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- PDB-1n4c: NMR Structure of the J-Domain and Clathrin Substrate Binding Doma... -

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Basic information

Entry
Database: PDB / ID: 1n4c
TitleNMR Structure of the J-Domain and Clathrin Substrate Binding Domain of Bovine Auxilin
ComponentsAuxilin
KeywordsPROTEIN BINDING / Four Helix Bundle
Function / homology
Function and homology information


regulation of clathrin coat assembly / synaptic vesicle recycling / synaptic vesicle uncoating / clathrin heavy chain binding / clathrin coat disassembly / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / clathrin-dependent endocytosis / clathrin-coated vesicle / clathrin binding / intracellular transport ...regulation of clathrin coat assembly / synaptic vesicle recycling / synaptic vesicle uncoating / clathrin heavy chain binding / clathrin coat disassembly / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / clathrin-dependent endocytosis / clathrin-coated vesicle / clathrin binding / intracellular transport / dephosphorylation / heat shock protein binding / protein tyrosine phosphatase activity / SH3 domain binding / presynapse / vesicle / postsynaptic density / molecular adaptor activity / protein domain specific binding / intracellular membrane-bounded organelle / cytoplasm
Similarity search - Function
Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. ...Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / C2 domain superfamily / Protein-tyrosine phosphatase-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsGruschus, J.M. / Han, C.J. / Greener, T. / Greene, L.E. / Ferretti, J.A. / Eisenberg, E.
Citation
Journal: Biochemistry / Year: 2004
Title: Structure of the functional fragment of auxilin required for catalytic uncoating of clathrin-coated vesicles.
Authors: Gruschus, J.M. / Han, C.J. / Greener, T. / Ferretti, J.A. / Greene, L.E. / Eisenberg, E.
#1: Journal: J.Biomol.NMR / Year: 2000
Title: H-1, 15N, and 13C NMR backbone assignments and secondary structure of the C-terminal recombinant fragment of auxilin including the J-domain
Authors: Han, C.J. / Gruschus, J.M. / Greener, T. / Greene, L.E. / Ferretti, J. / Eisenberg, E.
History
DepositionOct 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Auxilin


Theoretical massNumber of molelcules
Total (without water)20,5931
Polymers20,5931
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Auxilin /


Mass: 20593.453 Da / Num. of mol.: 1 / Fragment: Residues (737-845), J-Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: Q27974

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM Auxilin (20kD C-terminal construct) U-15N90% H20, 10% D2O
21.5mM Auxilin (20kD C-terminal construct) U-15N,13C90% H2O/10% D2O
Sample conditionsIonic strength: 60mM NaCl / pH: 4.5 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglioprocessing
X-PLOR3.851Brungerrefinement
TALOS1Cornilescudata analysis
XwinNMR2.1Brukercollection
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: Structure determined using 2810 distance restraints, 144 Phi and Psi dihedral restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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