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- PDB-1tqz: Solution structure of NECAP1 protein -

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Basic information

Entry
Database: PDB / ID: 1tqz
TitleSolution structure of NECAP1 protein
ComponentsNECAP1
KeywordsENDOCYTOSIS/EXOCYTOSIS / NECAP1 protein / endocytosis / structural genomics / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


clathrin vesicle coat / Golgi Associated Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin-coated pit / vesicle-mediated transport / endocytosis / protein transport
Similarity search - Function
NECAP, PHear domain / Protein of unknown function (DUF1681) / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Adaptin ear-binding coat-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsDenisov, A.Y. / Ritter, B. / McPherson, P.S. / Gehring, K.
CitationJournal: To be Published
Title: Solution structure of NECAP1 protein
Authors: Denisov, A.Y. / Ritter, B. / McPherson, P.S. / Gehring, K.
History
DepositionJun 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NECAP1


Theoretical massNumber of molelcules
Total (without water)15,1021
Polymers15,1021
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)10 / 200structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NECAP1


Mass: 15101.970 Da / Num. of mol.: 1 / Fragment: residues 1-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9CR95

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
121CBCA(CO)HN
13113C,15N-edited NOESY
14215N-edited NOESY
152HNHA
163IPAP-HSQC
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM NECAP1 protein U-15N,13C, 25 mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
21.5 mM NECAP1 protein U-15N, 25 mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
30.6 mM NECAP1 protein U-15N, 8 mg/ml Pf1-bacteriophages, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 75mM NaCl / pH: 7.2 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2Delargio et al.processing
XEASY1.3.13Bartels et al.data analysis
CNS1.1Brunger et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure was refined by using standard protocol in CNS with restraints from NOE distances, backbone torsion angles, hydrogen bonds and residual dipolar couplings
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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