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- EMDB-34233: Echovirus3 empty particle in complex with 6D10 Fab (upright) -

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Basic information

Entry
Database: EMDB / ID: EMD-34233
TitleEchovirus3 empty particle in complex with 6D10 Fab (upright)
Map data
Sample
  • Complex: Echovirus3 empty particle in complex with 6D10 Fab (upright)
    • Complex: 6D10 Fab
      • Protein or peptide: Heavy chain of 6D10
      • Protein or peptide: Light chain of 6D10
    • Virus: Echovirus E3
      • Protein or peptide: VP1
      • Protein or peptide: VP0
      • Protein or peptide: VP3
KeywordsE3 Full particle / Echovirus3 Full particle / antibody / 6D10 / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / viral capsid / host cell / nucleoside-triphosphate phosphatase ...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 / viral capsid / host cell / 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 / symbiont entry into host cell / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesMus musculus (house mouse) / Echovirus E3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang X / Fu W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Viruses / Year: 2022
Title: Structural Basis for the Immunogenicity of the C-Terminus of VP1 of Echovirus 3 Revealed by the Binding of a Neutralizing Antibody.
Authors: Shuai Qi / Wangjun Fu / Jinyan Fan / Li Zhang / Binyang Zheng / Kang Wang / Xiangxi Wang / Ling Zhu / Xinjian Li / Yuxia Zhang /
Abstract: Echovirus 3 (E3), a serotype of human enterovirus B (HEV-B), causes severe diseases in infants. Here, we determined the structures of E3 with a monoclonal antibody (MAb) 6D10 by cryo-EM to ...Echovirus 3 (E3), a serotype of human enterovirus B (HEV-B), causes severe diseases in infants. Here, we determined the structures of E3 with a monoclonal antibody (MAb) 6D10 by cryo-EM to comprehensively understand the specificities and the immunological characteristic of this serotype. The solved cryo-EM structures of the F-, A-, and E-particles of E3 bound with 6D10 revealed the structural features of the virus-antibody interface. Importantly, the structures of E-particles bound with 6D10 revealed for the first time the nature of the C-terminus of VP1 for HEV-Bs at the structural level. The highly immunogenic nature of this region in the E-particles provides new strategies for vaccine development for HEV-Bs.
History
DepositionSep 6, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34233.png

Downloads & links

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Map

FileDownload / File: emd_34233.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 380 pix.
= 513. Å		1.35 Å/pix.
x 380 pix.
= 513. Å		1.35 Å/pix.
x 380 pix.
= 513. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.03
Minimum - Maximum-0.10215283 - 0.1711003
Average (Standard dev.)0.00085927296 (±0.0081698205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 513.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34233_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34233_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Echovirus3 empty particle in complex with 6D10 Fab (upright)

EntireName: Echovirus3 empty particle in complex with 6D10 Fab (upright)
Components
  • Complex: Echovirus3 empty particle in complex with 6D10 Fab (upright)
    • Complex: 6D10 Fab
      • Protein or peptide: Heavy chain of 6D10
      • Protein or peptide: Light chain of 6D10
    • Virus: Echovirus E3
      • Protein or peptide: VP1
      • Protein or peptide: VP0
      • Protein or peptide: VP3

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Supramolecule #1: Echovirus3 empty particle in complex with 6D10 Fab (upright)

SupramoleculeName: Echovirus3 empty particle in complex with 6D10 Fab (upright)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #3: 6D10 Fab

SupramoleculeName: 6D10 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: Echovirus E3

SupramoleculeName: Echovirus E3 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 / NCBI-ID: 47516 / Sci species name: Echovirus E3 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E3
Molecular weightTheoretical: 26.940322 KDa
SequenceString: YHSRTESSIE NFLCRAACVY IATYASAGGT PTERYASWRI NTRQMVQLRR KFELFTYLRF DMEITFVITS TQDPGTQLAQ DMPVLTHQI MYIPPGGPVP NSATDFAWQS STNPSIFWTE GCAPARMSVP FISIGNAYSN FYDGWSHFTQ EGVYGFNSLN N MGHIYVRH ...String:
YHSRTESSIE NFLCRAACVY IATYASAGGT PTERYASWRI NTRQMVQLRR KFELFTYLRF DMEITFVITS TQDPGTQLAQ DMPVLTHQI MYIPPGGPVP NSATDFAWQS STNPSIFWTE GCAPARMSVP FISIGNAYSN FYDGWSHFTQ EGVYGFNSLN N MGHIYVRH VNEQSLGVST STLRVYFKPK HVRAWVPRPP RLSPYVKSSN VNFKPTAVTT ERKDINDVGT LRPVGYTNH

UniProtKB: Genome polyprotein

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Macromolecule #2: VP0

MacromoleculeName: VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E3
Molecular weightTheoretical: 28.069537 KDa
SequenceString: RVRSITLGNS TITTQECANV VVGYGVWPSY LQDNEATAED QPTQPDVATC RFYTLDSIQW QKESDGWWWK FPEALKNMGL FGQNMEYHY LGRSGYTIHV QCNASKFHQG CLLVVCVPEA EMGCSDVERE VVAASLSSED TAKSFSRTES NGQHTVQTVV Y NAGMGVGV ...String:
RVRSITLGNS TITTQECANV VVGYGVWPSY LQDNEATAED QPTQPDVATC RFYTLDSIQW QKESDGWWWK FPEALKNMGL FGQNMEYHY LGRSGYTIHV QCNASKFHQG CLLVVCVPEA EMGCSDVERE VVAASLSSED TAKSFSRTES NGQHTVQTVV Y NAGMGVGV GNLTIFPHQW INLRTNNSAT IVMPYINSVP MDNMFRHYNF TLMIIPFAKL EYTEQASNYV PITVTVAPMC AE YNGLRLA SHQ

UniProtKB: Genome polyprotein

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E3
Molecular weightTheoretical: 25.896449 KDa
SequenceString: MLTPGSNQFL TSDDFQSPSA MPQFDVTPEM KIPGEVHNLM EIAEVDSVVP VNNTKENINS MEAYRIPVTG GDQLHTQVFG FQMQPGLNS VFKRTLLGEI LNYYAHWSGS VKLTFVFCGS AMATGKFLLA YSPPGASPPQ NRKQAMLGTH VIWDVGLQSS C VLCIPWIS ...String:
MLTPGSNQFL TSDDFQSPSA MPQFDVTPEM KIPGEVHNLM EIAEVDSVVP VNNTKENINS MEAYRIPVTG GDQLHTQVFG FQMQPGLNS VFKRTLLGEI LNYYAHWSGS VKLTFVFCGS AMATGKFLLA YSPPGASPPQ NRKQAMLGTH VIWDVGLQSS C VLCIPWIS QTHYRLVQQD EYTSAGYVTC WYQTGLIVPP GAPPSCTILC FASACNDFSV RNLRDTPFIE QTQLLQ

UniProtKB: Genome polyprotein

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Macromolecule #4: Heavy chain of 6D10

MacromoleculeName: Heavy chain of 6D10 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.9382 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
EVQLQQSGPE LARPWASVKI SCQAFYTFSN YGMQWVKQSP GQGLEWIGPF YPGNADTSYN QKFKGKATLT ADKSSSTAYM QFSSLTSED SAVYYCARVV ATTDFDYWGQ GTTVTVSS

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Macromolecule #5: Light chain of 6D10

MacromoleculeName: Light chain of 6D10 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.652158 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
YIEASQSPSS LAVSVGEKVT MSCKSSQSLL YSSNQKNYLA WFQQKPGQSP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVKAEDL AVYYCQQYYS YPYTFGGGTK LKIKR

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24188
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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