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- PDB-4c0y: Cryo-EM reconstruction of empty enterovirus 71 in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 4c0y
TitleCryo-EM reconstruction of empty enterovirus 71 in complex with a neutralizing antibody E18
Components
  • (FAB EV18 4 D6-1 F1 G9) x 2
  • VP1
  • VP2
  • VP3
KeywordsVIRUS/IMMUNE SYSTEM / VIRUS-IMMUNE SYSTEM COMPLEX / EV71 / ANTIBODY / E18 / NEUTRALIZING / PATHOGEN
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Picornavirus coat protein / 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) ...Picornavirus coat protein / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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 speciesHUMAN ENTEROVIRUS 71
MUS MUSCULUS (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16 Å
AuthorsPlevka, P. / Perera, R. / Cardosa, J. / Suksatu, A. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Neutralizing antibodies can initiate genome release from human enterovirus 71.
Authors: Pavel Plevka / Pei-Yin Lim / Rushika Perera / Jane Cardosa / Ampa Suksatu / Richard J Kuhn / Michael G Rossmann /
Abstract: Antibodies were prepared by immunizing mice with empty, immature particles of human enterovirus 71 (EV71), a picornavirus that causes severe neurological disease in young children. The capsid ...Antibodies were prepared by immunizing mice with empty, immature particles of human enterovirus 71 (EV71), a picornavirus that causes severe neurological disease in young children. The capsid structure of these empty particles is different from that of the mature virus and is similar to "A" particles encountered when picornaviruses recognize a potential host cell before genome release. The monoclonal antibody E18, generated by this immunization, induced a conformational change when incubated at temperatures between 4 °C and 37 °C with mature virus, transforming infectious virions into A particles. The resultant loss of genome that was observed by cryo-EM and a fluorescent SYBR Green dye assay inactivated the virus, establishing the mechanism by which the virus is inactivated and demonstrating that the E18 antibody has potential as an anti-EV71 therapy. The antibody-mediated virus neutralization by the induction of genome release has not been previously demonstrated. Furthermore, the present results indicate that antibodies with genome-release activity could also be produced for other picornaviruses by immunization with immature particles.
History
DepositionAug 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Aug 21, 2019Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.4Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.5May 8, 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_initial_refinement_model / pdbx_struct_oper_list
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_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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-2434
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  • Superimposition on EM map
  • EMDB-2434
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
X: FAB EV18 4 D6-1 F1 G9
Y: FAB EV18 4 D6-1 F1 G9


Theoretical massNumber of molelcules
Total (without water)124,3845
Polymers124,3845
Non-polymers00
Water00
1
A: VP1
B: VP2
C: VP3
X: FAB EV18 4 D6-1 F1 G9
Y: FAB EV18 4 D6-1 F1 G9
x 60


Theoretical massNumber of molelcules
Total (without water)7,463,047300
Polymers7,463,047300
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
A: VP1
B: VP2
C: VP3
X: FAB EV18 4 D6-1 F1 G9
Y: FAB EV18 4 D6-1 F1 G9
x 5


  • icosahedral pentamer
  • 622 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)621,92125
Polymers621,92125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
X: FAB EV18 4 D6-1 F1 G9
Y: FAB EV18 4 D6-1 F1 G9
x 6


  • icosahedral 23 hexamer
  • 746 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)746,30530
Polymers746,30530
Non-polymers00
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))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.809017, 0.309017), (0.809017, 0.309017, -0.5), (0.309017, 0.5, 0.809017)
3generate(-0.309017, -0.5, 0.809017), (0.5, -0.809017, -0.309017), (0.809017, 0.309017, 0.5)
4generate(-0.309017, 0.5, 0.809017), (-0.5, -0.809017, 0.309017), (0.809017, -0.309017, 0.5)
5generate(0.5, 0.809017, 0.309017), (-0.809017, 0.309017, 0.5), (0.309017, -0.5, 0.809017)
6generate(-1), (-1), (1)
7generate(-0.5, 0.809017, -0.309017), (-0.809017, -0.309017, 0.5), (0.309017, 0.5, 0.809017)
8generate(0.309017, 0.5, -0.809017), (-0.5, 0.809017, 0.309017), (0.809017, 0.309017, 0.5)
9generate(0.309017, -0.5, -0.809017), (0.5, 0.809017, -0.309017), (0.809017, -0.309017, 0.5)
10generate(-0.5, -0.809017, -0.309017), (0.809017, -0.309017, -0.5), (0.309017, -0.5, 0.809017)
11generate(1), (-1), (-1)
12generate(0.5, -0.809017, 0.309017), (-0.809017, -0.309017, 0.5), (-0.309017, -0.5, -0.809017)
13generate(-0.309017, -0.5, 0.809017), (-0.5, 0.809017, 0.309017), (-0.809017, -0.309017, -0.5)
14generate(-0.309017, 0.5, 0.809017), (0.5, 0.809017, -0.309017), (-0.809017, 0.309017, -0.5)
15generate(0.5, 0.809017, 0.309017), (0.809017, -0.309017, -0.5), (-0.309017, 0.5, -0.809017)
16generate(-1), (1), (-1)
17generate(-0.5, 0.809017, -0.309017), (0.809017, 0.309017, -0.5), (-0.309017, -0.5, -0.809017)
18generate(0.309017, 0.5, -0.809017), (0.5, -0.809017, -0.309017), (-0.809017, -0.309017, -0.5)
19generate(0.309017, -0.5, -0.809017), (-0.5, -0.809017, 0.309017), (-0.809017, 0.309017, -0.5)
20generate(-0.5, -0.809017, -0.309017), (-0.809017, 0.309017, 0.5), (-0.309017, 0.5, -0.809017)
21generate(-1), (-1), (1)
22generate(-0.809017, -0.309017, 0.5), (-0.309017, -0.5, -0.809017), (0.5, -0.809017, 0.309017)
23generate(-0.5, 0.809017, 0.309017), (-0.809017, -0.309017, -0.5), (-0.309017, -0.5, 0.809017)
24generate(0.5, 0.809017, -0.309017), (-0.809017, 0.309017, -0.5), (-0.309017, 0.5, 0.809017)
25generate(0.809017, -0.309017, -0.5), (-0.309017, 0.5, -0.809017), (0.5, 0.809017, 0.309017)
26generate(1), (-1), (-1)
27generate(0.809017, 0.309017, -0.5), (-0.309017, -0.5, -0.809017), (-0.5, 0.809017, -0.309017)
28generate(0.5, -0.809017, -0.309017), (-0.809017, -0.309017, -0.5), (0.309017, 0.5, -0.809017)
29generate(-0.5, -0.809017, 0.309017), (-0.809017, 0.309017, -0.5), (0.309017, -0.5, -0.809017)
30generate(-0.809017, 0.309017, 0.5), (-0.309017, 0.5, -0.809017), (-0.5, -0.809017, -0.309017)
31generate(1), (1), (1)
32generate(0.809017, 0.309017, -0.5), (0.309017, 0.5, 0.809017), (0.5, -0.809017, 0.309017)
33generate(0.5, -0.809017, -0.309017), (0.809017, 0.309017, 0.5), (-0.309017, -0.5, 0.809017)
34generate(-0.5, -0.809017, 0.309017), (0.809017, -0.309017, 0.5), (-0.309017, 0.5, 0.809017)
35generate(-0.809017, 0.309017, 0.5), (0.309017, -0.5, 0.809017), (0.5, 0.809017, 0.309017)
36generate(-1), (1), (-1)
37generate(-0.809017, -0.309017, 0.5), (0.309017, 0.5, 0.809017), (-0.5, 0.809017, -0.309017)
38generate(-0.5, 0.809017, 0.309017), (0.809017, 0.309017, 0.5), (0.309017, 0.5, -0.809017)
39generate(0.5, 0.809017, -0.309017), (0.809017, -0.309017, 0.5), (0.309017, -0.5, -0.809017)
40generate(0.809017, -0.309017, -0.5), (0.309017, -0.5, 0.809017), (-0.5, -0.809017, -0.309017)
41generate(1), (-1), (-1)
42generate(0.309017, 0.5, 0.809017), (-0.5, 0.809017, -0.309017), (-0.809017, -0.309017, 0.5)
43generate(0.809017, 0.309017, 0.5), (0.309017, 0.5, -0.809017), (-0.5, 0.809017, 0.309017)
44generate(0.809017, -0.309017, 0.5), (0.309017, -0.5, -0.809017), (0.5, 0.809017, -0.309017)
45generate(0.309017, -0.5, 0.809017), (-0.5, -0.809017, -0.309017), (0.809017, -0.309017, -0.5)
46generate(1), (1), (1)
47generate(0.309017, 0.5, 0.809017), (0.5, -0.809017, 0.309017), (0.809017, 0.309017, -0.5)
48generate(0.809017, 0.309017, 0.5), (-0.309017, -0.5, 0.809017), (0.5, -0.809017, -0.309017)
49generate(0.809017, -0.309017, 0.5), (-0.309017, 0.5, 0.809017), (-0.5, -0.809017, 0.309017)
50generate(0.309017, -0.5, 0.809017), (0.5, 0.809017, 0.309017), (-0.809017, 0.309017, 0.5)
51generate(-1), (-1), (1)
52generate(-0.309017, -0.5, -0.809017), (-0.5, 0.809017, -0.309017), (0.809017, 0.309017, -0.5)
53generate(-0.809017, -0.309017, -0.5), (0.309017, 0.5, -0.809017), (0.5, -0.809017, -0.309017)
54generate(-0.809017, 0.309017, -0.5), (0.309017, -0.5, -0.809017), (-0.5, -0.809017, 0.309017)
55generate(-0.309017, 0.5, -0.809017), (-0.5, -0.809017, -0.309017), (-0.809017, 0.309017, 0.5)
56generate(-1), (1), (-1)
57generate(-0.309017, -0.5, -0.809017), (0.5, -0.809017, 0.309017), (-0.809017, -0.309017, 0.5)
58generate(-0.809017, -0.309017, -0.5), (-0.309017, -0.5, 0.809017), (-0.5, 0.809017, 0.309017)
59generate(-0.809017, 0.309017, -0.5), (-0.309017, 0.5, 0.809017), (0.5, 0.809017, -0.309017)
60generate(-0.309017, 0.5, -0.809017), (0.5, 0.809017, 0.309017), (0.809017, -0.309017, -0.5)

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Components

#1: Protein VP1


Mass: 32832.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ENTEROVIRUS 71 / Strain: MY104-9-SAR-97 / References: UniProt: A9X4C2
#2: Protein VP2


Mass: 27800.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ENTEROVIRUS 71 / Strain: MY104-9-SAR-97 / References: UniProt: A9X4C2
#3: Protein VP3


Mass: 26524.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ENTEROVIRUS 71 / Strain: MY104-9-SAR-97 / References: UniProt: A9X4C2
#4: Antibody FAB EV18 4 D6-1 F1 G9


Mass: 18485.723 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: SEQUENCE MODELLED AS POLY-UNK / Source: (natural) MUS MUSCULUS (house mouse)
#5: Antibody FAB EV18 4 D6-1 F1 G9


Mass: 18741.035 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: SEQUENCE MODELLED AS POLY-UNK / Source: (natural) MUS MUSCULUS (house mouse)

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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: FAB FRAGMENT OF E18 ANTIBODY BOUND TO EMPTY EV71 VIRIONS
Type: VIRUS
Buffer solutionName: NTE BUFFER, 10 MM TRIS- HCL, PH 8.0, 0.5 M NACL, AND 1 MM EDTA
pH: 8
Details: NTE BUFFER, 10 MM TRIS- HCL, PH 8.0, 0.5 M NACL, AND 1 MM EDTA
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: PLUNGING INTO LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG/UT / Date: Sep 10, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49500 X / Nominal defocus max: 4500 nm / Nominal defocus min: 750 nm / Cs: 2 mm
Specimen holderTemperature: 119 K
Image recordingElectron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 112

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Processing

EM software
IDNameVersionCategory
1EMfitmodel fitting
2EMAN13D reconstruction
3EMAN23D reconstruction
CTF correctionDetails: CTF DETERMINED FOR ALL PARTICLES FROM ONE FILM, PHASE FLIP
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 16 Å / Num. of particles: 418 / Nominal pixel size: 2.48 Å / Actual pixel size: 2.48 Å
Magnification calibration: CORRELATION WITH ELECTRON DENSITY CALCULATED FROM X-RAY BASED MODEL OF THE VIRUS CAPSID
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2434. (DEPOSITION ID: 11887).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: RCRIT / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 3ZFE

3zfe


Accession code: 3ZFE / Source name: PDB / Type: experimental model
RefinementHighest resolution: 16 Å
Refinement stepCycle: LAST / Highest resolution: 16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8074 0 0 0 8074

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