[English] 日本語
Yorodumi
- EMDB-36223: Cryo-EM structure of the GI.4 Chiba VLP complexed with the CV-1A1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36223
TitleCryo-EM structure of the GI.4 Chiba VLP complexed with the CV-1A1 Fv-clasp
Map data
Sample
  • Complex: Viral protein 1 with its antibody fragments
    • Protein or peptide: VP1
    • Protein or peptide: VH,SARAH
    • Protein or peptide: VL,SARAH
KeywordsNOROVIRUS / GI.4 / VIRUS LIKE PARTICLE / human monoclonal antibody / Fv-clasp / VIRUS
Biological speciesNorovirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsHosaka T / Katsura K / Kimura-Someya T / Someya Y / Shirouzu M
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21fk0108121 Japan
Japan Agency for Medical Research and Development (AMED)JP22fk0108121 Japan
CitationJournal: To Be Published
Title: Structural analyses of the GI.4 norovirus by cryo-electron microscopy and X-ray crystallography reveal binding sites for human monoclonal antibodies
Authors: Kimura-Someya T / Katsura K / Kato-Murayama M / Hosaka T / Uchikubo-Kamo T / Ihara K / Hanada K / Murayama K / Shirouzu M / Someya Y
History
DepositionMay 19, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36223.png

Downloads & links

-
Map

FileDownload / File: emd_36223.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.47 Å/pix.
x 500 pix.
= 735. Å		1.47 Å/pix.
x 500 pix.
= 735. Å		1.47 Å/pix.
x 500 pix.
= 735. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.47 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.5610304 - 3.3488245
Average (Standard dev.)0.004567188 (±0.12802236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 735.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_36223_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_36223_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_36223_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_36223_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Viral protein 1 with its antibody fragments

EntireName: Viral protein 1 with its antibody fragments
Components
  • Complex: Viral protein 1 with its antibody fragments
    • Protein or peptide: VP1
    • Protein or peptide: VH,SARAH
    • Protein or peptide: VL,SARAH

-
Supramolecule #1: Viral protein 1 with its antibody fragments

SupramoleculeName: Viral protein 1 with its antibody fragments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Norovirus

-
Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Details: GenBank ID AB042808 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Norovirus
Molecular weightTheoretical: 58.108332 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASKDATPSA DGATGAGQLV PEVNTADPIP IDPVAGSSTA APVAGQVNLI DPWIINNFVQ APQGEFTISP NNTPGDVLFD LQLGPHLNP FLSHLSQMYN GWVGNMRVRV VLAGNAFTAG KVIICCVPPG FQSRTLSIAQ ATLFPHVIAD VRTLDPVEVP L EDVRNVLY ...String:
MASKDATPSA DGATGAGQLV PEVNTADPIP IDPVAGSSTA APVAGQVNLI DPWIINNFVQ APQGEFTISP NNTPGDVLFD LQLGPHLNP FLSHLSQMYN GWVGNMRVRV VLAGNAFTAG KVIICCVPPG FQSRTLSIAQ ATLFPHVIAD VRTLDPVEVP L EDVRNVLY HNNDTQPTMR LLCMLYTPLR TGGASGGTDS FVVAGRVLTC PGPDFNFLFL VPPTVEQKTR PFTVPNIPLK YL SNSRIPN PIEGMSLSPD QTQNVQFQNG RCTIDGQPLG TTPVSVSQLC KFRGRITSGQ RVLNLTELDG SPFMAFAAPA PAG FPDLGS CDWHIEMSKI PNSSTQNNPI VTNSVKPNSQ QFVPHLSSIT LDENVSSGGD YIGTIQWTSP PSDSGGANTN FWKI PDYGS SLAEASQLAP AVYPPGFNEV IVYFMASIPG PNQSGSPNLV PCLLPQEYIT HFISEQAPIQ GEAALLHYVD PDTNR NLGE FKLYPGGYLT CVPNSSSTGP QQLPLDGVFV FASWVSRFYQ LKPVGTAGPA RGRLGVRR

-
Macromolecule #2: VH,SARAH

MacromoleculeName: VH,SARAH / type: protein_or_peptide / ID: 2
Details: VH-SARAH chimera of linker (residues (-6)-0), VH (residues 1-118), and SARAH (residues 119-171)
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.847254 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSSGSSGEVQ LVESGAEVKK PGASVKVSCK ASGYTFTSLY MHWVRQAPGQ GLEWMGMINP SGGGTWNAQK FQGRVTMTRD TSTSTVYME LRSLRSDDTA MYYCARDSDQ YSQGLGYWGQ GTLVTVCSGS DYEFLKSWTV EDLQKRLLAL DPMMEQEIEE I RQKYQSKR QPILDAIEAK

-
Macromolecule #3: VL,SARAH

MacromoleculeName: VL,SARAH / type: protein_or_peptide / ID: 3
Details: VL-SARAH chimera of linker (residues (-6)-0), VL (residues 1-112), and SARAH (residues 113-162)
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.19315 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSSGSSGQSA LTQPASVSGS PGQSITISCT GTSSDVGGYN YVSWYQQHPG KAPKLMIYDV SKRPSGVSNR FSGSKSGNTA SLTISGLQA KDEADYYCSS YTSSSTWVFG GGTKLTVLGG SDYEFLKSWT VEDLQKRLLA LDPMMEQEIE EIRQKYQCKR Q PILDAIEA K

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6out

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47125
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