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- PDB-2klv: Membrane-bound structure of the Pf1 major coat protein in DHPC micelle -

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Basic information

Entry
Database: PDB / ID: 2klv
TitleMembrane-bound structure of the Pf1 major coat protein in DHPC micelle
ComponentsCapsid protein G8P
KeywordsMEMBRANE PROTEIN / alignment / alpha helix / Capsid protein / Membrane / Transmembrane / Virion
Function / homology
Function and homology information


helical viral capsid / host cell membrane / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #230 / Inovirus Coat protein B / Capsid protein G8P / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudomonas phage Pf1 (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsPark, S. / Son, W. / Mukhopadhyay, R. / Valafar, H. / Opella, S.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Phage-induced alignment of membrane proteins enables the measurement and structural analysis of residual dipolar couplings with dipolar waves and lambda-maps.
Authors: Park, S.H. / Son, W.S. / Mukhopadhyay, R. / Valafar, H. / Opella, S.J.
History
DepositionJul 8, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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

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Assembly

Deposited unit
A: Capsid protein G8P


Theoretical massNumber of molelcules
Total (without water)4,6121
Polymers4,6121
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)15 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Capsid protein G8P / / Gene 8 protein / G8P / Coat protein B / Major coat protein


Mass: 4612.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage Pf1 (virus) / Gene: VIII / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: P03621

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D 1H-15N NOESY
1411H-15N IPAP

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Sample preparation

DetailsContents: 1 mM [U-98% 13C; U-98% 15N] Pf1 major coat protein-1, 100 mM DHPC micelle
Solvent system: 100 mM DHPC micelle
SampleConc.: 1 mM / Component: Pf1 major coat protein-1 / Isotopic labeling: [U-98% 13C; U-98% 15N]
Sample conditionspH: 6.7 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR NIH / Developer: Schwieters, C.D. et al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 15

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