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- PDB-1if0: PSEUDO-ATOMIC MODEL OF BACTERIOPHAGE HK97 PROCAPSID (PROHEAD II) -

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Entry
Database: PDB / ID: 1if0
TitlePSEUDO-ATOMIC MODEL OF BACTERIOPHAGE HK97 PROCAPSID (PROHEAD II)
DescriptorMAJOR CAPSID PROTEIN GP5
KeywordsVIRUS / Bacteriophage / Virus / Capsid / cryoEM / Pseudo-atomic model. / Icosahedral virus
Specimen sourceEnterobacteria phage HK97 / virus
MethodElectron microscopy (12 Å resolution / Particle / Single particle)
AuthorsConway, J.F. / Wikoff, W.R. / Cheng, N. / Duda, R.L. / Hendrix, R.W. / Johnson, J.E. / Steven, A.C.
CitationScience, 2001, 292, 744-748

primary. Science, 2001, 292, 744-748 StrPapers
Virus maturation involving large subunit rotations and local refolding.
J F Conway / W R Wikoff / N Cheng / R L Duda / R W Hendrix / J E Johnson / A C Steven

#1. Science, 2000, 289, 2129-2133
Topologically Linked Protein Rings in the Bacteriophage HK97 Capsid
Wikoff, W.R. / Liljas, L. / Duda, R.L. / Tsuruta, H. / Hendrix, R.W. / Johnson, J.E.

#2. Science, 1995, 253, 86-99
Proteolytic and Conformational Control of Virus Capsid Maturation: The Bacteriophage HK97 System
Conway, J.F. / Duda, R.L. / Cheng, N. / Hendrix, R.W. / Steven, A.C.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 11, 2001 / Release: May 2, 2001
RevisionDateData content typeGroupProviderType
1.0May 2, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
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Assembly

Deposited unit
A: PROTEIN (MAJOR CAPSID PROTEIN GP5)
B: PROTEIN (MAJOR CAPSID PROTEIN GP5)
C: PROTEIN (MAJOR CAPSID PROTEIN GP5)
D: PROTEIN (MAJOR CAPSID PROTEIN GP5)
E: PROTEIN (MAJOR CAPSID PROTEIN GP5)
F: PROTEIN (MAJOR CAPSID PROTEIN GP5)
G: PROTEIN (MAJOR CAPSID PROTEIN GP5)


Theoretical massNumber of molelcules
Total (without water)197,9587
Polyers197,9587
Non-polymers00
Water0
#1
A: PROTEIN (MAJOR CAPSID PROTEIN GP5)
B: PROTEIN (MAJOR CAPSID PROTEIN GP5)
C: PROTEIN (MAJOR CAPSID PROTEIN GP5)
D: PROTEIN (MAJOR CAPSID PROTEIN GP5)
E: PROTEIN (MAJOR CAPSID PROTEIN GP5)
F: PROTEIN (MAJOR CAPSID PROTEIN GP5)
G: PROTEIN (MAJOR CAPSID PROTEIN GP5)
x 60


Theoretical massNumber of molelcules
Total (without water)11,877,495420
Polyers11,877,495420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3
A: PROTEIN (MAJOR CAPSID PROTEIN GP5)
B: PROTEIN (MAJOR CAPSID PROTEIN GP5)
C: PROTEIN (MAJOR CAPSID PROTEIN GP5)
D: PROTEIN (MAJOR CAPSID PROTEIN GP5)
E: PROTEIN (MAJOR CAPSID PROTEIN GP5)
F: PROTEIN (MAJOR CAPSID PROTEIN GP5)
G: PROTEIN (MAJOR CAPSID PROTEIN GP5)
x 5


  • icosahedral pentamer
  • 990 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)989,79135
Polyers989,79135
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: PROTEIN (MAJOR CAPSID PROTEIN GP5)
B: PROTEIN (MAJOR CAPSID PROTEIN GP5)
C: PROTEIN (MAJOR CAPSID PROTEIN GP5)
D: PROTEIN (MAJOR CAPSID PROTEIN GP5)
E: PROTEIN (MAJOR CAPSID PROTEIN GP5)
F: PROTEIN (MAJOR CAPSID PROTEIN GP5)
G: PROTEIN (MAJOR CAPSID PROTEIN GP5)
x 6


  • icosahedral 23 hexamer
  • 1.19 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,187,75042
Polyers1,187,75042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
#5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Polypeptide(L)
PROTEIN (MAJOR CAPSID PROTEIN GP5) / BACTERIOPHAGE HK97 CAPSID PROTEIN / Coordinate model: Cα atoms only


Mass: 28279.750 Da / Num. of mol.: 7 / Source: (gene. exp.) Enterobacteria phage HK97 / virus / References: UniProt: P49861

Cellular component

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: BACTERIOPHAGE HK97 PROCAPSID (PROHEAD II) / Type: VIRUS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingFilm or detector model: GENERIC FILM
Image scansScanner model: ZEISS SCAI

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Processing

Particle selectionNumber of particles selected: 2939
SymmetryPoint symmetry: I
3D reconstructionResolution: 12 Å / Resolution method: OTHER / Number of particles: 981
Details: IMAGE RECONSTRUCTION INCLUDING CONTRAST TRANSFER CORRECTION, WAS DONE AS DESCRIBED IN T.S.Baker & R.H.Cheng, J.Struct.Biol. 116, 120-130 (1996) and J.F.Conway & A.C.Steven, J.Struct.Biol. 128, 106 (1999). Nine focal pairs were analyzed, yielding 2939 particles, of which 981 were included in the final map. This map was calculated to 12 Angstroms, its resolution as assessed by Fourier Ring Correlation (cutoff 2 sigma), as calculated between reprojections of two maps from half data sets.
Symmetry type: POINT
Atomic model buildingRef space: REAL
Least-squares processHighest resolution: 12 Å
Refine hist #LASTHighest resolution: 12 Å
Number of atoms included #LASTProtein: 1792 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1792
Least-squares process
*PLUS
Highest resolution: 12 Å

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