[English] 日本語
Yorodumi
- EMDB-34547: Spike 3-up RBD with THSC20.HVTR04 (Fab4): State - II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34547
TitleSpike 3-up RBD with THSC20.HVTR04 (Fab4): State - II
Map dataState - II: Spike 3-up RBD with THSC20.HVTR04 (Fab4)
Sample
  • Complex: Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [State II - 3-up RBD]
    • Complex: THSC20.HVTR04(Fab4)
    • Complex: Wuhan SARS-CoV-2 Spike protein
KeywordsMonoclonal antibodies / SARS-CoV-2 / Cryo-EM / IMMUNE SYSTEM
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.152 Å
AuthorsRencilin CF / Ansari MY / Chatterjee A / Deshpande S / Mukherjee S / Singh R / Jayatheertha S / Reddy PM / Das P / Hingankar N ...Rencilin CF / Ansari MY / Chatterjee A / Deshpande S / Mukherjee S / Singh R / Jayatheertha S / Reddy PM / Das P / Hingankar N / Rathore D / Varadarajan R / Bhattacharya J / Dutta S
Funding support India, United States, 4 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/INF/22/SP22844/2017 India
Science and Engineering Research Board (SERB)SERB-EMR/2016/000608 and SERB-IPA/2020/000094 India
Bill & Melinda Gates FoundationINV-030592 United States
Department of Biotechnology (DBT, India)IA/TSG/19/1/600019 India
CitationJournal: To Be Published
Title: Spike 2-up RBD with THSC20.HVTR04 (Fab4): State - I
Authors: Rencilin CF / Ansari MY / Chatterjee A / Deshpande S / Mukherjee S / Singh R / Jayatheertha S / Reddy PM / Das P / Hingankar N / Rathore D / Varadarajan R / Bhattacharya J / Dutta S
History
DepositionOct 22, 2022-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_34547.png

Downloads & links

-
Map

FileDownload / File: emd_34547.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationState - II: Spike 3-up RBD with THSC20.HVTR04 (Fab4)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.92 Å/pix.
x 336 pix.
= 309.12 Å		0.92 Å/pix.
x 336 pix.
= 309.12 Å		0.92 Å/pix.
x 336 pix.
= 309.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.89
Minimum - Maximum-11.080886 - 24.540545000000002
Average (Standard dev.)-0.000000000001392 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 309.12 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: State - II: Spike 3-up RBD with THSC20.HVTR04 (Fab4)-half map 1

Fileemd_34547_half_map_1.map
AnnotationState - II: Spike 3-up RBD with THSC20.HVTR04 (Fab4)-half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: State - II: Spike 3-up RBD with THSC20.HVTR04 (Fab4)-half map 2

Fileemd_34547_half_map_2.map
AnnotationState - II: Spike 3-up RBD with THSC20.HVTR04 (Fab4)-half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [...

EntireName: Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [State II - 3-up RBD]
Components
  • Complex: Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [State II - 3-up RBD]
    • Complex: THSC20.HVTR04(Fab4)
    • Complex: Wuhan SARS-CoV-2 Spike protein

-
Supramolecule #1: Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [...

SupramoleculeName: Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [State II - 3-up RBD]
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

-
Supramolecule #2: THSC20.HVTR04(Fab4)

SupramoleculeName: THSC20.HVTR04(Fab4) / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: Wuhan SARS-CoV-2 Spike protein

SupramoleculeName: Wuhan SARS-CoV-2 Spike protein / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Wuhan

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.25 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

31100

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.152 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93959
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