[English] 日本語
Yorodumi
- EMDB-75894: Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 5H03 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75894
TitleCryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 5H03
Map data
SampleEnterovirus != Human enterovirus D68

Enterovirus

  • Virus: Human enterovirus D68
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: 5H03 Fab heavy chain
    • Protein or peptide: 5H03 Fab light chain
KeywordsEV-D68 / B3 subclade / 5H03 neutralizing antibody / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


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 / virion component / ribonucleoside triphosphate phosphatase activity / host cell / nucleoside-triphosphate phosphatase ...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 / virion component / ribonucleoside triphosphate phosphatase activity / host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont-mediated suppression of host innate immune response / 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 / symbiont entry into host cell / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
: / Picornavirus coat protein / 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 / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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
Similarity search - Component
Biological speciesHuman enterovirus D68 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsCheng J / Lei H / Pletnev S / Morano NC / Zhang B / Du H / Rubin S / Moss DL / Krug PW / Kanekiyo M ...Cheng J / Lei H / Pletnev S / Morano NC / Zhang B / Du H / Rubin S / Moss DL / Krug PW / Kanekiyo M / Pierson TC / Ruckwardt TJ / Shapiro L / Kwong PD / Zhou T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 5H03
Authors: Cheng J / Lei H / Pletnev S / Morano NC / Zhang B / Du H / Rubin S / Moss DL / Krug PW / Kanekiyo M / Pierson TC / Ruckwardt TJ / Shapiro L / Kwong PD / Zhou T
History
DepositionMar 6, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75894.png

Downloads & links

-
Map

FileDownload / File: emd_75894.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.15900187 - 0.47172534
Average (Standard dev.)0.00053492613 (±0.02759156)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 531.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_75894_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_75894_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Enterovirus

EntireName: Enterovirus
Components
  • Virus: Human enterovirus D68
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: 5H03 Fab heavy chain
    • Protein or peptide: 5H03 Fab light chain

-
Supramolecule #1: Human enterovirus D68

SupramoleculeName: Human enterovirus D68 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 42789 / Sci species name: Human enterovirus D68 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SUBSPECIES / Virus enveloped: No / Virus empty: Yes

-
Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 25.735379 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VSETLVENFL SRAALVSKRS FEYKDHTSST AQTDKNFFKW TINTRSFVQL RRKLELFTYL RFDAEITILT TVAVNGSNNN TYVGLPDLT LQAMFVPTGA LTPEKQDSFH WQSGSNASVF FKISDPPARM TIPFMCINSA YSVFYDGFAG FEKTGLYGIN P ADTIGNLC ...String:
VSETLVENFL SRAALVSKRS FEYKDHTSST AQTDKNFFKW TINTRSFVQL RRKLELFTYL RFDAEITILT TVAVNGSNNN TYVGLPDLT LQAMFVPTGA LTPEKQDSFH WQSGSNASVF FKISDPPARM TIPFMCINSA YSVFYDGFAG FEKTGLYGIN P ADTIGNLC VRIVNEHQPV GFTVTVRVYM KPKHIKAWAP RPPRTLPYMS IANANYKGKE RAPNALNAII G

UniProtKB: Genome polyprotein

-
Macromolecule #2: Capsid protein VP0

MacromoleculeName: Capsid protein VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 23.797006 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ANYCCAYGEW PNYLPDHEAV AIDKPTQPET ATDRFYTLRS VKWEATSTGW WWKLPDALNN IGMFGQNVQH HYLYRSGFLI HVQCNATKF HQGALLVVAI PEHQRGAHNT TTSPGFDDIM KGEAGGTFNH PYVLDDGTSL ACATIFPHQW INLRTNNSAT I VLPWMNAA ...String:
ANYCCAYGEW PNYLPDHEAV AIDKPTQPET ATDRFYTLRS VKWEATSTGW WWKLPDALNN IGMFGQNVQH HYLYRSGFLI HVQCNATKF HQGALLVVAI PEHQRGAHNT TTSPGFDDIM KGEAGGTFNH PYVLDDGTSL ACATIFPHQW INLRTNNSAT I VLPWMNAA PMDFPLRHNQ WTLAIIPVVP LGTRTMSSMV PITVSIAPMC CEFN

UniProtKB: Genome polyprotein

-
Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 27.170895 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GVPTYLLPGS GQFLTTDDHS SAPVLPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMATGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSITLIIP ...String:
GVPTYLLPGS GQFLTTDDHS SAPVLPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMATGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSITLIIP WISGSHYRMF NNDAKSTNAN VGYVTCFMQT NLIVPSESSD TCSLIGFIAA KDDFSLRLMR DSPDIGQIDH LH GAEAAYQ

UniProtKB: Genome polyprotein

-
Macromolecule #4: 5H03 Fab heavy chain

MacromoleculeName: 5H03 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.768218 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LAQPGGSLGL SCAASGFTFS DYAMTWVRQA SGKGLEWVGY IRTKYNDHAT EYAASVKGRF IISRDDSKNT LFLQMSSLT TEDTAVYYCC REGEFCLGSD CYTSGLDSWG QGVVVTVSS

-
Macromolecule #5: 5H03 Fab light chain

MacromoleculeName: 5H03 Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.764249 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDTVT ITCRASQRFV SSLAWYQQKP GKAPKLLIYS ASNLQSGVPS RFSGRKSGTD FILTIRSLQP EDIGNYYCQ QFYSYPLTFG GGTKVEIK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 54.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wdt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 48000
Initial angle assignmentType: ANGULAR RECONSTITUTION
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