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- PDB-6qwp: Crystal structure of T7 bacteriophage portal protein, 13mer, clos... -

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Basic information

Entry
Database: PDB / ID: 6qwp
TitleCrystal structure of T7 bacteriophage portal protein, 13mer, closed valve
ComponentsPortal protein
KeywordsVIRAL PROTEIN / DNA packaging
Function / homologyPortal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / Portal protein
Function and homology information
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsFabrega-Ferrer, M. / Cuervo, A. / Machon, C. / Fernandez, F.J. / Perez-Luque, R. / Pous, J. / Vega, M.C. / Carrascosa, J.L. / Coll, M.
Funding support Spain, 7items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU 2014-54181 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2014-53550-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-83720-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
Spanish Ministry of Science, Innovation, and UniversitiesSEV-2013-0347 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2011-09071 Spain
European Commission653706
CitationJournal: Nat Commun / Year: 2019
Title: Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism.
Authors: Ana Cuervo / Montserrat Fàbrega-Ferrer / Cristina Machón / José Javier Conesa / Francisco J Fernández / Rosa Pérez-Luque / Mar Pérez-Ruiz / Joan Pous / M Cristina Vega / José L Carrascosa / Miquel Coll /
Abstract: Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been ...Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been packaged, the tail components assemble on the portal to render the mature infective virion. The tail tightly seals the ejection conduit until infection, when its interaction with the host membrane triggers the opening of the channel and the viral genome is delivered to the host cell. Using high-resolution cryo-electron microscopy and X-ray crystallography, here we describe various structures of the T7 bacteriophage portal and fiber-less tail complex, which suggest a possible mechanism for DNA retention and ejection: a portal closed conformation temporarily retains the genome before the tail is assembled, whereas an open portal is found in the tail. Moreover, a fold including a seven-bladed β-propeller domain is described for the nozzle tail protein.
History
DepositionMar 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein
M: Portal protein


Theoretical massNumber of molelcules
Total (without water)785,95913
Polymers785,95913
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)261.570, 261.570, 256.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
12A
22B
32C
42D
52F
62G
72H
82I
92J
102K
112L
122M

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 92
2112B1 - 92
3112C1 - 92
4112D1 - 92
5112E1 - 92
6112F1 - 92
7112G1 - 92
8112H1 - 92
9112I1 - 92
10112J1 - 92
11112K1 - 92
12112L1 - 92
13112M1 - 92
1214A104 - 303
2214B104 - 303
3214C104 - 303
4214D104 - 303
5214E104 - 303
6214F104 - 303
7214G104 - 303
8214H104 - 303
9214I104 - 303
10214J104 - 303
11214K104 - 303
12214L104 - 303
13214M104 - 303
1314A314 - 500
2314B314 - 500
3314C314 - 500
4314D314 - 500
5314E314 - 500
6314F314 - 500
7314G314 - 500
8314H314 - 500
9314I314 - 500
10314J314 - 500
11314K314 - 500
12314L314 - 500
13314M314 - 500
1122A93 - 103
2122B93 - 103
3122C93 - 103
4122D93 - 103
5122F93 - 103
6122G93 - 103
7122H93 - 103
8122I93 - 103
9122J93 - 103
10122K93 - 103
11122L93 - 103
12122M93 - 103

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.954145, -0.05946, -0.293381), (-0.052006, 0.932242, -0.358078), (0.294794, 0.356916, 0.886402)116.18602, 140.10556, -97.05845
3given(0.827134, -0.222098, -0.516257), (-0.199893, 0.742269, -0.639593), (0.525254, 0.632226, 0.56956)248.10345, 301.10437, -98.57867
4given(0.64378, -0.44693, -0.621129), (-0.414653, 0.478455, -0.774044), (0.643125, 0.755867, 0.122699)365.44907, 443.04828, -2.22337
5given(0.457485, -0.674471, -0.579479), (-0.644027, 0.198023, -0.738929), (0.613136, 0.711249, -0.343785)437.35211, 536.94165, 163.9929
6given(0.304153, -0.864567, -0.400018), (-0.843055, -0.048769, -0.535611), (0.443564, 0.500145, -0.743711)450.75372, 563.2674, 371.12442
7given(0.217575, -0.967652, -0.127713), (-0.95965, -0.188201, -0.20893), (0.178136, 0.168018, -0.969555)402.0174, 510.3931, 567.24438
8given(0.213495, -0.959822, 0.182106), (-0.969271, -0.184789, 0.162378), (-0.122203, -0.211177, -0.969779)299.97961, 390.45444, 708.25879
9given(0.295282, -0.845755, 0.444417), (-0.870314, -0.046206, 0.490326), (-0.394161, -0.531566, -0.749716)174.03224, 234.27484, 757.73212
10given(0.451852, -0.651342, 0.609576), (-0.68254, 0.187578, 0.706366), (-0.574429, -0.735233, -0.35981)48.79412, 78.0159, 709.39874
11given(0.640234, -0.421326, 0.642328), (-0.449871, 0.472134, 0.758093), (-0.622669, -0.774322, 0.112734)-47.5732, -44.78502, 573.35229
12given(0.822419, -0.206948, 0.529905), (-0.222147, 0.740699, 0.634047), (-0.523715, -0.639169, 0.563192)-91.90186, -105.82227, 379.01068
13given(0.953109, -0.053655, 0.297833), (-0.059735, 0.931439, 0.358961), (-0.296673, -0.35992, 0.884558)-75.18449, -89.29419, 171.64975
14given(1), (1), (1)
15given(0.953547, -0.055809, -0.296029), (-0.057956, 0.930345, -0.362076), (0.295616, 0.362413, 0.883893)115.54377, 141.90102, -98.35442
16given(0.827652, -0.217543, -0.517365), (-0.20681, 0.738744, -0.641472), (0.521748, 0.637912, 0.566433)246.832, 302.76138, -99.66563
17given(0.640373, -0.447507, -0.624227), (-0.431557, 0.462664, -0.774403), (0.635359, 0.765297, 0.103153)366.51352, 448.04932, 0.20696
18given(0.308881, -0.860283, -0.405592), (-0.850381, -0.058811, -0.522871), (0.425964, 0.506413, -0.749734)451.39429, 561.9967, 370.80103
19given(0.212524, -0.968248, -0.131643), (-0.962408, -0.18409, -0.199704), (0.169129, 0.169136, -0.970973)403.59769, 505.6283, 567.26678
20given(0.206268, -0.961571, 0.181202), (-0.968803, -0.174692, 0.175793), (-0.137383, -0.211809, -0.967607)300.99667, 381.80533, 707.74463
21given(0.288347, -0.848681, 0.443392), (-0.86795, -0.036105, 0.495338), (-0.404375, -0.527671, -0.747023)175.65697, 228.5235, 755.49146
22given(0.446761, -0.651791, 0.612841), (-0.676591, 0.202027, 0.708103), (-0.585345, -0.730995, -0.350738)47.93676, 71.45512, 704.84131
23given(0.637482, -0.420272, 0.645746), (-0.447371, 0.480451, 0.754338), (-0.627277, -0.769765, 0.118261)-49.02803, -47.00481, 569.83514
24given(0.821762, -0.200309, 0.533464), (-0.222842, 0.748657, 0.624384), (-0.524451, -0.631973, 0.57058)-95.6636, -106.02158, 373.78186
25given(0.953703, -0.046677, 0.297107), (-0.065168, 0.932339, 0.355664), (-0.293606, -0.35856, 0.886132)-77.72601, -88.45371, 170.53725

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Components

#1: Protein
Portal protein / Gene product 8 / Gp8 / Head-to-tail connector


Mass: 60458.387 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03728

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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

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15 % tacsimate, 0.1 M HEPES pH 7.0, 12 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0679 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0679 Å / Relative weight: 1
ReflectionResolution: 3.4→58.56 Å / Num. obs: 110605 / % possible obs: 95.7 % / Redundancy: 3.4 % / CC1/2: 0.969 / Rmerge(I) obs: 0.025 / Net I/σ(I): 5.9
Reflection shellResolution: 3.4→3.52 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→58.56 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.856 / SU B: 40.024 / SU ML: 0.586 / Cross valid method: THROUGHOUT / ESU R Free: 0.647 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27534 5822 5 %RANDOM
Rwork0.22977 ---
obs0.23203 110605 95.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 81.824 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0 Å2
2--0.18 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 3.4→58.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49530 0 0 0 49530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01450284
X-RAY DIFFRACTIONr_bond_other_d0.0010.01746072
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.65968016
X-RAY DIFFRACTIONr_angle_other_deg0.8741.629108290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01156292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37322.7752717
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.642159178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.75215377
X-RAY DIFFRACTIONr_chiral_restr0.0590.26604
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0256563
X-RAY DIFFRACTIONr_gen_planes_other0.0020.028385
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8288.32425246
X-RAY DIFFRACTIONr_mcbond_other4.8278.32325245
X-RAY DIFFRACTIONr_mcangle_it8.03812.47331512
X-RAY DIFFRACTIONr_mcangle_other8.03812.47331513
X-RAY DIFFRACTIONr_scbond_it4.4618.65825038
X-RAY DIFFRACTIONr_scbond_other4.4618.65725036
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.68112.81536504
X-RAY DIFFRACTIONr_long_range_B_refined11.73197.28855289
X-RAY DIFFRACTIONr_long_range_B_other11.73197.29155290
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A6538medium positional0.170.5
11B6538medium positional0.150.5
11C6538medium positional0.140.5
11D6538medium positional0.180.5
11E6538medium positional0.190.5
11F6538medium positional0.140.5
11G6538medium positional0.140.5
11H6538medium positional0.140.5
11I6538medium positional0.160.5
11J6538medium positional0.160.5
11K6538medium positional0.160.5
11L6538medium positional0.150.5
11M6538medium positional0.170.5
22A95medium positional0.020.5
22B95medium positional0.020.5
22C95medium positional0.020.5
22D95medium positional0.020.5
22F95medium positional0.020.5
22G95medium positional0.020.5
22H95medium positional0.020.5
22I95medium positional0.020.5
22J95medium positional0.010.5
22K95medium positional0.010.5
22L95medium positional0.020.5
22M95medium positional0.020.5
11A495tight thermal9.560.5
11B495tight thermal12.010.5
11C495tight thermal8.440.5
11D495tight thermal6.980.5
11E495tight thermal7.450.5
11F495tight thermal6.740.5
11G495tight thermal5.570.5
11H495tight thermal4.850.5
11I495tight thermal6.970.5
11J495tight thermal9.990.5
11K495tight thermal12.380.5
11L495tight thermal7.270.5
11M495tight thermal6.610.5
22A64tight thermal10.790.5
22B64tight thermal6.740.5
22C64tight thermal23.980.5
22D64tight thermal15.790.5
22F64tight thermal16.150.5
22G64tight thermal11.470.5
22H64tight thermal11.780.5
22I64tight thermal7.270.5
22J64tight thermal11.050.5
22K64tight thermal19.770.5
22L64tight thermal11.010.5
22M64tight thermal11.860.5
11A6538medium thermal11.972
11B6538medium thermal10.12
11C6538medium thermal8.832
11D6538medium thermal8.292
11E6538medium thermal10.082
11F6538medium thermal7.572
11G6538medium thermal7.832
11H6538medium thermal7.492
11I6538medium thermal7.82
11J6538medium thermal11.442
11K6538medium thermal11.652
11L6538medium thermal8.352
11M6538medium thermal7.512
22A95medium thermal9.612
22B95medium thermal7.132
22C95medium thermal20.412
22D95medium thermal13.222
22F95medium thermal14.112
22G95medium thermal11.712
22H95medium thermal10.012
22I95medium thermal12.782
22J95medium thermal15.492
22K95medium thermal17.112
22L95medium thermal10.952
22M95medium thermal15.962
LS refinement shellResolution: 3.401→3.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 434 -
Rwork0.367 8241 -
obs--97.22 %

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