% D2OggPacSH3_PRR_13CK122P13090% H2O/10% D2O
solution10229 uM unlabeled ggPacSH3, 1.145 mM selectively 13C P129 K133 PRR, 90% H2O/10% D2OggPacSH3_PRR_13CP129K13390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
250 uMPacsin 3 SH3[U-13C; U-15N]1
1.25 mMPRRunlabeled1
250 uMPacsin 3 SH3[U-13C; U-15N]7
576 uMPacsin 3 SH3[U-13C; U-15N]6
2.88 mMPRRunlabeled6
256.8 uMPacsin 3 SH3unlabeled4
1.284 mMPRRselectively 13C P124 and 15N A1254
256.8 uMPacsin 3 SH3[U-13C; U-15N]5
1.284 mMPRRselectively 13C P1285
235 uMPacsin 3 SH3unlabeled8
1.175 mMPRRselectively 13C P1268
235 uMPacsin 3 SH3unlabeled9
1.175 mMPRRselectively 13C K122 P1309
229 uMPacsin 3 SH3unlabeled10
1.145 mMPRRselectively 13C P129 K13310
Sample conditionsIonic strength: 100 mM / Label: NMR-buffer complex / pH: 7.0 / Pressure: AMBIENT Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE9502
Bruker AVANCEBrukerAVANCE8003
Bruker AVANCEBrukerAVANCE6004

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Processing

SoftwareName: CYANA / Version: 3.97 / Classification: refinement
NMR software
NameVersionDeveloperClassification
CYANA3.9Guentertstructure calculation
CARA3.9Keller and Wuthrichchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
TopSpinBruker Biospinprocessing
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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