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- PDB-2hf6: Solution structure of human zeta-COP -

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Basic information

Entry
Database: PDB / ID: 2hf6
TitleSolution structure of human zeta-COP
ComponentsCoatomer subunit zeta-1
KeywordsPROTEIN TRANSPORT / COP I
Function / homology
Function and homology information


COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / transport vesicle / intracellular protein transport / Golgi membrane / endoplasmic reticulum membrane / cytosol
Similarity search - Function
Beta-Lactamase - #60 / Coatomer subunit zeta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Coatomer subunit zeta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsYu, W. / Jin, C. / Xia, B.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Solution structure of human zeta-COP: direct evidences for structural similarity between COP I and clathrin-adaptor coats
Authors: Yu, W. / Lin, J. / Jin, C. / Xia, B.
History
DepositionJun 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 30, 2011Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coatomer subunit zeta-1


Theoretical massNumber of molelcules
Total (without water)17,0501
Polymers17,0501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Coatomer subunit zeta-1 / Zeta-1 coat protein / Zeta-1 COP / zeta-COP


Mass: 17049.582 Da / Num. of mol.: 1 / Fragment: residues 1-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPZ1, COPZ / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P61923

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB,CBCA(CO)NH
121HNCO,HN(CA)CO
131HC(C)H COSY
141HC(C)H TOCSY
1513D 13C-separated NOESY
1613D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.5mM zeta-COP, 20mM Potassium phosphate (pH 7.0), 50mM NaCl, 1mM EDTA , 20mM DTT, 10mM PMSF, 0.01% sodium azide, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipecyana 2.0F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
NMRView5B. A. Johnson and R. A. Blevinsdata analysis
DIANAcyana2.0Guntert, P., Mumenthaler, C. & W thrich, Kstructure solution
Amber7David A. Case, et. al.refinement
XwinNMR3.5Brukercollection
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: torsion angle dynamics performed by DYANA; simulated annealing performed by AMBER
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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