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- PDB-6qx5: Crystal structure of T7 bacteriophage portal protein, 12mer, clos... -

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Basic information

Entry
Database: PDB / ID: 6qx5
TitleCrystal structure of T7 bacteriophage portal protein, 12mer, 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: 3.6 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 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)656,86712
Polymers656,86712
Non-polymers00
Water0
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)165.850, 191.330, 260.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
12A
22C
32D
42E
52F
62G
72H
82I
92J
102K
112L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 149
2111B1 - 149
3111C1 - 149
4111D1 - 149
5111E1 - 149
6111F1 - 149
7111G1 - 149
8111H1 - 149
9111I1 - 149
10111J1 - 149
11111K1 - 149
12111L1 - 149
1211A156 - 197
2211B156 - 197
3211C156 - 197
4211D156 - 197
5211E156 - 197
6211F156 - 197
7211G156 - 197
8211H156 - 197
9211I156 - 197
10211J156 - 197
11211K156 - 197
12211L156 - 197
1311A206 - 308
2311B206 - 308
3311C206 - 308
4311D206 - 308
5311E206 - 308
6311F206 - 308
7311G206 - 308
8311H206 - 308
9311I206 - 308
10311J206 - 308
11311K206 - 308
12311L206 - 308
1411A310 - 600
2411B310 - 600
3411C310 - 600
4411D310 - 600
5411E310 - 600
6411F310 - 600
7411G310 - 600
8411H310 - 600
9411I310 - 600
10411J310 - 600
11411K310 - 600
12411L310 - 600
1121A150 - 155
2121C150 - 155
3121D150 - 155
4121E150 - 155
5121F150 - 155
6121G150 - 155
7121H150 - 155
8121I150 - 155
9121J150 - 155
10121K150 - 155
11121L150 - 155

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.866658, -0.314873, -0.386987), (0.316918, 0.946527, -0.060405), (0.385313, -0.070292, 0.920105)13.74574, 16.27501, 20.04833
3given(0.503067, -0.545413, -0.670409), (0.55518, 0.798436, -0.232969), (0.662343, -0.254999, 0.70447)12.68721, 34.74511, 42.40779
4given(0.005022, -0.621196, -0.783639), (0.650144, 0.597448, -0.469434), (0.759794, -0.507121, 0.406868)-2.46104, 50.51884, 61.28991
5given(-0.493664, -0.530624, -0.68901), (0.576277, 0.393763, -0.716139), (0.651307, -0.750593, 0.1114)-28.15008, 59.55662, 71.46659
6given(-0.862518, -0.290461, -0.414361), (0.352474, 0.242674, -0.903809), (0.363076, -0.925603, -0.106931)-57.19338, 59.38174, 69.97346
7given(-0.998896, 0.030493, -0.035742), (0.040795, 0.185596, -0.981779), (-0.023304, -0.982153, -0.186635)-81.3335, 50.21046, 57.67261
8given(-0.869102, 0.349556, 0.349961), (-0.280219, 0.235077, -0.930707), (-0.407602, -0.906945, -0.106354)-94.74227, 34.23911, 37.61187
9given(-0.51012, 0.57484, 0.639795), (-0.518418, 0.38806, -0.762006), (-0.68631, -0.720395, 0.10005)-93.88575, 16.10963, 16.24717
10given(-0.011922, 0.654879, 0.755639), (-0.615757, 0.590604, -0.521566), (-0.787846, -0.471509, 0.396205)-79.07475, 0.29867, -2.41777
11given(0.490327, 0.563553, 0.664821), (-0.540866, 0.794911, -0.27492), (-0.683405, -0.224779, 0.694573)-53.89626, -8.69461, -12.70981
12given(0.866311, 0.319159, 0.384242), (-0.314212, 0.946184, -0.077497), (-0.388298, -0.053597, 0.919974)-24.74512, -9.17865, -12.01938
13given(1), (1), (1)
14given(0.513734, -0.536098, -0.669834), (0.556463, 0.802451, -0.215454), (0.653013, -0.262052, 0.710565)13.68029, 34.91588, 41.47792
15given(0.002171, -0.620679, -0.784062), (0.654292, 0.593823, -0.46827), (0.756239, -0.511988, 0.407395)-2.74228, 50.83501, 60.78305
16given(-0.498561, -0.528886, -0.686816), (0.58102, 0.384109, -0.717549), (0.643314, -0.756796, 0.115792)-28.76484, 60.1029, 70.47677
17given(-0.858473, -0.291278, -0.422114), (0.356745, 0.252156, -0.899528), (0.368452, -0.922808, -0.112557)-56.32381, 59.33386, 70.64983
18given(-0.998746, 0.034656, -0.036132), (0.041995, 0.186971, -0.981467), (-0.027258, -0.981754, -0.188192)-81.46301, 50.27188, 57.46802
19given(-0.868671, 0.342706, 0.357721), (-0.284107, 0.246908, -0.926455), (-0.405826, -0.906416, -0.117117)-95.20092, 33.18712, 38.66594
20given(-0.500862, 0.577382, 0.6448), (-0.516525, 0.398384, -0.757953), (-0.694506, -0.712685, 0.098696)-94.32053, 15.41677, 15.97742
21given(-0.005539, 0.657855, 0.753124), (-0.617459, 0.590163, -0.52005), (-0.786584, -0.467903, 0.40293)-79.05041, 0.25389, -3.0531
22given(0.483504, 0.567749, 0.666247), (-0.539927, 0.792523, -0.283524), (-0.688987, -0.22264, 0.689731)-53.86355, -8.25709, -12.47769
23given(0.862169, 0.332095, 0.382594), (-0.326282, 0.941698, -0.082133), (-0.387564, -0.054021, 0.920259)-24.48246, -8.90699, -12.09084

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Components

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


Mass: 54738.953 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / 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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M CaCl2, 0.1 M sodium acetate pH 4.6 and 30 % (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.6→49.23 Å / Num. obs: 82010 / % possible obs: 89.7 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.9
Reflection shellResolution: 3.6→3.73 Å / Num. unique obs: 5972

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QWP

6qwp


Resolution: 3.6→49.23 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.88 / SU B: 212.101 / SU ML: 1.223 / Cross valid method: THROUGHOUT / ESU R Free: 0.942 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33441 4317 5 %RANDOM
Rwork0.28393 ---
obs0.28643 82010 89.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 181.058 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å2-0 Å2
2---5.49 Å20 Å2
3---6.53 Å2
Refinement stepCycle: LAST / Resolution: 3.6→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45048 0 0 0 45048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01345732
X-RAY DIFFRACTIONr_bond_other_d0.0030.01743332
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.64661872
X-RAY DIFFRACTIONr_angle_other_deg1.1521.572100608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37955724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05822.672472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.933158316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.05815348
X-RAY DIFFRACTIONr_chiral_restr0.0560.26012
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0251120
X-RAY DIFFRACTIONr_gen_planes_other0.0030.029060
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_it8.11912.71122968
X-RAY DIFFRACTIONr_mcbond_other8.11712.71122967
X-RAY DIFFRACTIONr_mcangle_it13.55419.05928668
X-RAY DIFFRACTIONr_mcangle_other13.55419.05928669
X-RAY DIFFRACTIONr_scbond_it6.86913.23622764
X-RAY DIFFRACTIONr_scbond_other6.8713.23622762
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.96419.65733204
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 / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A715919.07
11B715918.06
11C715918.67
11D715917.82
11E715920.31
11F715918.03
11G715920.31
11H715919.25
11I715918.86
11J715919.74
11K715918.99
11L715918.01
22A7823.87
22C7811.99
22D7818.47
22E7823.33
22F7818.53
22G7812.88
22H7813.74
22I7817.71
22J7820.95
22K7817.97
22L7821.44
LS refinement shellResolution: 3.603→3.697 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.556 220 -
Rwork0.492 4170 -
obs--62.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.96251.5512-0.76142.5842-1.22092.14260.27470.08970.0824-0.5048-0.2218-0.09760.31480.7857-0.05290.41410.21290.05550.3696-0.01870.7667-9.3999-34.081832.6472
22.07631.50220.38837.4818-1.56781.0834-0.18760.14880.1806-0.3213-0.2461-0.1213-0.19760.31940.43370.51380.03580.00320.52320.08730.575-9.634112.746829.2636
32.75221.1914-1.94961.6129-1.1153.57030.06260.4146-0.1654-0.7398-0.01530.10960.38390.2202-0.04730.56450.1967-0.16430.2025-0.04280.5967-31.1613-41.265323.5904
40.34490.12281.08837.15940.78523.8255-0.19720.12120.06070.12250.15670.1748-0.31330.32790.04050.50430.02460.14160.37370.11350.6609-17.84833.370917.7238
52.06480.5585-1.14241.5236-0.88492.92150.13750.4501-0.0138-0.80270.04340.41150.54250.0304-0.18090.57770.1057-0.3860.1333-0.00070.9207-55.7914-40.422823.966
66.1420.4338-0.28062.18032.63124.6326-0.60451.2660.603-0.8982-0.0213-0.1726-0.6856-0.08470.62580.94470.0353-0.04420.29270.14350.9813-32.1859-2.037210.8163
71.14850.2075-0.3691.0392-0.57523.94610.14480.37560.0875-0.36280.07050.51910.1993-0.2596-0.21540.28830.0136-0.37930.1380.04651.1634-76.8103-31.722433.4958
87.3888-0.35282.09570.16030.35442.07670.46191.65550.3322-0.115-0.0853-0.2114-0.29990.5041-0.37660.82310.0186-0.19520.38950.17830.9562-48.9467-1.860110.3419
91.2583-0.00820.77361.1077-0.73393.95220.1475-0.00290.2262-0.20280.02590.7149-0.0772-0.5615-0.17350.08620.0458-0.07320.1048-0.08581.4339-88.517-17.690349.8187
103.7481.0679-2.95893.3241-1.77795.75040.19480.14020.0335-0.56660.1271-0.1832-0.2001-0.2886-0.32180.45670.0362-0.11810.33710.10.7228-63.62833.442216.0793
111.497-0.62581.16121.3276-0.90653.03790.1426-0.0830.08220.0106-0.0160.8484-0.1623-0.4947-0.12660.08740.03420.2450.1129-0.1371.7667-87.7357-2.02668.6691
126.05971.8962-0.02541.1042-1.53864.8681-0.57820.26090.52620.06640.19350.0674-1.1952-0.53540.38470.89550.4216-0.1170.28480.19431.3103-72.244712.578726.8221
131.8481-1.26920.74281.8775-1.09832.6980.14530.0680.21470.3887-0.19450.5437-0.6769-0.33160.04920.36170.02730.38710.1211-0.20691.5325-74.722611.125884.8683
142.4502-1.58913.31852.4554-0.8477.6850.20210.09670.2698-0.8666-0.4653-0.0954-1.03850.14110.26310.79920.0838-0.16160.20260.04441.1876-72.467223.163139.5378
151.2997-1.07130.77332.0354-0.6972.07040.0614-0.27830.18820.3572-0.11680.4801-0.6033-0.22010.05530.6304-0.15910.35660.1723-0.24141.2814-53.021318.28194.0024
162.2532-0.039-0.32972.44851.33290.8069-0.11080.50950.4051-1.0276-0.11570.1461-0.5747-0.15180.22650.80980.1949-0.03550.20350.09251.2507-64.513132.309950.7222
171.312-1.25030.08142.6386-0.31941.50930.0884-0.24590.46590.6161-0.17640.0863-0.5760.28830.0880.5896-0.31510.07030.2055-0.17881.0854-28.336417.279993.9703
180.0966-0.06870.13617.1422-0.28020.33470.0040.18010.3642-1.1388-0.4558-0.4673-0.26740.46230.45181.0298-0.1160.01430.87970.43761.5013-50.137937.759157.7826
190.73390.0822-0.08454.5178-0.4120.74360.1839-0.24130.51960.3717-0.2395-0.2889-0.29340.53160.05560.283-0.3071-0.08540.4618-0.04820.824-7.28158.793184.4954
203.6641-3.50353.97577.2093-1.49585.7108-0.08130.31220.5518-0.2843-0.2708-1.081-0.42570.39420.3520.6567-0.31090.02080.17380.05561.2612-33.421937.893658.5287
210.93580.5062-0.06133.2929-0.42510.96120.00790.02060.364-0.0725-0.0743-0.5023-0.1410.71680.06640.0363-0.1182-0.05190.55550.05190.86894.5608-5.308168.0867
222.9455-3.73131.72967.2978-2.44042.8340.16110.2380.3313-0.7528-0.3619-0.6101-0.3965-0.14450.20070.6782-0.2290.07670.3724-0.01590.931-18.554932.53952.6717
231.20061.1534-0.63813.8563-0.98481.41350.2841-0.04670.2055-0.1059-0.3132-0.3596-0.03930.80330.02910.12990.06720.0510.56620.10080.70723.7901-21.061948.9379
240.90470.26020.96826.8082-0.66321.93140.05390.1250.25130.0181-0.2897-0.0121-0.3506-0.17130.23580.4746-0.07490.09370.48390.04450.699-9.818823.343642.0647
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 428
2X-RAY DIFFRACTION2A429 - 600
3X-RAY DIFFRACTION3B1 - 428
4X-RAY DIFFRACTION4B429 - 600
5X-RAY DIFFRACTION5C1 - 428
6X-RAY DIFFRACTION6C429 - 600
7X-RAY DIFFRACTION7D1 - 428
8X-RAY DIFFRACTION8D429 - 600
9X-RAY DIFFRACTION9E1 - 428
10X-RAY DIFFRACTION10E429 - 600
11X-RAY DIFFRACTION11F1 - 428
12X-RAY DIFFRACTION12F429 - 600
13X-RAY DIFFRACTION13G1 - 428
14X-RAY DIFFRACTION14G429 - 600
15X-RAY DIFFRACTION15H1 - 428
16X-RAY DIFFRACTION16H429 - 600
17X-RAY DIFFRACTION17I1 - 428
18X-RAY DIFFRACTION18I429 - 600
19X-RAY DIFFRACTION19J1 - 428
20X-RAY DIFFRACTION20J429 - 600
21X-RAY DIFFRACTION21K1 - 428
22X-RAY DIFFRACTION22K429 - 600
23X-RAY DIFFRACTION23L1 - 428
24X-RAY DIFFRACTION24L429 - 600

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