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- PDB-2fte: Bacteriophage HK97 Expansion Intermediate IV -

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Basic information

Entry
Database: PDB / ID: 2fte
TitleBacteriophage HK97 Expansion Intermediate IV
Componentsmajor capsid protein
KeywordsVIRUS/VIRAL PROTEIN / Bacteriophage / HK97 / capsid protein / expansion intermediate / VIRUS-VIRAL PROTEIN COMPLEX
Function / homologyPhage 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
AuthorsGan, L. / Speir, J.A. / Conway, J.F. / Lander, G. / Cheng, N. / Firek, B.A. / Hendrix, R.W. / Duda, R.L. / Liljas, L. / Johnson, J.E.
Citation
Journal: Structure / Year: 2006
Title: Capsid conformational sampling in HK97 maturation visualized by X-ray crystallography and cryo-EM.
Authors: Lu Gan / Jeffrey A Speir / James F Conway / Gabriel Lander / Naiqian Cheng / Brian A Firek / Roger W Hendrix / Robert L Duda / Lars Liljas / John E Johnson /
Abstract: Maturation of the bacteriophage HK97 capsid from a precursor (Prohead II) to the mature state (Head II) involves a 60 A radial expansion. The mature particle is formed by 420 copies of the major ...Maturation of the bacteriophage HK97 capsid from a precursor (Prohead II) to the mature state (Head II) involves a 60 A radial expansion. The mature particle is formed by 420 copies of the major capsid protein organized on a T = 7 laevo lattice with each subunit covalently crosslinked to two neighbors. Well-characterized pH 4 expansion intermediates make HK97 valuable for investigating quaternary structural dynamics. Here, we use X-ray crystallography and cryo-EM to demonstrate that in the final transition in maturation (requiring neutral pH), pentons in Expansion Intermediate IV (EI-IV) reversibly sample 14 A translations and 6 degrees rotations relative to a fixed hexon lattice. The limit of this trajectory corresponds to the Head II conformation that is secured at this extent only by the formation of the final class of covalent crosslinks. Mutants that cannot crosslink or EI-IV particles that have been rendered incapable of forming the final crosslink remain in the EI-IV state.
#1: Journal: Mol Cell / Year: 2004
Title: Control of crosslinking by quaternary structure changes during bacteriophage HK97 maturation.
Authors: Lu Gan / James F Conway / Brian A Firek / Naiqian Cheng / Roger W Hendrix / Alasdair C Steven / John E Johnson / Robert L Duda /
Abstract: Radical structural changes drive the maturation of the capsid of HK97, a lambda-like, dsDNA bacteriophage of Escherichia coli. These include expansion from approximately 560 to approximately 660 A in ...Radical structural changes drive the maturation of the capsid of HK97, a lambda-like, dsDNA bacteriophage of Escherichia coli. These include expansion from approximately 560 to approximately 660 A in diameter, metamorphosis from a round to an angular shape, and formation of covalent crosslinks between adjacent capsomers. Analogous transformations also occur in unrelated viruses and protein complexes. We find that expansion and crosslinking happen concurrently during maturation at low pH. Expansion causes residues on three different subunits to move up to 35 A to form 420 active sites that each catalyze the formation of a lysine-asparagine crosslink between adjacent subunits, making crosslink formation an indirect reporter of structural change. Intermediate crosslinking patterns support a previously proposed model of expansion, while hydrophobic properties aid in distinguishing discrete intermediates. A structure derived from cryo-EM images reveals the free intermediate conformation of penton arms, supporting our model for coordinated movement of hexons and pentons on the capsid lattice.
History
DepositionJan 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Nov 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.length_a / _cell.length_b / _cell.length_c
Revision 1.5Feb 14, 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

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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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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
Water0
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: (Hermann–Mauguin notation: 532 / 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.) Enterobacteria phage HK97 (virus) / Genus: Lambda-like viruses / Gene: 5 / Plasmid: pT7-Hd2.9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / 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

Component
IDNameTypeDetailsParent-ID
1Bacteriophage HK97 Expansion Intermediate IVVIRUSThe structure was monodisperse.0
2major capsid proteinstructural molecule activity1
Details of virusHost category: BACTERIA(EUBACTERIA) / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Escherichia coli
Buffer solutionName: 50mM Citric Acid pH 4.0, 200mM KCl / pH: 4 / Details: 50mM Citric Acid pH 4.0, 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 FIELDBright-field microscopy / Nominal magnification: 50000 X
Image recordingElectron dose: 15 e/Å2

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Processing

EM software
IDNameCategory
1CNSmodel fitting
2Omodel fitting
3OTHER3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionNominal pixel size: 1.4 Å
Details: THE ENTIRE STRUCTURE WAS MODELED AS ALA AND GLY. THE MISSING ATOMS ARE SUPPRESSED DUE TO TOO MANY TO LIST. RESIDUES 159 to 172 IN CHAIN G WERE DELETED DUE TO DISORDER.
Symmetry type: POINT
Atomic model buildingB value: 374 / Protocol: RIGID BODY FIT / Space: RECIPROCAL
Target criteria: vector reciprocal space target and manual correction with O
Details: METHOD--Rigid body and manual fitting REFINEMENT PROTOCOL--rigid body, magnification optimized using van der Waals constraints and real-space correlation coefficient
Atomic model buildingPDB-ID: 2FSY
Accession code: 2FSY / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms9392 0 0 0 9392

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