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

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Basic information

Entry
Database: PDB / ID: 2frp
TitleBacteriophage HK97 Expansion Intermediate IV
ComponentsMajor capsid protein
KeywordsVIRUS / Bacteriophage / HK97 / Capsid Protein / Expansion Intermediate / icosahedral VIRUS
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.5 Å
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.
CitationJournal: 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.
History
DepositionJan 19, 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 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / cell / database_2 / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
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 30


  • crystal asymmetric unit, crystal frame
  • 6.47 MDa, 210 polymers
Theoretical massNumber of molelcules
Total (without water)6,468,967210
Polymers6,468,967210
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)1008.967, 1008.967, 728.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.65450308, -0.34145899, -0.67456151), (-0.34951162, 0.65450152, -0.67042375), (0.67042426, 0.67456041, 0.30902938)107.70026, 108.96299, -210.86535
3generate(0.09547577, -0.90200387, -0.42103969), (-0.90698068, 0.09547481, -0.41020691), (0.41020883, 0.42103741, -0.80898456)283.22567, 284.00608, -130.32195
4generate(0.09547481, -0.90698068, 0.41020691), (-0.90200387, 0.09547577, 0.42103969), (-0.42103741, -0.41020883, -0.80898456)284.00608, 283.22567, 130.32195
5generate(0.65450152, -0.34951162, 0.67042375), (-0.34145899, 0.65450308, 0.67456151), (-0.67456041, -0.67042426, 0.30902938)108.96299, 107.70026, 210.86535
6generate(-0.28018776, -0.71981224, -0.63511138), (-0.71981224, -0.28018776, 0.63511138), (-0.63510932, 0.63510932, -0.43962448)313.558, 313.558
7generate(-0.35759508, -0.80386656, 0.47531502), (0.05260363, 0.49082404, 0.86967024), (-0.93239401, 0.33599053, -0.13322895)338.8718, 71.58095, 93.50354
8generate(0.36557636, -0.08339914, 0.92703743), (0.44592855, 0.8899282, -0.09579082), (-0.81700729, 0.44840966, 0.36252942)112.53954, -52.65529, 57.78837
9generate(0.8899282, 0.44592855, 0.09579082), (-0.08339914, 0.36557636, -0.92703743), (-0.44840966, 0.81700729, 0.36252942)-52.65529, 112.53954, -57.78837
10generate(0.49082404, 0.05260363, -0.86967024), (-0.80386656, -0.35759508, -0.47531502), (-0.33599053, 0.93239401, -0.13322895)71.58095, 338.8718, -93.50354
11generate(0.91341804, -0.38408939, 0.13469227), (-0.06500063, -0.46432803, -0.88327576), (0.40179995, 0.79804392, -0.44909001)73.79138, 239.76662, -188.11032
12generate(0.82237959, -0.47242382, -0.31703014), (-0.47242457, -0.8775312, 0.0821853), (-0.31702716, 0.0821844, -0.94484839)101.91328, 368.42372, 36.81841
13generate(0.49082291, -0.80386699, -0.3359931), (0.05260305, -0.35759295, 0.93239486), (-0.86966895, -0.47531572, -0.13322997)205.85774, 204.59501, 210.86535
14generate(0.37694805, -0.92037572, 0.10400955), (0.78451189, 0.37694975, 0.49239221), (-0.49239323, -0.10401025, 0.86413617)241.97705, -25.3138, 93.50354
15generate(0.6381262, -0.66093888, 0.3949091), (0.71182882, 0.31098385, -0.62975394), (0.29341775, 0.68296929, 0.66892393)160.35555, -3.57655, -153.07698
16generate(-0.46432803, -0.06500063, 0.88327576), (-0.38408939, 0.91341804, -0.13469227), (-0.79804392, -0.40179995, -0.44909001)239.76662, 73.79138, 188.11032
17generate(0.31098385, 0.71182882, 0.62975394), (-0.66093888, 0.6381262, -0.3949091), (-0.68296929, -0.29341775, 0.66892393)-3.57655, 160.35555, 153.07698
18generate(0.37694975, 0.78451189, -0.49239221), (-0.92037572, 0.37694805, -0.10400955), (0.10401025, 0.49239323, 0.86413617)-25.3138, 241.97705, -93.50354
19generate(-0.35759295, 0.05260305, -0.93239486), (-0.80386699, 0.49082291, 0.3359931), (0.47531572, 0.86966895, -0.13322997)204.59501, 205.85774, -210.86535
20generate(-0.8775312, -0.47242457, -0.0821853), (-0.47242382, 0.82237959, 0.31703014), (-0.0821844, 0.31702716, -0.94484839)368.42372, 101.91328, -36.81841
21generate(0.91341793, -0.06500036, 0.40179824), (-0.38409129, -0.46432628, 0.79804493), (0.13469362, -0.88327481, -0.44909166)23.76494, 289.79306, 117.36181
22generate(0.88992852, -0.08340042, -0.44841133), (0.44592719, 0.36557869, 0.81700789), (0.09579027, -0.9270365, 0.36252676)30.33233, 29.55192, 130.32195
23generate(0.31098454, -0.66094032, -0.68297018), (0.71182863, 0.63812714, -0.29341851), (0.62975181, -0.39490905, 0.66892229)211.64472, -54.86572, -36.81841
24generate(-0.02333311, -0.99947957, 0.02227404), (0.04614629, -0.02333361, -0.99866273), (0.99866154, -0.0222745, 0.04666671)317.13455, 153.20245, -153.07698
25generate(0.34899119, -0.63116841, 0.69269779), (-0.63116947, -0.70468729, -0.32410122), (0.69269876, -0.32410113, -0.6443039)201.01846, 366.21329, -57.78837
26generate(-0.46432628, -0.38409129, -0.79804493), (-0.06500036, 0.91341793, -0.40179824), (0.88327481, -0.13469362, -0.44909166)289.79306, 23.76494, -117.36181
27generate(-0.70468729, -0.63116947, 0.32410122), (-0.63116841, 0.34899119, -0.69269779), (0.32410113, -0.69269876, -0.6443039)366.21329, 201.01846, 57.78837
28generate(-0.02333361, 0.04614629, 0.99866273), (-0.99947957, -0.02333311, -0.02227404), (0.0222745, -0.99866154, 0.04666671)153.20245, 317.13455, 153.07698
29generate(0.63812714, 0.71182863, 0.29341851), (-0.66094032, 0.31098454, 0.68297018), (0.39490905, -0.62975181, 0.66892229)-54.86572, 211.64472, 36.81841
30generate(0.36557869, 0.44592719, -0.81700789), (-0.08340042, 0.88992852, 0.44841133), (0.9270365, -0.09579027, 0.36252676)29.55192, 30.33233, -130.32195

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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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 50mM Citric Acid pH 4.0, 0.2M Magnesium Acetate Hexahydrate, 0.1M KCl, 25% MPD, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.18076 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 7.5→40 Å / Num. obs: 306300 / % possible obs: 65 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): -1.5 / Rmerge(I) obs: 0.201 / Χ2: 1.589
Reflection shellResolution: 7.5→7.63 Å / % possible obs: 20.6 % / Rmerge(I) obs: 0.258 / Num. unique obs: 4813 / Χ2: 1.54 / % possible all: 20.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
Blu-Icedata collection
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OHG

1ohg


Resolution: 7.5→40 Å / σ(F): 0 / Stereochemistry target values: vector
RfactorNum. reflection% reflection
Rwork0.421 --
obs0.421 305895 64.7 %
Rfree-0 0 %
all-305895 -
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 60.177 Å2
Refinement stepCycle: LAST / Resolution: 7.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14631 0 0 0 14631
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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