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- PDB-7cmk: E30 E-particle in complex with 6C5 -

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Basic information

Entry
Database: PDB / ID: 7cmk
TitleE30 E-particle in complex with 6C5
Components
  • Heavy chain
  • Light chain
  • VP1
  • VP2
  • VP3
KeywordsVIRUS / Echovirus B / mature / neutralizing MAb
Function / homology
Function and homology information


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 genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...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 genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 superfamily / 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 VP4 superfamily / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEchovirus E30
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang, K. / Zhu, F. / Rao, Z. / Wang, X.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesKJZD-SW-L05 China
CitationJournal: Nat Commun / Year: 2020
Title: Serotype specific epitopes identified by neutralizing antibodies underpin immunogenic differences in Enterovirus B.
Authors: Kang Wang / Binyang Zheng / Li Zhang / Lunbiao Cui / Xuan Su / Qian Zhang / Zhenxi Guo / Yu Guo / Wei Zhang / Ling Zhu / Fengcai Zhu / Zihe Rao / Xiangxi Wang /
Abstract: Echovirus 30 (E30), a serotype of Enterovirus B (EV-B), recently emerged as a major causative agent of aseptic meningitis worldwide. E30 is particularly devastating in the neonatal population and ...Echovirus 30 (E30), a serotype of Enterovirus B (EV-B), recently emerged as a major causative agent of aseptic meningitis worldwide. E30 is particularly devastating in the neonatal population and currently no vaccine or antiviral therapy is available. Here we characterize two highly potent E30-specific monoclonal antibodies, 6C5 and 4B10, which efficiently block binding of the virus to its attachment receptor CD55 and uncoating receptor FcRn. Combinations of 6C5 and 4B10 augment the sum of their individual anti-viral activities. High-resolution structures of E30-6C5-Fab and E30-4B10-Fab define the location and nature of epitopes targeted by the antibodies. 6C5 and 4B10 engage the capsid loci at the north rim of the canyon and in-canyon, respectively. Notably, these regions exhibit antigenic variability across EV-Bs, highlighting challenges in development of broad-spectrum antibodies. Our structures of these neutralizing antibodies of E30 are instructive for development of vaccines and therapeutics against EV-B infections.
History
DepositionJul 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _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-30408
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
H: Heavy chain
L: Light chain


Theoretical massNumber of molelcules
Total (without water)142,5005
Polymers142,5005
Non-polymers00
Water00
1
A: VP1
B: VP2
C: VP3
H: Heavy chain
L: Light chain
x 60


Theoretical massNumber of molelcules
Total (without water)8,550,015300
Polymers8,550,015300
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
H: Heavy chain
L: Light chain
x 5


  • icosahedral pentamer
  • 713 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)712,50125
Polymers712,50125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
H: Heavy chain
L: Light chain
x 6


  • icosahedral 23 hexamer
  • 855 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)855,00230
Polymers855,00230
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
6
A: VP1
B: VP2
C: VP3
H: Heavy chain
L: Light chain
x 60


  • crystal asymmetric unit, crystal frame
  • 8.55 MDa, 300 polymers
Theoretical massNumber of molelcules
Total (without water)8,550,015300
Polymers8,550,015300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.95105651, -3.0E-8), (0.95105652, 0.309017, 3.0E-8), (-3.0E-8, -4.0E-8, 1)
3generate(-0.809017, -0.58778525, -7.0E-8), (0.58778526, -0.80901699, 2.0E-8), (-8.0E-8, -2.0E-8, 1)
4generate(-0.80901699, 0.58778525, -7.0E-8), (-0.58778526, -0.809017, -3.0E-8), (-7.0E-8, 3.0E-8, 1)
5generate(0.309017, 0.95105651, -2.0E-8), (-0.95105652, 0.30901699, -4.0E-8), (-2.0E-8, 4.0E-8, 1)
6generate(-0.63819654, 0.26286557, -0.72360684), (0.26286558, -0.809017, -0.52573111), (-0.72360685, -0.5257311, 0.44721354)
7generate(0.05278646, 0.68819093, -0.72360681), (-0.68819094, -0.50000001, -0.52573114), (-0.72360681, 0.52573114, 0.44721354)
8generate(0.67082041, 0.16245981, -0.72360679), (-0.68819094, 0.49999999, -0.52573114), (0.27639322, 0.85065081, 0.44721358)
9generate(0.36180339, -0.58778525, -0.7236068), (0.26286558, 0.80901699, -0.5257311), (0.89442719, -2.0E-8, 0.4472136)
10generate(-0.44721358, -0.52573108, -0.72360683), (0.85065083, -0.52573108), (0.27639316, -0.85065082, 0.44721358)
11generate(-0.05278646, 0.68819094, 0.72360681), (0.68819094, -0.5, 0.52573114), (0.72360681, 0.52573114, -0.44721354)
12generate(0.63819654, 0.26286558, 0.72360684), (-0.26286559, -0.80901699, 0.5257311), (0.72360684, -0.5257311, -0.44721354)
13generate(0.44721358, -0.52573107, 0.72360683), (-0.85065083, 0.52573108), (-0.27639316, -0.85065083, -0.44721358)
14generate(-0.3618034, -0.58778525, 0.7236068), (-0.26286557, 0.809017, 0.52573111), (-0.89442719, -3.0E-8, -0.4472136)
15generate(-0.67082041, 0.16245982, 0.72360679), (0.68819095, 0.5, 0.52573114), (-0.27639321, 0.85065081, -0.44721358)
16generate(-0.309017, -0.95105651, 2.0E-8), (-0.95105652, 0.309017, -3.0E-8), (3.0E-8, -4.0E-8, -1)
17generate(-1), (1), (-1)
18generate(-0.30901699, 0.95105651, 3.0E-8), (0.95105652, 0.30901699, 4.0E-8), (2.0E-8, 3.0E-8, -1)
19generate(0.809017, 0.58778525, 7.0E-8), (0.58778525, -0.809017, 2.0E-8), (7.0E-8, 2.0E-8, -1)
20generate(0.80901699, -0.58778525, 7.0E-8), (-0.58778526, -0.80901699, -2.0E-8), (8.0E-8, -2.0E-8, -1)
21generate(-0.13819665, -0.95105651, 0.27639318), (0.42532544, -0.30901699, -0.8506508), (0.89442717, -4.0E-8, 0.44721364)
22generate(-0.94721362, -0.16245981, 0.27639315), (-0.16245981, -0.5, -0.85065082), (0.27639314, -0.85065081, 0.44721362)
23generate(-0.44721358, 0.85065083, 0.27639317), (-0.52573108, -0.85065083), (-0.72360683, -0.52573107, 0.44721358)
24generate(0.67082041, 0.68819094, 0.27639321), (-0.16245981, 0.49999999, -0.85065082), (-0.72360679, 0.52573114, 0.44721358)
25generate(0.86180338, -0.42532543, 0.27639322), (0.42532544, 0.30901699, -0.8506508), (0.27639322, 0.85065079, 0.44721362)
26generate(-0.36180339, 0.58778525, 0.7236068), (0.26286559, 0.80901699, -0.5257311), (-0.89442719, 2.0E-8, -0.4472136)
27generate(0.44721358, 0.52573108, 0.72360683), (0.85065083, -0.52573108), (-0.27639317, 0.85065082, -0.44721357)
28generate(0.63819654, -0.26286557, 0.72360684), (0.26286557, -0.809017, -0.52573111), (0.72360684, 0.5257311, -0.44721353)
29generate(-0.05278646, -0.68819093, 0.72360681), (-0.68819095, -0.5, -0.52573114), (0.72360682, -0.52573114, -0.44721354)
30generate(-0.67082041, -0.16245981, 0.72360679), (-0.68819094, 0.5, -0.52573114), (-0.27639321, -0.85065082, -0.44721358)
31generate(-0.44721357, 0.52573107, -0.72360683), (-0.85065083, 0.52573108), (0.27639317, 0.85065083, 0.44721358)
32generate(0.3618034, 0.58778525, -0.7236068), (-0.26286558, 0.80901699, 0.52573111), (0.89442719, 2.0E-8, 0.4472136)
33generate(0.67082041, -0.16245982, -0.72360679), (0.68819094, 0.50000001, 0.52573114), (0.27639321, -0.85065081, 0.44721357)
34generate(0.05278646, -0.68819094, -0.72360682), (0.68819094, -0.49999999, 0.52573114), (-0.72360682, -0.52573114, 0.44721353)
35generate(-0.63819654, -0.26286558, -0.72360684), (-0.26286558, -0.80901699, 0.5257311), (-0.72360684, 0.5257311, 0.44721354)
36generate(0.94721362, -0.16245981, -0.27639315), (0.16245981, -0.49999999, 0.85065082), (-0.27639315, -0.85065081, -0.44721362)
37generate(0.13819664, -0.95105651, -0.27639318), (-0.42532544, -0.30901699, 0.8506508), (-0.89442717, -4.0E-8, -0.44721364)
38generate(-0.86180338, -0.42532544, -0.27639322), (-0.42532544, 0.309017, 0.8506508), (-0.27639322, 0.85065078, -0.44721362)
39generate(-0.67082041, 0.68819093, -0.27639321), (0.16245981, 0.5, 0.85065082), (0.72360679, 0.52573114, -0.44721358)
40generate(0.44721358, 0.85065082, -0.27639317), (0.52573108, 0.85065083), (0.72360683, -0.52573108, -0.44721358)
41generate(-0.13819665, 0.42532544, 0.89442717), (-0.95105652, -0.30901699, -4.0E-8), (0.27639318, -0.85065078, 0.44721364)
42generate(0.36180339, 0.26286558, 0.89442719), (-0.58778525, 0.809017, -2.0E-8), (-0.7236068, -0.5257311, 0.4472136)
43generate(0.36180339, -0.26286557, 0.89442719), (0.58778526, 0.80901699, 2.0E-8), (-0.7236068, 0.5257311, 0.44721361)
44generate(-0.13819665, -0.42532543, 0.89442717), (0.95105652, -0.309017, 3.0E-8), (0.27639318, 0.85065079, 0.44721365)
45generate(-0.44721367, 0.89442716), (-1), (0.89442716, 0.44721367)
46generate(-0.44721358, -0.85065082, 0.27639316), (0.52573108, 0.85065083), (-0.72360684, 0.52573108, 0.44721358)
47generate(-0.94721362, 0.16245982, 0.27639315), (0.16245981, -0.5, 0.85065081), (0.27639315, 0.85065082, 0.44721362)
48generate(-0.13819664, 0.95105651, 0.27639318), (-0.42532544, -0.30901699, 0.85065079), (0.89442717, 4.0E-8, 0.44721364)
49generate(0.86180338, 0.42532544, 0.27639322), (-0.42532544, 0.309017, 0.85065079), (0.27639322, -0.85065079, 0.44721361)
50generate(0.67082041, -0.68819094, 0.27639321), (0.16245982, 0.50000001, 0.85065082), (-0.72360679, -0.52573114, 0.44721357)
51generate(0.94721362, 0.16245981, -0.27639315), (-0.16245982, -0.50000001, -0.85065082), (-0.27639314, 0.85065081, -0.44721361)
52generate(0.44721358, -0.85065083, -0.27639317), (-0.52573108, -0.85065083), (0.72360684, 0.52573107, -0.44721357)
53generate(-0.67082041, -0.68819094, -0.27639321), (-0.16245981, 0.5, -0.85065081), (0.72360679, -0.52573114, -0.44721358)
54generate(-0.86180338, 0.42532543, -0.27639322), (0.42532545, 0.30901699, -0.85065079), (-0.27639322, -0.85065079, -0.44721362)
55generate(0.13819665, 0.95105651, -0.27639318), (0.42532544, -0.309017, -0.85065079), (-0.89442717, 4.0E-8, -0.44721364)
56generate(-0.36180339, 0.26286557, -0.89442719), (0.58778526, 0.809017, 3.0E-8), (0.7236068, -0.5257311, -0.44721361)
57generate(0.13819665, 0.42532543, -0.89442717), (0.95105652, -0.30901699, 4.0E-8), (-0.27639318, -0.85065079, -0.44721365)
58generate(0.44721367, -0.89442716), (-1), (-0.89442716, -0.44721367)
59generate(0.13819665, -0.42532544, -0.89442717), (-0.95105652, -0.309017, -3.0E-8), (-0.27639317, 0.85065079, -0.44721364)
60generate(-0.36180339, -0.26286558, -0.89442719), (-0.58778525, 0.80901699, -2.0E-8), (0.72360681, 0.5257311, -0.4472136)

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Components

#1: Protein VP1


Mass: 33091.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E30 / References: UniProt: A0A0F6T703*PLUS
#2: Protein VP2


Mass: 36428.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E30 / References: UniProt: A0A0F6T703*PLUS
#3: Protein VP3


Mass: 26157.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E30 / References: UniProt: A8BJF8*PLUS
#4: Antibody Heavy chain


Mass: 23332.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#5: Antibody Light chain


Mass: 23490.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Has protein modificationY

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Echovirus E30 in complex with 6C5COMPLEXThe complex is obtained by mixing E30 with 6C5all0NATURAL
2E30COMPLEXE30 particles purified from the cells inoculated with live E30#1-#31NATURAL
36C5-FabCOMPLEXFab fragment generated by proteolytic cleavage of IgG antibody.#4-#51NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Echovirus E3041846
33Mus musculus (house mouse)10090
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11NONOSEROTYPEVIRION
22
33
Natural host
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens9606
12
13
Virus shell
IDEntity assembly-IDDiameter (nm)Triangulation number (T number)
11303
12
13
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 25

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2RELION3image acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2120 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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