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- PDB-5ku0: expanded poliovirus in complex with VHH 17B -

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Basic information

Entry
Database: PDB / ID: 5ku0
Titleexpanded poliovirus in complex with VHH 17B
Components
  • VHH 17B
  • VP1
  • VP2
  • VP3
KeywordsVirus/Immune System / poliovirus / VHH / nanobody / 80S / expanded / single domain antibody / Virus-Immune System complex
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesCamelus dromedarius (Arabian camel)
Poliovirus type 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsStrauss, M. / Schotte, L. / Filman, D.J. / Hogle, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI020566 United States
CitationJournal: J Virol / Year: 2017
Title: Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State.
Authors: Mike Strauss / Lise Schotte / Krishanthi S Karunatilaka / David J Filman / James M Hogle /
Abstract: By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs ...By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion.
IMPORTANCE: When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The ...IMPORTANCE: When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productive-infection events.
History
DepositionJul 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Feb 1, 2017Group: Database references / Other
Revision 1.3Feb 8, 2017Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / em_software / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 18, 2018Group: Data collection / Experimental preparation / Category: em_sample_support / em_software
Item: _em_sample_support.grid_type / _em_software.image_processing_id / _em_software.name
Revision 1.6Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
1: VP1
2: VP2
3: VP3
7: VHH 17B


Theoretical massNumber of molelcules
Total (without water)94,0094
Polymers94,0094
Non-polymers00
Water0
1
1: VP1
2: VP2
3: VP3
7: VHH 17B
x 60


Theoretical massNumber of molelcules
Total (without water)5,640,546240
Polymers5,640,546240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: VP1
2: VP2
3: VP3
7: VHH 17B
x 5


  • icosahedral pentamer
  • 470 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)470,04620
Polymers470,04620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: VP1
2: VP2
3: VP3
7: VHH 17B
x 6


  • icosahedral 23 hexamer
  • 564 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)564,05524
Polymers564,05524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
111
21A
31D
41E
51F
61V
71W
81X
122
22B
32G
42J
52L
62N
133
23C
33H
43I
53K
63M
73T
83U
147
24S

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111157 - 213
2111A57 - 213
3111D57 - 213
4111E57 - 213
5111F57 - 213
6111V57 - 213
7111W57 - 213
8111X57 - 213
12111232 - 279
2211A232 - 279
3211D232 - 279
4211E232 - 279
5211F232 - 279
6211V232 - 279
7211W232 - 279
8211X232 - 279
112121 - 43
2121B1 - 43
3121G1 - 43
4121J1 - 43
5121L1 - 43
6121N1 - 43
1221253 - 159
2221B53 - 159
3221G53 - 159
4221J53 - 159
5221L53 - 159
6221N53 - 159
13212174 - 269
2321B174 - 269
3321G174 - 269
4321J174 - 269
5321L174 - 269
6321N174 - 269
14212944 - 952
2421B944 - 952
3421G944 - 952
4421J944 - 952
5421L944 - 952
6421N944 - 952
113131 - 231
2131C1 - 231
3131H1 - 231
4131I1 - 231
5131K1 - 231
6131M1 - 231
7131T1 - 231
8131U1 - 231
114171 - 124
2141S1 - 124

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.309144, 0.808989, -0.499966), (-0.809006, 0.500073, 0.308929), (0.49994, 0.308971, 0.809072)0.00981, 0.00369, 0.00989
3given(-0.808964, 0.500041, -0.309088), (-0.500262, -0.309451, 0.808689), (0.30873, 0.808825, 0.500487)0.01365, 0.04245, -0.03099
4given(-0.809097, -0.499858, 0.309039), (0.500091, -0.309427, 0.808804), (-0.308662, 0.808948, 0.500331)-0.01921, 0.04919, -0.01675
5given(0.309031, -0.809148, 0.49978), (0.809181, 0.499823, 0.308874), (-0.499726, 0.30896, 0.809208)0.03113, 0.03092, -0.00643
6given(-0.999998, 0.000951, 0.00191), (-0.00095, -0.999999, 0.000349), (0.00191, 0.000347, 0.999998)-0.18948, -0.08299, 0.05395
7given(-0.30775, 0.809254, 0.500397), (-0.809406, -0.499128, 0.309408), (0.500152, -0.309804, 0.808622)-0.04319, -0.01047, 0.02411
8given(-0.30872, -0.808434, 0.501125), (0.809578, -0.499898, -0.307711), (0.499275, 0.310703, 0.808819)-0.15344, -0.16333, 0.11735
9given(1), (1), (1)
10given(0.309468, 0.808023, -0.501326), (-0.808509, 0.501099, 0.308565), (0.500542, 0.309836, 0.808369)0.19425, -0.08516, -0.04227
11given(0.308778, -0.809219, 0.49982), (0.808932, 0.499836, 0.309504), (-0.500285, 0.308753, 0.808942)0.02479, -0.06332, -0.0026
12given(-0.30911, 0.809023, 0.499932), (-0.809026, -0.500026, 0.308952), (0.499928, -0.308958, 0.809084)0.02664, 0.00473, -0.02497
13given(-0.309293, -0.809293, 0.499381), (0.809263, -0.499783, -0.308725), (0.499431, 0.308644, 0.80951)0.08907, -0.04705, -0.03361
14given(-0.500495, 0.308003, 0.809098), (0.309121, -0.80939, 0.499332), (0.808671, 0.500022, 0.309885)0.09098, 0.06147, -0.05983
15given(1), (1), (1)
16given(0.309297, 0.808483, -0.50069), (-0.808733, 0.500612, 0.308769), (0.500286, 0.309424, 0.808685)0.09494, -0.01915, 0.00492
17given(0.308815, -0.808744, 0.500566), (0.808912, 0.500157, 0.309039), (-0.500295, 0.309477, 0.808659)-0.08284, -0.01324, 0.01174
18given(-0.999999, 0.001177, 5.6E-5), (-0.001177, -0.999999, 0.001245), (5.8E-5, 0.001245, 0.999999)0.02886, -0.18735, 0.0263
19given(-0.308187, 0.8082, 0.50183), (-0.809336, -0.499988, 0.3082), (0.499996, -0.311166, 0.808195)-0.28393, 0.1148, 0.03783
20given(-0.308247, -0.808583, 0.501175), (0.808828, -0.500091, -0.309364), (0.50078, 0.310004, 0.808157)-0.19218, 0.04805, 0.02588
21given(-0.80839, 0.500336, -0.310113), (-0.501097, -0.308475, 0.808545), (0.308882, 0.809016, 0.500085)0.056, 0.00085, 0.00201
22given(-0.809443, -0.499672, 0.308431), (0.499417, -0.309555, 0.809172), (-0.308844, 0.809014, 0.500112)0.01532, 0.01176, -0.00079
23given(1), (1), (1)
24given(0.309916, 0.807809, -0.501395), (-0.810026, 0.500457, 0.305615), (0.497806, 0.311427, 0.809446)0.17813, 0.44031, -0.09558

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Components

#1: Protein VP1


Mass: 25291.594 Da / Num. of mol.: 1 / Fragment: UNP reisdues 636-858 / Source method: isolated from a natural source / Source: (natural) Poliovirus type 1 (strain Mahoney) / Strain: Mahoney / References: UniProt: P03300
#2: Protein VP2


Mass: 29677.301 Da / Num. of mol.: 1 / Fragment: UNP residues 70-338 / Source method: isolated from a natural source / Source: (natural) Poliovirus type 1 (strain Mahoney) / Strain: Mahoney / References: UniProt: P03300
#3: Protein VP3


Mass: 25777.613 Da / Num. of mol.: 1 / Fragment: UNP residues 342-571 / Source method: isolated from a natural source / Source: (natural) Poliovirus type 1 (strain Mahoney) / Strain: Mahoney / References: UniProt: P03300
#4: Antibody VHH 17B


Mass: 13262.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli K-12 (bacteria)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: expanded poliovirus in complex with VHH 17B / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 9 MDa / Experimental value: NO
Source (natural)Organism: Poliovirus type 1 (strain Mahoney)
Buffer solutionpH: 7
SpecimenConc.: 0.45 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0151 / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND3CTF correction
7Cootmodel fitting
8Cootother
9RELION1.3initial Euler assignment
10FREALIGN9final Euler assignment
11Relion 1.3classification
12GeFrealign3D reconstruction
13e2boxer.pyparticle selection
14REFMAC 5.8.01245model refinement
15FREALIGN9.093D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17654 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Details: using both Fourier amplitudes and phases
RefinementResolution: 4.2→98.94 Å / Cor.coef. Fo:Fc: 0.758 / SU B: 87.301 / SU ML: 1.061 / ESU R: 0.95
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.43953 --
obs0.43953 280350 99.99 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 24.819 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å2-0.29 Å20.65 Å2
2---0.54 Å20.5 Å2
3---1.8 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.01942502
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.8781.94857968
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg1.50155216
ELECTRON MICROSCOPYr_dihedral_angle_2_deg17.59923.5431840
ELECTRON MICROSCOPYr_dihedral_angle_3_deg8.596156622
ELECTRON MICROSCOPYr_dihedral_angle_4_deg8.12815242
ELECTRON MICROSCOPYr_chiral_restr0.1370.26474
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.02132438
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 4.2→4.427 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.536 40849 -
Rfree-0 -
obs--100 %

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