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- EMDB-30303: E30 F-particle in complex with 4B10 -

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Basic information

Entry
Database: EMDB / ID: EMD-30303
TitleE30 F-particle in complex with 4B10
Map data
Sample
  • Complex: E30 F-particle in complex with 4B10
    • Complex: E30 F-particle in complex with 4B10
      • Protein or peptide: Light chain
      • Protein or peptide: Heavy chain
    • Complex: E30 F-particle in complex with 4B10
      • Protein or peptide: VP1
      • Protein or peptide: VP2
      • Protein or peptide: VP3
      • Protein or peptide: VP4
  • Ligand: SPHINGOSINE
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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / viral capsid ...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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / viral capsid / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / 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 / 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 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) / 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 / 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 / VP4
Similarity search - Component
Biological speciesMus musculus (house mouse) / Echovirus E30 / Mouse (mice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang K / Zheng B / Zhang L / Cui L / Su X / Zhang Q / Guo Y / Zhu L / Zhu F / Rao Z / Wang X
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
DepositionMay 28, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateSep 16, 2020-
Current statusSep 16, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7c80
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7c80
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30303.png

Downloads & links

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Map

FileDownload / File: emd_30303.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.313 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.04586241 - 0.078852184
Average (Standard dev.)0.0000607643 (±0.0046068933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 603.98 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3131.3131.313
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z603.980603.980603.980
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS460460460
D min/max/mean-0.0460.0790.000

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Supplemental data

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Sample components

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Entire : E30 F-particle in complex with 4B10

EntireName: E30 F-particle in complex with 4B10
Components
  • Complex: E30 F-particle in complex with 4B10
    • Complex: E30 F-particle in complex with 4B10
      • Protein or peptide: Light chain
      • Protein or peptide: Heavy chain
    • Complex: E30 F-particle in complex with 4B10
      • Protein or peptide: VP1
      • Protein or peptide: VP2
      • Protein or peptide: VP3
      • Protein or peptide: VP4
  • Ligand: SPHINGOSINE

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Supramolecule #1: E30 F-particle in complex with 4B10

SupramoleculeName: E30 F-particle in complex with 4B10 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: E30 F-particle in complex with 4B10

SupramoleculeName: E30 F-particle in complex with 4B10 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: E30 F-particle in complex with 4B10

SupramoleculeName: E30 F-particle in complex with 4B10 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Echovirus E30

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Macromolecule #1: Light chain

MacromoleculeName: Light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 24.32683 KDa
SequenceString: DIELTQSPAT LSVTPGDSVS LSCRASQSIS NSLHWYQQRS HESPRRLIKT ASAEKAKSIS GIPSRFSVSR GNTSFTLSIN SVETEDFGM YFCQQAYAGS KLQPHTGAGT KLEIKRADAA PTVSIFPPSS EQLTSGGASV VCFLNNFYPK DINVKWKIDG S ERQNGVLN ...String:
DIELTQSPAT LSVTPGDSVS LSCRASQSIS NSLHWYQQRS HESPRRLIKT ASAEKAKSIS GIPSRFSVSR GNTSFTLSIN SVETEDFGM YFCQQAYAGS KLQPHTGAGT KLEIKRADAA PTVSIFPPSS EQLTSGGASV VCFLNNFYPK DINVKWKIDG S ERQNGVLN SWTDQDSKDS TYSMSSTLTL TKDEYERHNS YTCEATHKTS TSPIVKSFNR NEC

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Macromolecule #2: Heavy chain

MacromoleculeName: Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 21.729221 KDa
SequenceString: QVQLQQSGGG LVKPGGSLKL SCAASGFTFS SYWMHWVQTP EKRLEWVATI SSGGGDTYYG DSVKGPATIS RDNAKNTLYL QMSSLKSED TAMYACTGAG GSTYYFDYWG QGTTVTVSSP AAASTAASMV TLGCLVKGYF PEPVTVTWNS GSLSSGVHTF P AVLQSDLY ...String:
QVQLQQSGGG LVKPGGSLKL SCAASGFTFS SYWMHWVQTP EKRLEWVATI SSGGGDTYYG DSVKGPATIS RDNAKNTLYL QMSSLKSED TAMYACTGAG GSTYYFDYWG QGTTVTVSSP AAASTAASMV TLGCLVKGYF PEPVTVTWNS GSLSSGVHTF P AVLQSDLY TLSSSVTVPS STWPSETVTC NVAHPASSTK VDKKIVPR

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Macromolecule #3: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 3 / 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 #4: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E30
Molecular weightTheoretical: 28.878502 KDa
SequenceString: SPTVEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPT YLSDHEATAV DQPTQPDVAT CRFYTLESVK WESSSAGWWW KFPEALSDM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGAATTDH AFNHTKLSNI GQAMEFSAKK S TDQTGPQT ...String:
SPTVEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPT YLSDHEATAV DQPTQPDVAT CRFYTLESVK WESSSAGWWW KFPEALSDM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGAATTDH AFNHTKLSNI GQAMEFSAKK S TDQTGPQT AVHNAGMGVA VGNLTIFPHQ WINLRTNNSA TIVMPYINSV PMDNMYRHYN FTLMVIPFAK LEHSPQASTY VP ITVTVAP MCAEYNGLRL AGHQ

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Macromolecule #5: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 5 / 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 #6: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E30
Molecular weightTheoretical: 7.6475 KDa
SequenceString:
(MYR)GAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDSASNS LNRQDFTQDP SKFTEPVKDV MIKTLPALN

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Macromolecule #7: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE / Sphingosine

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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

Concentration2.0 mg/mL
BufferpH: 7.4 / Component - Name: PBS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0025 µm / Nominal defocus min: 0.0012 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 998 / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 18328
CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 1841

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