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- PDB-1inz: SOLUTION STRUCTURE OF THE EPSIN N-TERMINAL HOMOLOGY (ENTH) DOMAIN... -

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Basic information

Entry
Database: PDB / ID: 1inz
TitleSOLUTION STRUCTURE OF THE EPSIN N-TERMINAL HOMOLOGY (ENTH) DOMAIN OF HUMAN EPSIN
ComponentsEPS15-INTERACTING PROTEIN(EPSIN)
KeywordsENDOCYTOSIS/EXOCYTOSIS / ALPHA-HELIX / EPSIN / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


negative regulation of sprouting angiogenesis / clathrin vesicle coat / molecular sequestering activity / clathrin binding / embryonic organ development / clathrin-coated pit / Notch signaling pathway / female pregnancy / EGFR downregulation / phospholipid binding ...negative regulation of sprouting angiogenesis / clathrin vesicle coat / molecular sequestering activity / clathrin binding / embryonic organ development / clathrin-coated pit / Notch signaling pathway / female pregnancy / EGFR downregulation / phospholipid binding / endocytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / in utero embryonic development / endosome / nucleus / plasma membrane / cytosol
Similarity search - Function
ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKoshiba, S. / Kigawa, T. / Kikuchi, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2001
Title: Solution structure of the epsin N-terminal homology (ENTH) domain of human epsin
Authors: Koshiba, S. / Kigawa, T. / Kikuchi, A. / Yokoyama, S.
History
DepositionDec 5, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2020Group: Data collection / Derived calculations / Structure summary
Category: entity / pdbx_nmr_software ...entity / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct
Item: _entity.pdbx_description / _pdbx_nmr_software.name / _struct.pdbx_descriptor
Revision 1.4Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: EPS15-INTERACTING PROTEIN(EPSIN)


Theoretical massNumber of molelcules
Total (without water)17,3091
Polymers17,3091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11670 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein EPS15-INTERACTING PROTEIN(EPSIN) / EH DOMAIN-BINDING MITOTIC PHOSPHOPROTEIN


Mass: 17308.641 Da / Num. of mol.: 1 / Fragment: ENTH DOMAIN(RESIDUES 1-144)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPSIN / Plasmid: PGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y6I3

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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
1324D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM epsin ENTH domain U-15N; 20mM NA phosphate buffer; 400mM NaCl; 2mM DTT; 0.01% sodium azide; 90% H2O, 10% D2O90% H2O/10% D2O
21mM epsin ENTH domain U-15N,13C; 20mM NA phosphate buffer; 400mM NaCl; 2mM DTT; 0.01% sodium azide; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 400mM / pH: 6.5 / Pressure: 1 atm / Temperature: 303.0 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1 and 2.6Brukercollection
NMRPipeDelaglioprocessing
NMRView4.0.3Johnsondata analysis
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers submitted total number: 20

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