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- PDB-6rh5: Solution structure and 1H, 13C and 15N chemical shift assignments... -

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Basic information

Entry
Database: PDB / ID: 6rh5
TitleSolution structure and 1H, 13C and 15N chemical shift assignments for NECAP1 PHear domain
ComponentsAdaptin ear-binding coat-associated protein 1
KeywordsENDOCYTOSIS / clathrin mediated endocytosis / regulation by phosphorylation / AP2 endocytic adaptor / NECAP SNX9
Function / homology
Function and homology information


presynaptic endocytosis / clathrin vesicle coat / Golgi Associated Vesicle Biogenesis / clathrin-coated pit / vesicle-mediated transport / protein transport / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / cytosol
Similarity search - Function
NECAP, PHear domain / Protein of unknown function (DUF1681) / PH-like domain superfamily
Similarity search - Domain/homology
Adaptin ear-binding coat-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics / simulated annealing / molecular dynamics
AuthorsOwen, D.J. / Neuhaus, D. / Yang, J.-C. / Herrmann, T.
Funding support United Kingdom, Czech Republic, 5items
OrganizationGrant numberCountry
Wellcome Trust090909/Z/09/Z United Kingdom
Wellcome Trust097040/Z/11/Z United Kingdom
Medical Research Council (United Kingdom)U105178934 United Kingdom
European Communitys Seventh Framework ProgrammePIOF-GA-2012-330268
Czech Science FoundationGA18-05360S Czech Republic
CitationJournal: Dev.Cell / Year: 2019
Title: Temporal Ordering in Endocytic Clathrin-Coated Vesicle Formation via AP2 Phosphorylation.
Authors: Wrobel, A.G. / Kadlecova, Z. / Kamenicky, J. / Yang, J.C. / Herrmann, T. / Kelly, B.T. / McCoy, A.J. / Evans, P.R. / Martin, S. / Muller, S. / Sroubek, F. / Neuhaus, D. / Honing, S. / Owen, D.J.
History
DepositionApr 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adaptin ear-binding coat-associated protein 1


Theoretical massNumber of molelcules
Total (without water)15,5621
Polymers15,5621
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8490 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Adaptin ear-binding coat-associated protein 1 / NECAP endocytosis-associated protein 1 / NECAP-1


Mass: 15562.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NECAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NC96

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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
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic12D 1H-13C HSQC aliphatic (constant time)
151isotropic12D 1H-13C HSQC aromatic (constant time)
1141isotropic13D HNCA
1131isotropic13D CBCA(CO)NH
1121isotropic13D HN(CA)CB
1111isotropic23D HBHA(CO)NH
1101isotropic23D (H)CCH-COSY (1H,13C,1H)
191isotropic23D (H)CCH-TOCSY (13C,13C,1H)
181isotropic33D 1H-15N NOESY tau(m) 150ms
171isotropic33D 1H-13C NOESY aliphatic tau(m) 150ms
161isotropic33D 1H-13C NOESY aromatic tau(m) 150ms

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-98% 13C; U-98% 15N] NECAP1 1-133, 70 mM [U-2H] sodium acetate, 95% H2O/5% D2O
Label: 15N,13C_H2O_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMNECAP1 1-133[U-98% 13C; U-98% 15N]1
70 mMsodium acetate[U-2H]1
Sample conditionsIonic strength: 70 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCE IIIBrukerAVANCE III8003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNchemical shift assignment
Sparky3.115Goddardchemical shift assignment
UNIO2.8.1Herrmannstructure calculation
Xplor-NIH2.28Schwieters, Kuszewski, Tjandra and Clorestructure calculation
Amber11Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Refinement
MethodSoftware ordinal
torsion angle dynamics4
simulated annealing5
molecular dynamics6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 30

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