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- PDB-3j3o: Conformational Shift of a Major Poliovirus Antigen Confirmed by I... -

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Basic information

Entry
Database: PDB / ID: 3j3o
TitleConformational Shift of a Major Poliovirus Antigen Confirmed by Immuno-Cryogenic Electron Microscopy: 160S Poliovirus and C3-Fab Complex
Components
  • (C3 antibody, ...) x 2
  • Protein VP1
  • Protein VP2
  • Protein VP3
  • Protein VP4
  • unknown peptide
KeywordsVIRUS/IMMUNE SYSTEM / antibody-antigen interaction / antibody-protein interaction / picornavirus / virus-antibody interaction / neutralizing antibody interaction / conformational change / 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 MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / 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 MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / 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 / structural molecule activity / virion attachment to host cell / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MYRISTIC ACID / SPHINGOSINE / Genome polyprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
unidentified (others)
Human poliovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.1 Å
AuthorsLin, J. / Cheng, N. / Hogle, J.M. / Steven, A.C. / Belnap, D.M.
CitationJournal: J Immunol / Year: 2013
Title: Conformational shift of a major poliovirus antigen confirmed by immuno-cryogenic electron microscopy.
Authors: Jun Lin / Naiqian Cheng / James M Hogle / Alasdair C Steven / David M Belnap /
Abstract: Small, interfacial conformational changes occur in some Ag-Ab interactions. Using cryogenic electron microscopy (cryo-EM), we have demonstrated such changes in a major antigenic site of a poliovirus ...Small, interfacial conformational changes occur in some Ag-Ab interactions. Using cryogenic electron microscopy (cryo-EM), we have demonstrated such changes in a major antigenic site of a poliovirus capsid protein. During cell entry, native human poliovirus (160S particle) converts to a cell entry intermediate (135S particle) and later to an RNA-released (80S) particle. By mixing particles with Fabs of the neutralizing C3 mAb, we labeled the external loop connecting the B and C β-strands (BC loop) of the capsid protein VP1 (residues 95-105) in the 160S and 135S states. We then determined three-dimensional structures by cryo-EM and enhanced their interpretability by fitting high-resolution coordinates of C3 Fab and the capsid proteins into the density maps. Binding of C3 to either 160S or 135S particles caused residues of the BC loop, located on the tip of a prominent peak known as the "mesa," to move by an estimated 5 Å. C3 Abs are neutralizing and can bind bivalently. The orientation of the bound Fabs in our reconstructions suggests that C3 neutralizes poliovirus by binding two adjacent BC loops on the same mesa and inhibiting conformational changes in the viral capsid.
History
DepositionApr 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_database_related / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_database_related.content_type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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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
  • EMDB-5291
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  • Superimposition on EM map
  • EMDB-5291
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: C3 antibody, light chain
H: C3 antibody, heavy chain
0: unknown peptide
1: Protein VP1
2: Protein VP2
3: Protein VP3
4: Protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,0299
Polymers145,5017
Non-polymers5282
Water0
1
L: C3 antibody, light chain
H: C3 antibody, heavy chain
0: unknown peptide
1: Protein VP1
2: Protein VP2
3: Protein VP3
4: Protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,761,745540
Polymers8,730,073420
Non-polymers31,672120
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
L: C3 antibody, light chain
H: C3 antibody, heavy chain
0: unknown peptide
1: Protein VP1
2: Protein VP2
3: Protein VP3
4: Protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 730 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)730,14545
Polymers727,50635
Non-polymers2,63910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
L: C3 antibody, light chain
H: C3 antibody, heavy chain
0: unknown peptide
1: Protein VP1
2: Protein VP2
3: Protein VP3
4: Protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 876 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)876,17454
Polymers873,00742
Non-polymers3,16712
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein/peptide , 1 types, 1 molecules 0

#3: Protein/peptide unknown peptide / Coordinate model: Cα atoms only


Mass: 437.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unidentified (others)

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Protein , 4 types, 4 molecules 1234

#4: Protein Protein VP1 / P1D / Virion protein 1 / Coordinate model: Cα atoms only


Mass: 33488.613 Da / Num. of mol.: 1 / Fragment: UNP residues 580-881 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Strain: Mahoney / References: UniProt: P03300
#5: Protein Protein VP2 / P1B / Virion protein 2 / Coordinate model: Cα atoms only


Mass: 30075.783 Da / Num. of mol.: 1 / Fragment: UNP residues 70-341 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Strain: Mahoney / References: UniProt: P03300
#6: Protein Protein VP3 / P1C / Virion protein 3 / Coordinate model: Cα atoms only


Mass: 26547.482 Da / Num. of mol.: 1 / Fragment: UNP residues 342-579 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Strain: Mahoney / References: UniProt: P03300
#7: Protein Protein VP4 / P1A / Virion protein 4 / Coordinate model: Cα atoms only


Mass: 7393.050 Da / Num. of mol.: 1 / Fragment: UNP residues 2-69 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Strain: Mahoney / References: UniProt: P03300

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Antibody , 2 types, 2 molecules LH

#1: Antibody C3 antibody, light chain / Coordinate model: Cα atoms only


Mass: 24080.750 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody C3 antibody, heavy chain / Coordinate model: Cα atoms only


Mass: 23478.137 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 2 types, 2 molecules

#8: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#9: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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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: Poliovirus 160S particle and C3 Fab complex / Type: VIRUS / Details: 160S icosahedral particle with Fab
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 20 mM Tris, 2 mM CaCl2 / pH: 7.5 / Details: 20 mM Tris, 2 mM CaCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE
Details: Vitrification carried out in ambient atmosphere. Ethane cooled by liquid nitrogen.
Method: Blotted manually before plunging

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38000 X / Calibrated magnification: 37587 X / Nominal defocus max: 1770 nm / Nominal defocus min: 730 nm / Cs: 2 mm / Astigmatism: Bsoft / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder
Image recordingElectron dose: 14 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 12
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1CHARMMmodel fitting
2EM3DR23D reconstruction
CTF correctionDetails: CTF and decay correction of each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Fourier Bessel / Resolution: 11.1 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 4184 / Nominal pixel size: 1.824 Å / Actual pixel size: 1.824 Å
Details: Reconstruction computed from focal pairs. Pairs not summed for reconstruction calculation.
Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1RIGID BODY FITREALREFINEMENT PROTOCOL--Rigid Body DETAILS--Atomic coordinates for C3 Fab (Nature Struct. Biol. 2, 232-243) (PDB entry 1FPT) were manually fitted using UCSF Chimera (Journal of Computational Chemistry 25, 1605-1612). A core-weighted, rigid-body fitting algorithm implemented in CHARRM (J Struct Biol 141, 63-76) was used to refine the fit.
2RIGID BODY FITREALREFINEMENT PROTOCOL--Rigid body DETAILS--The unmodified coordinates of PDB entry 1ASJ were placed into the cryo-EM density. The BC loop of VP1 was then modified based on the fitting (see primary citation for details).
Atomic model building

Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-ID 3D fitting-IDAccession codeInitial refinement model-ID
11FPT

1fpt

P11FPT1
21FPT

1fpt

H11FPT1
31FPT

1fpt

L11FPT1
41ASJ

1asj

21ASJ2
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 36 0 1326

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