[English] 日本語
Yorodumi
- EMDB-30304: E30 F-particle in complex with 6C5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30304
TitleE30 F-particle in complex with 6C5
Map data
Sample
  • Complex: E30 F-particle in complex with 6C5
    • Complex: E30 F-particle in complex with 6C5
      • Protein or peptide: VP1
      • Protein or peptide: VP2
      • Protein or peptide: VP3
      • Protein or peptide: VP4
    • Complex: E30 F-particle in complex with 6C5
      • Protein or peptide: Light chain
      • Protein or peptide: Heavy chain
  • 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 / 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 / viral capsid / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / DNA replication / RNA helicase activity / induction by virus of host autophagy / 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 / VP4
Similarity search - Component
Biological speciesEchovirus E30 / Mus musculus (house mouse) / Mouse (mice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7c81
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7c81
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30304.png

Downloads & links

-
Map

FileDownload / File: emd_30304.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: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.113505736 - 0.19352621
Average (Standard dev.)0.0019217716 (±0.0135751655)
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/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.1140.1940.002

-
Supplemental data

-
Sample components

+
Entire : E30 F-particle in complex with 6C5

EntireName: E30 F-particle in complex with 6C5
Components
  • Complex: E30 F-particle in complex with 6C5
    • Complex: E30 F-particle in complex with 6C5
      • Protein or peptide: VP1
      • Protein or peptide: VP2
      • Protein or peptide: VP3
      • Protein or peptide: VP4
    • Complex: E30 F-particle in complex with 6C5
      • Protein or peptide: Light chain
      • Protein or peptide: Heavy chain
  • Ligand: SPHINGOSINE

+
Supramolecule #1: E30 F-particle in complex with 6C5

SupramoleculeName: E30 F-particle in complex with 6C5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

+
Supramolecule #2: E30 F-particle in complex with 6C5

SupramoleculeName: E30 F-particle in complex with 6C5 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Echovirus E30

+
Supramolecule #3: E30 F-particle in complex with 6C5

SupramoleculeName: E30 F-particle in complex with 6C5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Mus musculus (house mouse)

+
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

+
Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / 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

+
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

+
Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / 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

+
Macromolecule #5: Light chain

MacromoleculeName: Light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
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

+
Macromolecule #6: Heavy chain

MacromoleculeName: Heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
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

+
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.4 / Component - Name: PBS / Details: pH = 7.4 PBS purchased from Thermo Fisher.
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 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK I

-
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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 16488
CTF correctionSoftware - Name: Gctf
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 10127
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: CC
Output model

PDB-7c81:
E30 F-particle in complex with 6C5

+
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