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- PDB-5ktz: expanded poliovirus in complex with VHH 12B -

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Basic information

Entry
Database: PDB / ID: 5ktz
Titleexpanded poliovirus in complex with VHH 12B
Components
  • Genome polyprotein
  • VHH 12B
  • VP1
  • VP2
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 speciesPoliovirus type 1
Camelus dromedarius (Arabian camel)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 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: Genome polyprotein
7: VHH 12B


Theoretical massNumber of molelcules
Total (without water)93,8194
Polymers93,8194
Non-polymers00
Water0
1
1: VP1
2: VP2
3: Genome polyprotein
7: VHH 12B
x 60


Theoretical massNumber of molelcules
Total (without water)5,629,131240
Polymers5,629,131240
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: Genome polyprotein
7: VHH 12B
x 5


  • icosahedral pentamer
  • 469 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)469,09420
Polymers469,09420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: VP1
2: VP2
3: Genome polyprotein
7: VHH 12B
x 6


  • icosahedral 23 hexamer
  • 563 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)562,91324
Polymers562,91324
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
117
21S
121
22A
32D
42E
52F
62V
72W
82X
132
23B
33G
43J
53L
63N
143
24C
34H
44I
54K
64M
74T
84U

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
111171 - 123
2111S1 - 123
1121157 - 213
2121A57 - 213
3121D57 - 213
4121E57 - 213
5121F57 - 213
6121V57 - 213
7121W57 - 213
8121X57 - 213
12211232 - 279
2221A232 - 279
3221D232 - 279
4221E232 - 279
5221F232 - 279
6221V232 - 279
7221W232 - 279
8221X232 - 279
113121 - 43
2131B1 - 43
3131G1 - 43
4131J1 - 43
5131L1 - 43
6131N1 - 43
1231253 - 159
2231B53 - 159
3231G53 - 159
4231J53 - 159
5231L53 - 159
6231N53 - 159
13312174 - 269
2331B174 - 269
3331G174 - 269
4331J174 - 269
5331L174 - 269
6331N174 - 269
14312943 - 952
2431B943 - 952
3431G943 - 952
4431J943 - 952
5431L943 - 952
6431N943 - 952
114131 - 231
2141C1 - 231
3141H1 - 231
4141I1 - 231
5141K1 - 231
6141M1 - 231
7141T1 - 231
8141U1 - 231

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.309383, 0.806618, -0.503636), (-0.810614, 0.500606, 0.303806), (0.497179, 0.314262, 0.808735)0.60251, 0.67415, -0.16108
3given(1), (1), (1)
4given(0.309633, 0.809055, -0.499556), (-0.808732, 0.500387, 0.309136), (0.50008, 0.308289, 0.809246)-0.07349, -0.05591, 0.04824
5given(-0.808898, 0.500432, -0.308628), (-0.499861, -0.308972, 0.80912), (0.309552, 0.808767, 0.500074)-0.09097, -0.01715, 0.00945
6given(-0.808854, -0.500213, 0.309099), (0.500147, -0.308843, 0.808993), (-0.309206, 0.808952, 0.499989)-0.00753, -0.00537, -0.01033
7given(0.309026, -0.80894, 0.500119), (0.808946, 0.500095, 0.30905), (-0.50011, 0.309065, 0.808931)-0.0226, 0.00745, 0.00571
8given(-0.999996, -0.001271, 0.002391), (0.001273, -0.999999, 0.000965), (0.00239, 0.000968, 0.999997)-0.38, -0.0924, 0.1067
9given(-0.30867, 0.809045, 0.500168), (-0.808903, -0.499921, 0.309445), (0.500399, -0.309071, 0.80875)-0.0105, -0.06353, 0.02033
10given(-0.307632, -0.80864, 0.501462), (0.810007, -0.499088, -0.307896), (0.499251, 0.311468, 0.808539)-0.29917, -0.20373, 0.1446
11given(1), (1), (1)
12given(0.310089, 0.808814, -0.499664), (-0.808598, 0.500793, 0.30883), (0.500014, 0.308263, 0.809296)-0.07558, -0.07294, 0.0409
13given(0.308584, -0.808721, 0.500746), (0.808779, 0.500165, 0.309374), (-0.500653, 0.309525, 0.808419)-0.12084, -0.04286, 0.04697
14given(-0.308646, 0.808782, 0.500609), (-0.809032, -0.499994, 0.308988), (0.500205, -0.309641, 0.808652)-0.07605, 0.00133, 0.0106
15given(-0.308361, -0.809131, 0.50022), (0.809184, -0.499576, -0.309266), (0.500135, 0.309404, 0.808786)-0.08581, 0.00444, 0.01555
16given(-0.49922, 0.308357, 0.80975), (0.309586, -0.80937, 0.499075), (0.809281, 0.499836, 0.308591)-0.09133, 0.05103, 0.00698
17given(1), (1), (1)
18given(0.309254, 0.809098, -0.499723), (-0.808846, 0.500146, 0.309228), (0.50013, 0.308569, 0.809108)-0.06699, -0.03854, 0.02336
19given(0.308991, -0.809179, 0.499753), (0.809236, 0.499754, 0.30884), (-0.499661, 0.30899, 0.809237)0.04022, 0.04944, -0.01805
20given(-1, 0.000245, -0.00026), (-0.000245, -1, 0.000569), (-0.00026, 0.000569, 1)0.03945, -0.09063, -0.00023
21given(-0.308469, 0.808917, 0.5005), (-0.809294, -0.499681, 0.308808), (0.49989, -0.309794, 0.808788)-0.07647, 0.04833, 0.00654
22given(-0.308233, -0.808746, 0.500921), (0.809115, -0.499807, -0.309074), (0.500326, 0.310036, 0.808425)-0.17509, -0.01513, 0.04045
23given(-0.808641, 0.499839, -0.310261), (-0.501011, -0.308667, 0.808525), (0.308364, 0.80925, 0.500026)0.11718, 0.02426, -0.01569
24given(-0.809196, -0.499984, 0.308575), (0.499657, -0.309302, 0.80912), (-0.309104, 0.808918, 0.500106)0.03431, 0.03012, -0.01432

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Components

#1: Protein VP1


Mass: 25291.594 Da / Num. of mol.: 1 / Fragment: UNP residues 636-858
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 1 (strain Mahoney) / Strain: Mahoney / Production host: Homo sapiens (human) / References: UniProt: P03300
#2: Protein VP2


Mass: 29677.301 Da / Num. of mol.: 1 / Fragment: UNP residues 70-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 1 (strain Mahoney) / Strain: Mahoney / Production host: Homo sapiens (human) / References: UniProt: P03300
#3: Protein Genome polyprotein


Mass: 25777.613 Da / Num. of mol.: 1 / Fragment: UNP residues 342-572
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 1 / Strain: Mahoney / Production host: Homo sapiens (human) / References: UniProt: P03300
#4: Antibody VHH 12B


Mass: 13072.334 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 12B / 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
1e2boxer.pyparticle selection
2SerialEMimage acquisition
4CTFFIND3CTF correction
7Cootmodel fitting
8Cootother
9RELION1.3initial Euler assignment
10FREALIGN9final Euler assignment
11Relion 1.3classification
12GeFrealign3D reconstruction
13REFMAC 5.8.01245model refinement
14FREALIGN9.093D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17627 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
Details: Fitting protocol: rigid body restraint of structurally conserved areas, and stereochemically restrained, icosahedrally restrained flexible fitting of areas that would otherwise disagree with ...Details: Fitting protocol: rigid body restraint of structurally conserved areas, and stereochemically restrained, icosahedrally restrained flexible fitting of areas that would otherwise disagree with the map. Refinement space: reciprocal, using both Fourier amplitudes and phases.
RefinementResolution: 4.3→98.6 Å / Cor.coef. Fo:Fc: 0.733 / SU B: 38.562 / SU ML: 0.589 / ESU R: 1.228
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.47088 --
obs0.47088 235686 99.99 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 24.691 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0.82 Å2-0.07 Å2
2---0.01 Å2-0.43 Å2
3----0.05 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.01942314
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg2.0471.94657698
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg0.27355220
ELECTRON MICROSCOPYr_dihedral_angle_2_deg5.02523.4621814
ELECTRON MICROSCOPYr_dihedral_angle_3_deg2.148156554
ELECTRON MICROSCOPYr_dihedral_angle_4_deg1.38815242
ELECTRON MICROSCOPYr_chiral_restr0.1510.26456
ELECTRON MICROSCOPYr_gen_planes_refined0.0010.02132266
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: 4.3→4.532 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.539 34480 -
Rfree-0 -
obs--99.97 %

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