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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 / Capsid / cryoEM / Pseudo-atomic model. / Icosahedral virus
Specimen sourceEnterobacteria phage HK97 / virus
MethodElectron microscopy (12 A resolution / Single particle / Vitreous ice (cryo EM))
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.

DateDeposition: Apr 11, 2001 / Release: May 2, 2001 / Last modification: Feb 24, 2009

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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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
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  • Deposited structure unit
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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)197,9607
Polyers197,9607
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)11,877,577420
Polyers11,877,577420
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)989,79835
Polyers989,79835
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)1,187,75842
Polyers1,187,75842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


  • 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


Mass: 28279.945 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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenAggregation state: PARTICLE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILLIPS CM200FEG

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Processing

Image selectionNumber of particles: 981
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionResolution: 12 A
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.
Atomic model buildingRef space: REAL
Least-squares processHighest resolution: 12 A
Refine hist #LASTHighest resolution: 12 A
Number of atoms included #LASTProtein: 1792 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1792
Least-squares process
*PLUS
Highest resolution: 12 A

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