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- PDB-2fs3: Bacteriophage HK97 K169Y Head I -

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Basic information

Entry
Database: PDB / ID: 2fs3
TitleBacteriophage HK97 K169Y Head I
ComponentsMajor capsid protein
KeywordsVIRUS / Bacteriophage / HK97 / capsid / 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: 4.2 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 20, 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 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / 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 / _cell.Z_PDB / _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)215,8707
Polymers215,8707
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)12,952,212420
Polymers12,952,212420
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)1,079,35135
Polymers1,079,35135
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
  • 1.3 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,295,22142
Polymers1,295,22142
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
  • 6.48 MDa, 210 polymers
Theoretical massNumber of molelcules
Total (without water)6,476,106210
Polymers6,476,106210
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)1009.643, 1009.643, 729.812
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(0.65447299, -0.33578672, -0.67743126), (-0.35512486, 0.65447257, -0.66749672), (0.66749646, 0.67743056, 0.30908842)107.17535, 110.21744, -211.5663
3generate(0.09539814, -0.89843918, -0.42861009), (-0.91039082, 0.09539788, -0.40260112), (0.4026014, 0.42860922, -0.80883001)283.6308, 285.51091, -130.75517
4generate(0.09539788, -0.91039082, 0.40260112), (-0.89843918, 0.09539814, 0.42861009), (-0.42860922, -0.4026014, -0.80883001)285.51091, 283.6308, 130.75517
5generate(0.65447257, -0.35512486, 0.66749672), (-0.33578672, 0.65447299, 0.67743126), (-0.67743056, -0.66749646, 0.30908842)110.21744, 107.17535, 211.5663
6generate(-0.2855323, -0.7144677, -0.63875422), (-0.7144677, -0.2855323, 0.63875422), (-0.63875462, 0.63875462, -0.42893541)314.6138, 314.6138
7generate(-0.35951411, -0.80443319, 0.47290182), (0.06016599, 0.48574734, 0.87202616), (-0.93119816, 0.34195874, -0.12623323)340.40384, 71.43097, 92.69143
8generate(0.36604225, -0.08540125, 0.9266711), (0.44895043, 0.88844255, -0.09545989), (-0.81514234, 0.45097234, 0.36354918)113.16014, -53.07424, 57.28645
9generate(0.88844255, 0.44895043, 0.09545989), (-0.08540125, 0.36604225, -0.9266711), (-0.45097234, 0.81514234, 0.36354918)-53.07424, 113.16014, -57.28645
10generate(0.48574734, 0.06016599, -0.87202616), (-0.80443319, -0.35951411, -0.47290182), (-0.34195874, 0.93119816, -0.12623323)71.43097, 340.40384, -92.69143
11generate(0.91564104, -0.3812891, 0.12736019), (-0.07037826, -0.46397369, -0.88304889), (0.39578852, 0.79959209, -0.45166735)73.24965, 241.36415, -188.04162
12generate(0.81968004, -0.47072567, -0.32640908), (-0.47072409, -0.87823028, 0.08443716), (-0.32640849, 0.08443729, -0.94144976)102.41397, 369.50673, 38.06374
13generate(0.48574794, -0.80443421, -0.34195832), (0.06016672, -0.35951443, 0.9311976), (-0.87202571, -0.47290132, -0.12623352)207.43845, 204.39636, 211.5663
14generate(0.37532753, -0.92124086, 0.10220101), (0.7886211, 0.3753262, 0.48703827), (-0.48703868, -0.10220074, 0.86738024)243.18283, -25.79004, 92.69143
15generate(0.64101607, -0.65972279, 0.3922558), (0.70793988, 0.31076683, -0.63422772), (0.2965136, 0.68424344, 0.66625107)160.2496, -2.9427, -154.27985
16generate(-0.46397369, -0.07037826, 0.88304889), (-0.3812891, 0.91564104, -0.12736019), (-0.79959209, -0.39578852, -0.45166735)241.36415, 73.24965, 188.04162
17generate(0.31076683, 0.70793988, 0.63422772), (-0.65972279, 0.64101607, -0.3922558), (-0.68424344, -0.2965136, 0.66625107)-2.9427, 160.2496, 154.27985
18generate(0.3753262, 0.7886211, -0.48703827), (-0.92124086, 0.37532753, -0.10220101), (0.10220074, 0.48703868, 0.86738024)-25.79004, 243.18283, -92.69143
19generate(-0.35951443, 0.06016672, -0.9311976), (-0.80443421, 0.48574794, 0.34195832), (0.47290132, 0.87202571, -0.12623352)204.39636, 207.43845, -211.5663
20generate(-0.87823028, -0.47072409, -0.08443716), (-0.47072567, 0.81968004, 0.32640908), (-0.08443729, 0.32640849, -0.94144976)369.50673, 102.41397, -38.06374
21generate(0.91564068, -0.07037964, 0.39578869), (-0.38128817, -0.46397286, 0.79959242), (0.12736157, -0.88304918, -0.45166781)24.34151, 290.27229, 118.87488
22generate(0.8884432, -0.08540216, -0.45097174), (0.4489506, 0.36604234, 0.81514165), (0.09546076, -0.92667137, 0.36354843)30.983, 29.10289, 130.75517
23generate(0.31076847, -0.65972285, -0.68424368), (0.70793948, 0.64101489, -0.29651439), (0.63422783, -0.39225664, 0.66625061)212.19983, -54.89293, -38.06374
24generate(-0.01905668, -0.99965003, 0.01834677), (0.03776463, -0.01905792, -0.99910484), (0.999105, -0.01834796, 0.0381146)317.5565, 154.3642, -154.27985
25generate(0.3547749, -0.63541589, 0.68584348), (-0.63541507, -0.70197791, -0.32167358), (0.68584442, -0.32167443, -0.65279698)201.45366, 367.68804, -57.28645
26generate(-0.46397286, -0.38128817, -0.79959242), (-0.07037964, 0.91564068, -0.39578869), (0.88304918, -0.12736157, -0.45166781)290.27229, 24.34151, -118.87488
27generate(-0.70197791, -0.63541507, 0.32167358), (-0.63541589, 0.3547749, -0.68584348), (0.32167443, -0.68584442, -0.65279698)367.68804, 201.45366, 57.28645
28generate(-0.01905792, 0.03776463, 0.99910484), (-0.99965003, -0.01905668, -0.01834677), (0.01834796, -0.999105, 0.0381146)154.3642, 317.5565, 154.27985
29generate(0.64101489, 0.70793948, 0.29651439), (-0.65972285, 0.31076847, 0.68424368), (0.39225664, -0.63422783, 0.66625061)-54.89293, 212.19983, 38.06374
30generate(0.36604234, 0.4489506, -0.81514165), (-0.08540216, 0.8884432, 0.45097174), (0.92667137, -0.09546076, 0.36354843)29.10289, 30.983, -130.75517

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Components

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


Mass: 30838.600 Da / Num. of mol.: 7 / Mutation: K169Y
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-K169Y / 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: 5

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 100mM Sodium Cacodylate, 300mM Magnesium Acetate Hexahydrate, 25% 1,6-Hexanediol, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C10.9
SYNCHROTRONAPS 23-ID-D20.689
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 23, 2003
MARMOSAIC 225 mm CCD2CCDDec 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.6891
ReflectionResolution: 4.2→30 Å / Num. obs: 1679512 / % possible obs: 63 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -1.5 / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.162 / Χ2: 1.006 / Net I/σ(I): 4.1
Reflection shellResolution: 4.2→4.27 Å / % possible obs: 21.8 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 28999 / Χ2: 0.934 / % possible all: 21.8

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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: 4.2→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.384 --
all0.384 --
obs0.384 1679512 63.1 %
Rfree--0 %
Solvent computationBsol: 64.826 Å2
Displacement parametersBiso mean: 80.999 Å2
Baniso -1Baniso -2Baniso -3
1-19.939 Å20 Å20 Å2
2--19.939 Å20 Å2
3----39.878 Å2
Refinement stepCycle: LAST / Resolution: 4.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14664 0 0 0 14664
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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