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- PDB-2fsy: Bacteriophage HK97 Pepsin-treated Expansion Intermediate IV -

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Basic information

Entry
Database: PDB / ID: 2fsy
TitleBacteriophage HK97 Pepsin-treated Expansion Intermediate IV
Componentsmajor capsid protein
KeywordsVIRUS / Bacteriophage / HK97 / capsid protein / expansion intermediate / icosahedral VIRUS
Function / homology
Function and homology information


viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding
Similarity search - Function
Major capsid protein gp5 / hypothetical protein PF0899 domain / Major capsid protein gp5 fold / hypothetical protein PF0899 fold / Phage capsid / Phage capsid family / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major capsid protein
Similarity search - Component
Biological speciesEnterobacteria phage HK97 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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 23, 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 / cell ...atom_site / 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 / _cell.Z_PDB / _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)1006.394, 1006.394, 728.693
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(0.65447776, -0.33645526, -0.67709473), (-0.35446579, 0.65447727, -0.66784212), (0.66784223, 0.67709436, 0.30907895)106.78404, 109.6042, -210.59017
3generate(0.09541056, -0.89886183, -0.42772018), (-0.90999296, 0.09541026, -0.40349651), (0.40349707, 0.42771945, -0.8088548)282.3844, 284.12736, -130.15188
4generate(0.09541026, -0.90999296, 0.40349651), (-0.89886183, 0.09541056, 0.42772018), (-0.42771945, -0.40349707, -0.8088548)284.12736, 282.3844, 130.15188
5generate(0.65447727, -0.35446579, 0.66784212), (-0.33645526, 0.65447776, 0.67709473), (-0.67709436, -0.66784223, 0.30907895)109.6042, 106.78404, 210.59017
6generate(-0.28490198, -0.71509802, -0.63833049), (-0.71509802, -0.28490198, 0.63833049), (-0.63833029, 0.63833029, -0.43019604)313.16, 313.16
7generate(-0.35928828, -0.80436861, 0.47318369), (0.05927632, 0.48634659, 0.87175316), (-0.93134231, 0.34125894, -0.12705831)338.7854, 71.14636, 92.39525
8generate(0.36598703, -0.08516654, 0.92671455), (0.44859538, 0.88861811, -0.09549787), (-0.81536236, 0.45067078, 0.36342884)112.60913, -52.80089, 57.10341
9generate(0.88861811, 0.44859538, 0.09549787), (-0.08516654, 0.36598703, -0.92671455), (-0.45067078, 0.81536236, 0.36342884)-52.80089, 112.60913, -57.10341
10generate(0.48634659, 0.05927632, -0.87175316), (-0.80436861, -0.35928828, -0.47318369), (-0.34125894, 0.93134231, -0.12705831)71.14636, 338.7854, -92.39525
11generate(0.91538234, -0.38162012, 0.12822347), (-0.06974737, -0.46401485, -0.88307744), (0.39649808, 0.79941003, -0.45136749)73.00351, 240.15649, -187.25529
12generate(0.8200017, -0.47092752, -0.3253074), (-0.47092712, -0.87814706, 0.08417359), (-0.32530661, 0.08417345, -0.94185464)101.92196, 367.81804, 37.75663
13generate(0.48634656, -0.80436905, -0.34125928), (0.05927645, -0.35928793, 0.93134215), (-0.87175286, -0.47318373, -0.12705862)206.37596, 203.5558, 210.59017
14generate(0.37551696, -0.92113987, 0.10241278), (0.78814003, 0.37551686, 0.48767009), (-0.48767053, -0.10241284, 0.86700016)242.01364, -25.6254, 92.39525
15generate(0.64067565, -0.65986665, 0.39256908), (0.70839893, 0.31079207, -0.63370289), (0.29615165, 0.68409335, 0.66656625)159.58493, -3.00493, -153.48676
16generate(-0.46401485, -0.06974737, 0.88307744), (-0.38162012, 0.91538234, -0.12822347), (-0.79941003, -0.39649808, -0.45136749)240.15649, 73.00351, 187.25529
17generate(0.31079207, 0.70839893, 0.63370289), (-0.65986665, 0.64067565, -0.39256908), (-0.68409335, -0.29615165, 0.66656625)-3.00493, 159.58493, 153.48676
18generate(0.37551686, 0.78814003, -0.48767009), (-0.92113987, 0.37551696, -0.10241278), (0.10241284, 0.48767053, 0.86700016)-25.6254, 242.01364, -92.39525
19generate(-0.35928793, 0.05927645, -0.93134215), (-0.80436905, 0.48634656, 0.34125928), (0.47318373, 0.87175286, -0.12705862)203.5558, 206.37596, -210.59017
20generate(-0.87814706, -0.47092712, -0.08417359), (-0.47092752, 0.8200017, 0.3253074), (-0.08417345, 0.32530661, -0.94185464)367.81804, 101.92196, -37.75663
21generate(0.91538219, -0.06974779, 0.39649772), (-0.3816202, -0.46401419, 0.79941025), (0.12822425, -0.88307748, -0.451368)24.17057, 288.98943, 118.19492
22generate(0.88861841, -0.08516713, -0.45067085), (0.44859515, 0.36598755, 0.81536213), (0.09549806, -0.92671459, 0.36342802)30.7756, 29.03264, 130.15188
23generate(0.31079279, -0.65986698, -0.68409352), (0.70839874, 0.64067544, -0.29615205), (0.63370257, -0.39256941, 0.66656575)211.23804, -54.65804, -37.75663
24generate(-0.0195593, -0.99963169, 0.0188119), (0.03875085, -0.01955985, -0.99905747), (0.99905742, -0.01881242, 0.03911915)316.16493, 153.57507, -153.48676
25generate(0.35409749, -0.63491797, 0.68665401), (-0.63491791, -0.70229558, -0.32196273), (0.68665465, -0.32196306, -0.6518019)200.55087, 365.96089, -57.10341
26generate(-0.46401419, -0.3816202, -0.79941025), (-0.06974779, 0.91538219, -0.39649772), (0.88307748, -0.12822425, -0.451368)288.98943, 24.17057, -118.19492
27generate(-0.70229558, -0.63491791, 0.32196273), (-0.63491797, 0.35409749, -0.68665401), (0.32196306, -0.68665465, -0.6518019)365.96089, 200.55087, 57.10341
28generate(-0.01955985, 0.03875085, 0.99905747), (-0.99963169, -0.0195593, -0.0188119), (0.01881242, -0.99905742, 0.03911915)153.57507, 316.16493, 153.48676
29generate(0.64067544, 0.70839874, 0.29615205), (-0.65986698, 0.31079279, 0.68409352), (0.39256941, -0.63370257, 0.66656575)-54.65804, 211.23804, 37.75663
30generate(0.36598755, 0.44859515, -0.81536213), (-0.08516713, 0.88861841, 0.45067085), (0.92671459, -0.09549806, 0.36342802)29.03264, 30.7756, -130.15188

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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: 5.2
Details: 100mM Sodium Citrate pH 3.5, 400mM Magnesium Acetate Hexahydrate, 25% 1,6-Hexanediol, pH 5.2, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111.181
SYNCHROTRONAPS 23-ID-D20.626
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMay 31, 2004
MARMOSAIC 300 mm CCD2CCDJul 22, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.1811
20.6261
ReflectionResolution: 3.8→50 Å / Num. obs: 2144154 / % possible obs: 59.9 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -1.5 / Rmerge(I) obs: 0.17 / Χ2: 1.847 / Net I/σ(I): 5.5
Reflection shellResolution: 3.8→3.87 Å / % possible obs: 26.7 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 48089 / Χ2: 1.453 / % possible all: 44.1

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Processing

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

1ohg


Resolution: 3.8→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.337 --
all0.337 --
Rfree-0 -
obs-2144154 59.9 %
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 98.385 Å2
Baniso -1Baniso -2Baniso -3
1-23.526 Å20 Å20 Å2
2--23.526 Å20 Å2
3----47.051 Å2
Refinement stepCycle: LAST / Resolution: 3.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14631 0 0 0 14631
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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