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- EMDB-30408: E30 E-particle in complex with 6C5 -

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Basic information

Entry
Database: EMDB / ID: EMD-30408
TitleE30 E-particle in complex with 6C5
Map data
Sample
  • Complex: Echovirus E30 in complex with 6C5
    • Complex: E30
      • Protein or peptide: VP1
      • Protein or peptide: VP2
      • Protein or peptide: VP3
    • Complex: 6C5-Fab
      • Protein or peptide: Heavy chain
      • Protein or peptide: Light chain
KeywordsEchovirus B / mature / VIRUS / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEchovirus E30 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang K / Zhu F
Funding support China, 1 items
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, 2020-
Header (metadata) releaseAug 12, 2020-
Map releaseAug 12, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0275
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0275
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cmk
  • Surface level: 0.0275
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7cmk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30408.png

Downloads & links

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Map

FileDownload / File: emd_30408.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 360 pix.
= 475.2 Å		1.32 Å/pix.
x 360 pix.
= 475.2 Å		1.32 Å/pix.
x 360 pix.
= 475.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0275 / Movie #1: 0.0275
Minimum - Maximum-0.066497274 - 0.12878916
Average (Standard dev.)0.0013532102 (±0.009332559)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 475.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z475.200475.200475.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-163-114-126
NX/NY/NZ210124170
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.0660.1290.001

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Supplemental data

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Sample components

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Entire : Echovirus E30 in complex with 6C5

EntireName: Echovirus E30 in complex with 6C5
Components
  • Complex: Echovirus E30 in complex with 6C5
    • Complex: E30
      • Protein or peptide: VP1
      • Protein or peptide: VP2
      • Protein or peptide: VP3
    • Complex: 6C5-Fab
      • Protein or peptide: Heavy chain
      • Protein or peptide: Light chain

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Supramolecule #1: Echovirus E30 in complex with 6C5

SupramoleculeName: Echovirus E30 in complex with 6C5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: The complex is obtained by mixing E30 with 6C5

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Supramolecule #2: E30

SupramoleculeName: E30 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Details: E30 particles purified from the cells inoculated with live E30
Source (natural)Organism: Echovirus E30

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Supramolecule #3: 6C5-Fab

SupramoleculeName: 6C5-Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Details: Fab fragment generated by proteolytic cleavage of IgG antibody.
Source (natural)Organism: Mus musculus (house mouse)

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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 E30
Molecular weightTheoretical: 33.091008 KDa
SequenceString: NDPESALNRA VGRVADTVAS GPVNTEQIPA LTAVETGHTS QVVPSDTMQT RHVINYHTRS ESSIENFMGR AACVYIAQYA TEKVNDELD RYTNWEITTR QVAQLRRKLE MFTYMRFDLE ITFVITSSQR TSTTYASDSP PLTHQVMYVP PGGPIPKSYE D FAWQTSTN ...String:
NDPESALNRA VGRVADTVAS GPVNTEQIPA LTAVETGHTS QVVPSDTMQT RHVINYHTRS ESSIENFMGR AACVYIAQYA TEKVNDELD RYTNWEITTR QVAQLRRKLE MFTYMRFDLE ITFVITSSQR TSTTYASDSP PLTHQVMYVP PGGPIPKSYE D FAWQTSTN PSVFWTEGNA PPRMSIPFMS VGNAYCNFYD GWSHFSQSGV YGYTTLNNMG HLYFRHVNKS TAYPVNSVAR VY FKPKHVK AWVPRAPRLC PYLKARNVNF NVQGVTESRN KITLDRSTHN PLANT

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E30
Molecular weightTheoretical: 36.428777 KDa
SequenceString: MGAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDSASNS LNRQDFTQDP SKFTEPVKDV MIKTLPALNS PTVEECGYSD RVRSITLGN STITTQECAN VVVGYGVWPT YLSDHEATAV DQPTQPDVAT CRFYTLESVK WESSSAGWWW KFPEALSDMG L FGQNMQYH ...String:
MGAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDSASNS LNRQDFTQDP SKFTEPVKDV MIKTLPALNS PTVEECGYSD RVRSITLGN STITTQECAN VVVGYGVWPT YLSDHEATAV DQPTQPDVAT CRFYTLESVK WESSSAGWWW KFPEALSDMG L FGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGAATTDH AFNHTKLSNI GQAMEFSAKK STDQTGPQTA VH NAGMGVA VGNLTIFPHQ WINLRTNNSA TIVMPYINSV PMDNMYRHYN FTLMVIPFAK LEHSPQASTY VPITVTVAPM CAE YNGLRL AGHQ

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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 E30
Molecular weightTheoretical: 26.157531 KDa
SequenceString: GLPTMNTPGS TQFLTSDDFQ SPSAMPQFDV TPEIQIPGQV RNLMEIAEVD SVVPVNNTEG HVNSMEAYRI PVRPQTSSGE QVFGFQLQP GHDSVLKHTL LGEILNYYAN WSGSMKLTFM YCGAAMATGK FLIAYSPPGA GVPGSRRDAM LGTHVIWDVG L QSSCVLCV ...String:
GLPTMNTPGS TQFLTSDDFQ SPSAMPQFDV TPEIQIPGQV RNLMEIAEVD SVVPVNNTEG HVNSMEAYRI PVRPQTSSGE QVFGFQLQP GHDSVLKHTL LGEILNYYAN WSGSMKLTFM YCGAAMATGK FLIAYSPPGA GVPGSRRDAM LGTHVIWDVG L QSSCVLCV PWISQTNYRY VTSDAYTDAG YITCWYQTSI VTPPDIPTTS TILCFVSACN DFSVRLLRDT PFITQQALFQ

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Macromolecule #4: Heavy chain

MacromoleculeName: Heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.332088 KDa
SequenceString: QVQLQQSGSE LVRPGASVKL SCRASGYTFT TYWMHWVKQR PGQGLEWIGN IYPHSGNTNY DERFKSKATL TVDTSSSTAY MQLSSLTSE DSAVYYCTRD LRGFAYWGQG TTVTVSSPKT TPPSVYPLAP AAASTAASMV TLGCLVKGYF PEPVTVTWNS G SLSSGVHT ...String:
QVQLQQSGSE LVRPGASVKL SCRASGYTFT TYWMHWVKQR PGQGLEWIGN IYPHSGNTNY DERFKSKATL TVDTSSSTAY MQLSSLTSE DSAVYYCTRD LRGFAYWGQG TTVTVSSPKT TPPSVYPLAP AAASTAASMV TLGCLVKGYF PEPVTVTWNS G SLSSGVHT FPAVLQSDLY TLSSSVTVPS STWPSETVTC NVAHPASSTK VDKKIVPR

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Macromolecule #5: Light chain

MacromoleculeName: Light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.490846 KDa
SequenceString: DIELTQSPAI MSASPGEKVT MTCSASSSLR YMHWYQQKSG TSPKRWIYDT YNLASGVPVR FSGSGSGTSY SLTISSMEAE DAATYYCQQ WSSNPPTFGA GTKLELKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
DIELTQSPAI MSASPGEKVT MTCSASSSLR YMHWYQQKSG TSPKRWIYDT YNLASGVPVR FSGSGSGTSY SLTISSMEAE DAATYYCQQ WSSNPPTFGA GTKLELKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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 / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 2120
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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