[English] 日本語
Yorodumi
- EMDB-38170: Cryo-EM structure of coxsackievirus A16 empty particle in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38170
TitleCryo-EM structure of coxsackievirus A16 empty particle in complex with Fab h1A6.2
Map data
Sample
  • Complex: Coxsackievirus A16 empty particle in complex with Fab h1A6.2
    • Complex: The Fab of h1A6.2
    • Virus: Coxsackievirus A16
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP3
KeywordsCryo-EM / coxsackievirus A16 / VIRUS
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / symbiont-mediated suppression of host gene expression / viral capsid / virion attachment to host cell / structural molecule activity
Similarity search - Function
Picornavirus coat protein / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesMus (mice) / Coxsackievirus A16
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsJiang Y / Huang Y / Zhu R / Zheng Q / Li S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of coxsackievirus A16 empty particle in complex with Fab h1A6.2
Authors: Jiang Y / Huang Y / Zhu R / Zheng Q / Li S / Xia N
History
DepositionNov 29, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38170.png

Downloads & links

-
Map

FileDownload / File: emd_38170.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: 3.5
Minimum - Maximum-18.290130000000001 - 35.877678000000003
Average (Standard dev.)-0.01666676 (±1.6575271)
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

-
Half map: #2

Fileemd_38170_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38170_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Coxsackievirus A16 empty particle in complex with Fab h1A6.2

EntireName: Coxsackievirus A16 empty particle in complex with Fab h1A6.2
Components
  • Complex: Coxsackievirus A16 empty particle in complex with Fab h1A6.2
    • Complex: The Fab of h1A6.2
    • Virus: Coxsackievirus A16
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP3

-
Supramolecule #1: Coxsackievirus A16 empty particle in complex with Fab h1A6.2

SupramoleculeName: Coxsackievirus A16 empty particle in complex with Fab h1A6.2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #3: The Fab of h1A6.2

SupramoleculeName: The Fab of h1A6.2 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Mus (mice)

-
Supramolecule #2: Coxsackievirus A16

SupramoleculeName: Coxsackievirus A16 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: all / NCBI-ID: 31704 / Sci species name: Coxsackievirus A16 / Virus type: VIRION / Virus isolate: OTHER / 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: Coxsackievirus A16
Molecular weightTheoretical: 33.106352 KDa
SequenceString: GDPIADMIDQ TVNNQVNRSL TALQVLPTAA NTEASSHRLG TGVVPALQAA ETGASSNASD KNLIETRCVL NHHSTQETAI GNFFSRAGL VSIITMPTTD TQNTDGYVNW DIDLMGYAQL RRKCELFTYM RFDAEFTFVV AKPNGVLVPQ LLQYMYVPPG A PKPTSRDS ...String:
GDPIADMIDQ TVNNQVNRSL TALQVLPTAA NTEASSHRLG TGVVPALQAA ETGASSNASD KNLIETRCVL NHHSTQETAI GNFFSRAGL VSIITMPTTD TQNTDGYVNW DIDLMGYAQL RRKCELFTYM RFDAEFTFVV AKPNGVLVPQ LLQYMYVPPG A PKPTSRDS FAWQTATNPS VFVKMTDPPA QVSVPFMSPA SAYQWFYDGY PTFGEHLQAN DLDYGQCPNN MMGTFSIRTV GT EKSPHSI TLRVYMRIKH VRAWIPRPLR NQPYLFKTNP NYKGNDIKCT STSRDKITTL

UniProtKB: Genome polyprotein

-
Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A16
Molecular weightTheoretical: 27.557104 KDa
SequenceString: SPSAEACGYS DRVAQLTIGN STITTQEAAN IVIAYGEWPE YCPDTDATAV DKPTRPDVSV NRFFTLDTKS WAKDSKGWYW KFPDVLTEV GVFGQNAQFH YLYRSGFCVH VQCNASKFHQ GALLVAVLPE YVLGTIAGGT GNENSHPPYA TTQPGQVGAV L THPYVLDA ...String:
SPSAEACGYS DRVAQLTIGN STITTQEAAN IVIAYGEWPE YCPDTDATAV DKPTRPDVSV NRFFTLDTKS WAKDSKGWYW KFPDVLTEV GVFGQNAQFH YLYRSGFCVH VQCNASKFHQ GALLVAVLPE YVLGTIAGGT GNENSHPPYA TTQPGQVGAV L THPYVLDA GIPLSQLTVC PHQWINLRTN NCATIIVPYM NTVPFDSALN HCNFGLLVIP VVPLDFNAGA TSEIPITVTI AP MCAEFAG LRQAVKQ

UniProtKB: Genome polyprotein

-
Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A16
Molecular weightTheoretical: 26.654295 KDa
SequenceString: GIPTELKPGT NQFLTTDDGV SAPILPGFHP TPPIHIPGEV HNLLEICRVE TILEVNNLKT NETTPMQRLC FPVSVQSKTG ELCAAFRAD PGRDGPWQST ILGQLCRYYT QWSGSLEVTF MFAGSFMATG KMLIAYTPPG GNVPADRITA MLGTHVIWDF G LQSSVTLV ...String:
GIPTELKPGT NQFLTTDDGV SAPILPGFHP TPPIHIPGEV HNLLEICRVE TILEVNNLKT NETTPMQRLC FPVSVQSKTG ELCAAFRAD PGRDGPWQST ILGQLCRYYT QWSGSLEVTF MFAGSFMATG KMLIAYTPPG GNVPADRITA MLGTHVIWDF G LQSSVTLV VPWISNTHYR AHARAGYFDY YTTGIITIWY QTNYVVPIGA PTTAYIVALA AAQDNFTMKL CKDTEDIEQT AN IQ

UniProtKB: Genome polyprotein

-
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) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32746
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