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- PDB-3ddx: HK97 bacteriophage capsid Expansion Intermediate-II model -

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Basic information

Entry
Database: PDB / ID: 3ddx
TitleHK97 bacteriophage capsid Expansion Intermediate-II model
ComponentsMajor capsid protein
KeywordsVIRUS / Bacteriophage / HK97 / Capsid Protein / Expansion Intermediate / Virion / 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 speciesBacteriophage HK97 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14 Å
AuthorsLee, K.K. / Gan, L. / Conway, J.F. / Hendrix, R.W. / Steven, A.C. / Johnson, J.E.
CitationJournal: Structure / Year: 2008
Title: Virus capsid expansion driven by the capture of mobile surface loops.
Authors: Kelly K Lee / Lu Gan / Hiro Tsuruta / Crystal Moyer / James F Conway / Robert L Duda / Roger W Hendrix / Alasdair C Steven / John E Johnson /
Abstract: The capsids of tailed-DNA bacteriophages first assemble as procapsids, which mature by converting into a new form that is strong enough to contain a densely packed viral chromosome. We demonstrate ...The capsids of tailed-DNA bacteriophages first assemble as procapsids, which mature by converting into a new form that is strong enough to contain a densely packed viral chromosome. We demonstrate that the intersubunit crosslinking that occurs during maturation of HK97 capsids actually promotes the structural transformation. Small-angle X-ray scattering and crosslinking assays reveal that a shift in the crosslink pattern accompanies conversion of a semimature particle, Expansion Intermediate-I/II, to a more mature state, Balloon. This transition occurs in a switch-like fashion. We find that crosslink formation shifts the global conformational balance to favor the balloon state. A pseudoatomic model of EI-I/II derived from cryo-EM provides insight into the relationship between crosslink formation and conformational switching.
History
DepositionJun 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
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.length_a / _cell.length_b / _cell.length_c
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.4Mar 5, 2025Group: Data processing / Structure summary / Category: em_3d_reconstruction / pdbx_entry_details / Item: _em_3d_reconstruction.resolution

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Structure visualization

Movie
  • 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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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)215,6327
Polymers215,6327
Non-polymers00
Water00
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)12,937,935420
Polymers12,937,935420
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: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
x 5


  • icosahedral pentamer
  • 1.08 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,078,16135
Polymers1,078,16135
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
x 6


  • icosahedral 23 hexamer
  • 1.29 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,293,79342
Polymers1,293,79342
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Major capsid protein / Gp5 / Head protein


Mass: 30804.607 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage HK97 (virus) / Gene: 5 / Plasmid: PT7-HD2.9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P49861
Has protein modificationN

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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 Expansion Intermediate II / Type: VIRUS
Buffer solutionName: 50mM Na-Acetate, 200mM KCl / pH: 4.18 / Details: 50mM Na-Acetate, 200mM KCl
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 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 X

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Processing

EM software
IDNameCategory
1CNSmodel fitting
2Omodel fitting
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 14 Å / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: Vector Reciprocal Space Target
Details: METHOD--manual and rigid body fitting. THE COORDINATES CONTAIN ONLY THE BACKBONE ATOMS. DURING RIGID BODY DOCKING OF THE PROTEIN MODEL INTO THE EM DENSITY, THE TWO SUBDOMAINS 104-125 AND 155- ...Details: METHOD--manual and rigid body fitting. THE COORDINATES CONTAIN ONLY THE BACKBONE ATOMS. DURING RIGID BODY DOCKING OF THE PROTEIN MODEL INTO THE EM DENSITY, THE TWO SUBDOMAINS 104-125 AND 155-175 OF EACH SUBUNIT WERE ALLOWED TO MOVE INDEPENDENTLY FROM THE REMAINDER OF THE RESIDUES (THE CORE OF EACH SUBUNIT). THAT IS WHY THE CONNECTIVITY OF THOSE SEGMENTS WITH THE REST OF THE SUBUNIT IS NOT WELL-PRESERVED. REFINEMENT PROTOCOL--Rigid Body, Magnification Optimized using Van Der Waals Constraints and Real-space Correlation Coefficient
Atomic model buildingPDB-ID: 1OHG

1ohg


Accession code: 1OHG / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms9653 0 0 0 9653

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