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- PDB-3j3p: Conformational Shift of a Major Poliovirus Antigen Confirmed by I... -

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Basic information

Entry
Database: PDB / ID: 3j3p
TitleConformational Shift of a Major Poliovirus Antigen Confirmed by Immuno-Cryogenic Electron Microscopy: 135S Poliovirus and C3-Fab Complex
Components
  • C3 antibody, heavy chain
  • C3 antibody, light chain
  • Protein VP1
  • Protein VP2
  • Protein VP3
KeywordsVIRUS/IMMUNE SYSTEM / 135S cell-entry intermediate particle / antibody-antigen interaction / antibody-protein interaction / picornavirus / virus-antibody interaction / antibody neutralization / neutralizing antibody interaction / conformational change / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding ...symbiont-mediated suppression of host translation initiation / positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / 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 / immunoglobulin mediated immune response / antigen processing and presentation / positive regulation of phagocytosis / complement activation, classical pathway / 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 / antigen binding / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / multivesicular body / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / response to bacterium / endocytosis involved in viral entry into host cell / : / positive regulation of immune response / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / antibacterial humoral response / 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 / extracellular space / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane / cytosol
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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ig gamma-2A chain C region, membrane-bound form / Genome polyprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human poliovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.1 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
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
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
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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-5292
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
L: C3 antibody, light chain
H: C3 antibody, heavy chain
1: Protein VP1
2: Protein VP2
3: Protein VP3


Theoretical massNumber of molelcules
Total (without water)137,6715
Polymers137,6715
Non-polymers00
Water0
1
L: C3 antibody, light chain
H: C3 antibody, heavy chain
1: Protein VP1
2: Protein VP2
3: Protein VP3
x 60


Theoretical massNumber of molelcules
Total (without water)8,260,246300
Polymers8,260,246300
Non-polymers00
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
1: Protein VP1
2: Protein VP2
3: Protein VP3
x 5


  • icosahedral pentamer
  • 688 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)688,35425
Polymers688,35425
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
L: C3 antibody, light chain
H: C3 antibody, heavy chain
1: Protein VP1
2: Protein VP2
3: Protein VP3
x 6


  • icosahedral 23 hexamer
  • 826 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)826,02530
Polymers826,02530
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#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) / References: UniProt: P01865*PLUS
#3: 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
#4: 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
#5: 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

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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 135S particle and C3 Fab complex / Type: VIRUS / Details: 135S 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: 38000 X / Nominal defocus max: 1630 nm / Nominal defocus min: 1120 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: 4
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: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 9810 / Nominal pixel size: 1.84 Å / Actual pixel size: 1.84 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 coordinates of PDB entry 1XYR were placed into the 135S-C3 cryo-EM map. BC loop coordinates were manipulated to fit the cryo-EM data (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
41XYR

1xyr

21XYR2
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 0 0 1163

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