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

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Basic information

Entry
Database: PDB / ID: 1if0
TitlePSEUDO-ATOMIC MODEL OF BACTERIOPHAGE HK97 PROCAPSID (PROHEAD II)
ComponentsPROTEIN (MAJOR CAPSID PROTEIN GP5)
KeywordsVIRUS / Bacteriophage / Capsid / cryoEM / Pseudo-atomic model. / Icosahedral virus
Function / homology: / Phage capsid / Phage capsid family / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Biological speciesEnterobacteria phage HK97 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsConway, J.F. / Wikoff, W.R. / Cheng, N. / Duda, R.L. / Hendrix, R.W. / Johnson, J.E. / Steven, A.C.
Citation
Journal: Science / Year: 2001
Title: Virus maturation involving large subunit rotations and local refolding.
Authors: J F Conway / W R Wikoff / N Cheng / R L Duda / R W Hendrix / J E Johnson / A C Steven /
Abstract: Large-scale conformational changes transform viral precursors into infectious virions. The structure of bacteriophage HK97 capsid, Head-II, was recently solved by crystallography, revealing a ...Large-scale conformational changes transform viral precursors into infectious virions. The structure of bacteriophage HK97 capsid, Head-II, was recently solved by crystallography, revealing a catenated cross-linked topology. We have visualized its precursor, Prohead-II, by cryoelectron microscopy and modeled the conformational change by appropriately adapting Head-II. Rigid-body rotations ( approximately 40 degrees) cause switching to an entirely different set of interactions; in addition, two motifs undergo refolding. These changes stabilize the capsid by increasing the surface area buried at interfaces and bringing the cross-link-forming residues, initially approximately 40 angstroms apart, close together. The inner surface of Prohead-II is negatively charged, suggesting that the transition is triggered electrostatically by DNA packaging.
#1: Journal: Science / Year: 2000
Title: Topologically Linked Protein Rings in the Bacteriophage HK97 Capsid
Authors: Wikoff, W.R. / Liljas, L. / Duda, R.L. / Tsuruta, H. / Hendrix, R.W. / Johnson, J.E.
#2: Journal: Science / Year: 1995
Title: Proteolytic and Conformational Control of Virus Capsid Maturation: The Bacteriophage HK97 System
Authors: Conway, J.F. / Duda, R.L. / Cheng, N. / Hendrix, R.W. / Steven, A.C.
History
DepositionApr 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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
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  • Biological unit as icosahedral 23 hexamer
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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)197,9587
Polymers197,9587
Non-polymers00
Water00
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
Polymers11,877,495420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Polymers989,79135
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
Polymers1,187,75042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

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


Mass: 28279.750 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK97 (virus) / Genus: Lambda-like viruses / Plasmid: PT7-5 / Production host: Escherichia coli (E. coli) / Strain (production host): PT7-HD2.9B / References: UniProt: P49861

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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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

MicroscopyModel: 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 selectionNum. of particles selected: 2939
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 12 Å / Resolution method: OTHER / Num. 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. ...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 buildingSpace: REAL
RefinementHighest resolution: 12 Å
Refinement stepCycle: LAST / Highest resolution: 12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 0 0 1792
Refinement
*PLUS
Highest resolution: 12 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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