[English] 日本語
Yorodumi
- EMDB-32983: Cryo-EM structure of Coxsackievirus B1 muture virion in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32983
TitleCryo-EM structure of Coxsackievirus B1 muture virion in complex with nAbs 8A10 and 5F5 (CVB1-M:8A10:5F5)
Map data
Sample
  • Complex: Cryo-EM structure of Coxsackievirus B1 muture virion in complex with nAbs 8A10 and 5F5 (CVB1-M:8A10:5F5)
    • Protein or peptide: 8A10 light chain
    • Protein or peptide: 8A10 heavy chain
    • Protein or peptide: Virion protein 1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: Capsid protein VP4
    • Protein or peptide: 5F5 light chain
    • Protein or peptide: 5F5 heavy chain
  • Ligand: PALMITIC ACID
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 / symbiont-mediated suppression of host gene expression ...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 / symbiont-mediated suppression of host gene expression / nucleoside-triphosphate phosphatase / channel activity / viral capsid / monoatomic ion transmembrane transport / host cell cytoplasm / DNA replication / RNA helicase activity / induction by virus of host autophagy / symbiont entry into host cell / 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 / cytoplasm
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 / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B1 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsZheng Q / Zhu R / Sun H / Cheng T / Li S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Host Microbe / Year: 2022
Title: Structural basis for the synergistic neutralization of coxsackievirus B1 by a triple-antibody cocktail.
Authors: Qingbing Zheng / Rui Zhu / Zhichao Yin / Longfa Xu / Hui Sun / Hai Yu / Yuanyuan Wu / Yichao Jiang / Qiongzi Huang / Yang Huang / Dongqing Zhang / Liqin Liu / Hongwei Yang / Maozhou He / ...Authors: Qingbing Zheng / Rui Zhu / Zhichao Yin / Longfa Xu / Hui Sun / Hai Yu / Yuanyuan Wu / Yichao Jiang / Qiongzi Huang / Yang Huang / Dongqing Zhang / Liqin Liu / Hongwei Yang / Maozhou He / Zhenhong Zhou / Yanan Jiang / Zhenqin Chen / Huan Zhao / Yuqiong Que / Zhibo Kong / Lizhi Zhou / Tingting Li / Jun Zhang / Wenxin Luo / Ying Gu / Tong Cheng / Shaowei Li / Ningshao Xia /
Abstract: Coxsackievirus B1 (CVB1) is an emerging pathogen associated with severe neonatal diseases including aseptic meningitis, myocarditis, and pancreatitis and also with the development of type 1 diabetes. ...Coxsackievirus B1 (CVB1) is an emerging pathogen associated with severe neonatal diseases including aseptic meningitis, myocarditis, and pancreatitis and also with the development of type 1 diabetes. We characterize the binding and therapeutic efficacies of three CVB1-specific neutralizing antibodies (nAbs) identified for their ability to inhibit host receptor engagement. High-resolution cryo-EM structures showed that these antibodies recognize different epitopes but with an overlapping region in the capsid VP2 protein and specifically the highly variable EF loop. Moreover, they perturb capsid-receptor interactions by binding various viral particle forms. Antibody combinations achieve synergetic neutralization via a stepwise capsid transition and virion disruption, indicating dynamic changes in the virion in response to multiple nAbs targeting the receptor-binding site. Furthermore, this three-antibody cocktail protects against lethal challenge in neonatal mice and limits pancreatitis and viral replication in a non-obese diabetic mouse model. These results illustrate the utility of nAbs for rational design of therapeutics against picornaviruses such as CVB.
History
DepositionFeb 28, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateSep 28, 2022-
Current statusSep 28, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32983.png

Downloads & links

-
Map

FileDownload / File: emd_32983.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 560 pix.
= 627.2 Å		1.12 Å/pix.
x 560 pix.
= 627.2 Å		1.12 Å/pix.
x 560 pix.
= 627.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.9036365 - 4.8207445
Average (Standard dev.)0.0015025062 (±0.24661605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 627.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Cryo-EM structure of Coxsackievirus B1 muture virion in complex w...

EntireName: Cryo-EM structure of Coxsackievirus B1 muture virion in complex with nAbs 8A10 and 5F5 (CVB1-M:8A10:5F5)
Components
  • Complex: Cryo-EM structure of Coxsackievirus B1 muture virion in complex with nAbs 8A10 and 5F5 (CVB1-M:8A10:5F5)
    • Protein or peptide: 8A10 light chain
    • Protein or peptide: 8A10 heavy chain
    • Protein or peptide: Virion protein 1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: Capsid protein VP4
    • Protein or peptide: 5F5 light chain
    • Protein or peptide: 5F5 heavy chain
  • Ligand: PALMITIC ACID

+
Supramolecule #1: Cryo-EM structure of Coxsackievirus B1 muture virion in complex w...

SupramoleculeName: Cryo-EM structure of Coxsackievirus B1 muture virion in complex with nAbs 8A10 and 5F5 (CVB1-M:8A10:5F5)
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Coxsackievirus B1

+
Macromolecule #1: 8A10 light chain

MacromoleculeName: 8A10 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.945163 KDa
SequenceString:
DIQMTQTKSS LSASLGDRVT ISCRASQDIS NYLNWYQQKP DGSVKLLIYY TSTLHSGVPS RFSGSGSGTD YSLTINSLEQ EDIATYFCQ QGNTFPFTFG GGTKLEIRR

+
Macromolecule #2: 8A10 heavy chain

MacromoleculeName: 8A10 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.323863 KDa
SequenceString:
QVQLQQSAAE LARPGASVKM SCKASGYTFT TYTMHWVKQR PGQGLEWIGY INPSSRYTEY NQKFKDKTTL TADKSSSTAY MQLSSLTFE DSAVYYCARR SEADRFVYWG QGTLVTVSA

+
Macromolecule #3: Virion protein 1

MacromoleculeName: Virion protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B1
Molecular weightTheoretical: 31.207117 KDa
SequenceString: GPVEESVDRA VARVADTISS RPTNSESIPA LTAAETGHTS QVVPSDTMQT RHVKNYHSRS ESSIENFLCR SACVYYATYT NNSKKGFAE WVINTRQVAQ LRRKLELFTY LRFDLELTFV ITSAQQPSTA SSVDAPVQTH QIMYVPPGGP VPTKVKDYAW Q TSTNPSVF ...String:
GPVEESVDRA VARVADTISS RPTNSESIPA LTAAETGHTS QVVPSDTMQT RHVKNYHSRS ESSIENFLCR SACVYYATYT NNSKKGFAE WVINTRQVAQ LRRKLELFTY LRFDLELTFV ITSAQQPSTA SSVDAPVQTH QIMYVPPGGP VPTKVKDYAW Q TSTNPSVF WTEGNAPPRM SIPFISIGNA YSCFYDGWTQ FSRNGVYGIN TLNNMGTLYM RHVNEAGQGP IKSTVRIYFK PK HVKAWVP RPPRLCQYEK QKNVNFSPIG VTTSRTDIIT T

+
Macromolecule #4: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B1
Molecular weightTheoretical: 29.122744 KDa
SequenceString: SPSAEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVQ WMKNSAGWWW KLPDALSQM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSNLNN TPEFSELSGG DSARMFTDTQ V GESNAKKV ...String:
SPSAEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVQ WMKNSAGWWW KLPDALSQM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSNLNN TPEFSELSGG DSARMFTDTQ V GESNAKKV QTAVWNAGMG VGVGNLTIFP HQWINLRTNN SATLVMPYIN SVPMDNMFRH NNLTLMIIPF VPLNYSEGSS PY VPITVTI APMCAEYNGL RLASNQ

+
Macromolecule #5: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus B1
Molecular weightTheoretical: 26.328764 KDa
SequenceString: GLPVMTTPGS TQFLTSDDFQ SPSAMPQFDV TPEMQIPGRV NNLMEIAEVD SVVPVNNTED NVSSLKAYQI PVQSNSDNGK QVFGFPLQP GANNVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GVPKNRKDAM LGTHVIWDVG L QSSCVLCV ...String:
GLPVMTTPGS TQFLTSDDFQ SPSAMPQFDV TPEMQIPGRV NNLMEIAEVD SVVPVNNTED NVSSLKAYQI PVQSNSDNGK QVFGFPLQP GANNVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GVPKNRKDAM LGTHVIWDVG L QSSCVLCV PWISQTHYRY VVEDEYTAAG YVTCWYQTNI VVPADVQSSC DILCFVSACN DFSVRMLKDT PFIRQDTFYQ

+
Macromolecule #6: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B1
Molecular weightTheoretical: 7.484246 KDa
SequenceString:
MGAQVSTQKT GAHETGLNAS GNSVIHYTNI NYYKDAASNS ANRQDFTQDP GKFTEPVKDI MVKTMPALN

+
Macromolecule #7: 5F5 light chain

MacromoleculeName: 5F5 light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.218443 KDa
SequenceString:
QIVLSQSPAI LSASPGEKVT MTCRASSSVS YLHWYQQKPG SSPKPWISAT SNLASGVPAR FSGSGSGTSY SLTISRVEAE DAATYYCQQ WSSNPLSFGG GTKLELK

+
Macromolecule #8: 5F5 heavy chain

MacromoleculeName: 5F5 heavy chain / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.50688 KDa
SequenceString:
EIQLQQSGPE LVKPGASVKV SCKASGYSFT DYNIYWVKQS HGKSLEWIGY VDPYNGNTNY NQKFKGKATL TVDKSSSTAF MHLNSLTSE VSTVYYCARG GGYYGGGYYG MDYWGQGTSV TVSS

+
Macromolecule #9: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 9 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81761
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more