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- PDB-1nh4: Structure of the coat protein in fd filamentous bacteriophage par... -

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Basic information

Entry
Database: PDB / ID: 1nh4
TitleStructure of the coat protein in fd filamentous bacteriophage particles
ComponentsMajor coat protein
KeywordsVIRUS / ALPHA HELIX / Helical virus
Function / homology
Function and homology information


helical viral capsid / host cell membrane / membrane => GO:0016020 / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #80 / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Capsid protein G8P / Capsid protein G8P
Similarity search - Component
Biological speciesEnterobacteria phage fd (virus)
MethodSOLID-STATE NMR / SOLID-STATE NMR SPECTROSCOPY
AuthorsZeri, A.C. / Mesleh, M.F. / Nevzorov, A.A. / Opella, S.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structure of the coat protein in fd filamentous bacteriophage particles determined by solid-state NMR spectroscopy
Authors: Zeri, A.C. / Mesleh, M.F. / Nevzorov, A.A. / Opella, S.J.
History
DepositionDec 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999Authors informed that the sequence of their protein is identical to residues 27-76 of the database ...Authors informed that the sequence of their protein is identical to residues 27-76 of the database reference sequence provided in GenBank entry 8698956 but that the source of their protein is different. Residue 21 was mutated from Tyr to Met.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major coat protein


Theoretical massNumber of molelcules
Total (without water)5,2121
Polymers5,2121
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 / -
Representative

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Components

#1: Protein/peptide Major coat protein


Mass: 5212.021 Da / Num. of mol.: 1 / Mutation: Y21M / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage fd (virus) / Genus: Inovirus / Species: Enterobacteria phage M13 / Strain: fd / References: UniProt: Q9T0Q9, UniProt: P69539*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experimentType: PISEMA
NMR detailsText: This structure was generated from the five-fold symmetry of PDB entry 1IFI, which has the symmetry that relates one pentamer to the next. This one has had the sidechains added using the program ...Text: This structure was generated from the five-fold symmetry of PDB entry 1IFI, which has the symmetry that relates one pentamer to the next. This one has had the sidechains added using the program SCWRL. The structure was determined by solid state nuclear magnetic resonance using the whole virus in suspension. A model of a section of the virion capsid was built with 20 copies of the protein arranged in agreement with previous studies by fiber diffraction (Marvin et al., J. Mol. Biol. 235, 260286 (1994)).

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Sample preparation

DetailsContents: 15N 50mg/ml virus particles in suspension, 5mM sodium borate buffer
Solvent system: 100% H2O
Sample conditionspH: 8.0 / Pressure: ambient / Temperature: 338 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 spectrometerManufacturer: Home-built / Field strength: 550 MHz

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Processing

NMR software
NameVersionDeveloperClassification
tecmaglibratecmagcollection
Felix97MSIprocessing
SCWRL2.1Dunbrack, R.refinement
RefinementMethod: SOLID-STATE NMR SPECTROSCOPY / Software ordinal: 1
Details: The first five N-terminal residues of the coat protein undergo isotropic movements at room temperature and structural parameters cannot be resolved.
NMR ensembleConformers submitted total number: 20

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