[English] 日本語
Yorodumi
- EMDB-26609: Structure of the VP5*/VP8* assembly from the human rotavirus stra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26609
TitleStructure of the VP5*/VP8* assembly from the human rotavirus strain CDC-9 - Reversed conformation
Map dataReconstructed, sharpen_map.
Sample
  • Virus: Rotavirus
    • Protein or peptide: Outer capsid protein VP5*
    • Protein or peptide: Intermediate capsid protein VP6
    • Protein or peptide: Outer capsid glycoprotein VP7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
Function / homology
Function and homology information


viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / membrane => GO:0016020 ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / membrane => GO:0016020 / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / membrane / metal ion binding
Similarity search - Function
Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 ...Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Viral capsid/haemagglutinin protein / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Intermediate capsid protein VP6 / Outer capsid glycoprotein VP7 / Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJenni S / Zongli L / Wang Y / Bessey T / Salgado EN / Schmidt AG / Greenberg HB / Jiang B / Harrison SC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)CA13202 United States
CitationJournal: J Virol / Year: 2022
Title: Rotavirus VP4 Epitope of a Broadly Neutralizing Human Antibody Defined by Its Structure Bound with an Attenuated-Strain Virion.
Authors: Simon Jenni / Zongli Li / Yuhuan Wang / Theresa Bessey / Eric N Salgado / Aaron G Schmidt / Harry B Greenberg / Baoming Jiang / Stephen C Harrison /
Abstract: Rotavirus live-attenuated vaccines, both mono- and pentavalent, generate broadly heterotypic protection. B-cells isolated from adults encode neutralizing antibodies, some with affinity for VP5*, that ...Rotavirus live-attenuated vaccines, both mono- and pentavalent, generate broadly heterotypic protection. B-cells isolated from adults encode neutralizing antibodies, some with affinity for VP5*, that afford broad protection in mice. We have mapped the epitope of one such antibody by determining the high-resolution cryo-EM structure of its antigen-binding fragment (Fab) bound to the virion of a candidate vaccine strain, CDC-9. The Fab contacts both the distal end of a VP5* β-barrel domain and the two VP8* lectin-like domains at the tip of a projecting spike. Its interactions with VP8* do not impinge on the likely receptor-binding site, suggesting that the mechanism of neutralization is at a step subsequent to initial attachment. We also examined structures of CDC-9 virions from two different stages of serial passaging. Nearly all the VP4 (cleaved to VP8*/VP5*) spikes on particles from the earlier passage (wild-type isolate) had transitioned from the "upright" conformation present on fully infectious virions to the "reversed" conformation that is probably the end state of membrane insertion, unable to mediate penetration, consistent with the very low infectivity of the wild-type isolate. About half the VP4 spikes were upright on particles from the later passage, which had recovered substantial infectivity but had acquired an attenuated phenotype in neonatal rats. A mutation in VP4 that occurred during passaging appears to stabilize the interface at the apex of the spike and could account for the greater stability of the upright spikes on the late-passage, attenuated isolate. Rotavirus live-attenuated vaccines generate broadly heterotypic protection, and B-cells isolated from adults encode antibodies that are broadly protective in mice. Determining the structural and mechanistic basis of broad protection can contribute to understanding the current limitations of vaccine efficacy in developing countries. The structure of an attenuated human rotavirus isolate (CDC-9) bound with the Fab fragment of a broadly heterotypic protective antibody shows that protection is probably due to inhibition of the conformational transition in the viral spike protein (VP4) critical for viral penetration, rather than to inhibition of receptor binding. A comparison of structures of CDC-9 virus particles at two stages of serial passaging supports a proposed mechanism for initial steps in rotavirus membrane penetration.
History
DepositionApr 7, 2022-
Header (metadata) releaseJul 27, 2022-
Map releaseJul 27, 2022-
UpdateAug 31, 2022-
Current statusAug 31, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26609.png

Downloads & links

-
Map

FileDownload / File: emd_26609.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstructed, sharpen_map.
Voxel sizeX=Y=Z: 1.231 Å
Density
Contour LevelBy EMDB: 0.015
Minimum - Maximum-0.049042273 - 0.09365009
Average (Standard dev.)-3.247502e-06 (±0.0064770686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 393.91998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_26609_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half map 1, reconstructed, masked.

Fileemd_26609_additional_1.map
AnnotationHalf map 1, reconstructed, masked.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half map 2, reconstructed, masked.

Fileemd_26609_additional_2.map
AnnotationHalf map 2, reconstructed, masked.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1, reconstructed.

Fileemd_26609_half_map_1.map
AnnotationHalf map 1, reconstructed.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2, reconstructed.

Fileemd_26609_half_map_2.map
AnnotationHalf map 2, reconstructed.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Rotavirus

EntireName: Rotavirus
Components
  • Virus: Rotavirus
    • Protein or peptide: Outer capsid protein VP5*
    • Protein or peptide: Intermediate capsid protein VP6
    • Protein or peptide: Outer capsid glycoprotein VP7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium

-
Supramolecule #1: Rotavirus

SupramoleculeName: Rotavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 10912 / Sci species name: Rotavirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host systemOrganism: Chlorocebus aethiops (grivet)

-
Macromolecule #1: Outer capsid protein VP5*

MacromoleculeName: Outer capsid protein VP5* / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus / Strain: CDC-9
Molecular weightTheoretical: 59.605254 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: AQVDEDIIVS KTSLWKEMQY NRDIIIRFKF GNSIVKMGGL GYKWSEISYK AANYQYNYLR DGEQVTAHTT CSVNGVNNFS YNGGFLPTD FGISRYEVIK ENSYVYVDYW DDSKAFRNIV YVRSLAANLN SVRCTGGSYH FSLPVGAWPV INGGAVSLHF A GVTLSTQF ...String:
AQVDEDIIVS KTSLWKEMQY NRDIIIRFKF GNSIVKMGGL GYKWSEISYK AANYQYNYLR DGEQVTAHTT CSVNGVNNFS YNGGFLPTD FGISRYEVIK ENSYVYVDYW DDSKAFRNIV YVRSLAANLN SVRCTGGSYH FSLPVGAWPV INGGAVSLHF A GVTLSTQF TDFVSLNSLR FRFSLTVDEP PFSILRTRTV NLYGLPAANP NNGNEYYEIS GRFSLISLVP TNDDYQTPIM NS VTVRQDL ERQLTNLREE FNSLSQEIAM AQLIDLALLP LDMFSMFSGI KSTIDLTKSM ATSVMKKFRK SKLATSISEM TNS LSDAAS SASRNVSIRS NLSAISNWTN VSNDVSNVTN SLNDISTQTS TIGKKLRLKE MITQTEGMSF DDISAAVLKT KIDM STQIG KNTLPDIVTE ASEKFIPKRS YRILKDDEVM EINTEGKFFA YKINTFDEVP FDVNKFAELV TDSPVISAII DFKTL KNLN DNYGITRTEA LNLIKSNPNM LRNFINQNNP IIRNRIEQLI LQCKL

-
Macromolecule #2: Intermediate capsid protein VP6

MacromoleculeName: Intermediate capsid protein VP6 / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus / Strain: CDC-9
Molecular weightTheoretical: 44.994965 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: MEVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIVT MNGNDFQTGG IGNLPIRNWT FDFGLLGTTL LNLDANYVET ARTTIEYFI DFIDNVCMDE MVRESQRNGV APQSEALRKL AGIKFKRINF NNSSEYIENW NLQNRRQRTG FVFHKPNIFP Y SASFTLNR ...String:
MEVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIVT MNGNDFQTGG IGNLPIRNWT FDFGLLGTTL LNLDANYVET ARTTIEYFI DFIDNVCMDE MVRESQRNGV APQSEALRKL AGIKFKRINF NNSSEYIENW NLQNRRQRTG FVFHKPNIFP Y SASFTLNR SQPMHDNLMG TMWLNAGSEI QVAGFDYSCA LNAPANIQQF EHIVQLRRAL TTATITLLPD AERFSFPRVI NS ADGATTW FFNPIILRPN NVEVEFLLNG QIINTYQARF GTIVARNFDT IRLSFQLMRP PNMTPAVNAL FPQAQPFQHH ATV GLTLRI ESAVCESVLA DANETLLANV TAVRQEYAIP VGPVFPPGMN WTELITNYSP SREDNLQRVF TVASIRSMLI K

-
Macromolecule #3: Outer capsid glycoprotein VP7

MacromoleculeName: Outer capsid glycoprotein VP7 / type: protein_or_peptide / ID: 3 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus / Strain: CDC-9
Molecular weightTheoretical: 37.435934 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: MYGIEYTTIL IFLISIILLN YILKSVTRIM DYIIYRFLLI FVALFALTKA QNYGLNIPIT GSMDTVYSNS TREEVFLTST LCLYYPTEA STQISDGEWK DSLSQMFLIK GWPTGSVYFK EYSNIVDFSV DPQLYCDYNL VLMKYDQSLE LDMSELADLI L NEWLCNPM ...String:
MYGIEYTTIL IFLISIILLN YILKSVTRIM DYIIYRFLLI FVALFALTKA QNYGLNIPIT GSMDTVYSNS TREEVFLTST LCLYYPTEA STQISDGEWK DSLSQMFLIK GWPTGSVYFK EYSNIVDFSV DPQLYCDYNL VLMKYDQSLE LDMSELADLI L NEWLCNPM DITLYYYQQS GESNKWISMG SSCTVKVCPL NTQTLGIGCQ TTNVDSFETV AENEKLAIVD VVDGINHKIN LT TTTCTIR NCKKLGPREN VAVIQVGGAN ILDITADPTT NPQIERMMRV NWKRWWQVFY TIVDYINQIV QVMSKRSRSL NSA AFYYRV

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 35 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 72 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 359970
FSC plot (resolution estimation)

+
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