[English] 日本語
Yorodumi
- EMDB-35961: Immune complex of W328-6H2 Fab binding the RBD of SARS-CoV-2 WT 6... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35961
TitleImmune complex of W328-6H2 Fab binding the RBD of SARS-CoV-2 WT 6p spike protein
Map dataImmune complex of W328-6H2 Fab binding the RBD of SARS-CoV-2 WT 6p spike protein
Sample
  • Complex: SARS-CoV-2 WT 6p in complex with W328-6H2 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 2 wild-type 6p
      • Complex: W328-6H2 Fab
KeywordsComplex / SARS-CoV-2 WT / antibody / Homo sapiens / RBD / Fab / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsNan XY / Li YJ
Funding support China, 1 items
OrganizationGrant numberCountry
Other government22277017 China
CitationJournal: To Be Published
Title: Immune complex of W328-6H2 Fab binding the RBD of SARS-CoV-2 WT 6p spike protein
Authors: Nan XY / Li YJ
History
DepositionApr 17, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35961.png

Downloads & links

-
Map

FileDownload / File: emd_35961.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationImmune complex of W328-6H2 Fab binding the RBD of SARS-CoV-2 WT 6p spike protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.21 Å/pix.
x 192 pix.
= 424.32 Å		2.21 Å/pix.
x 192 pix.
= 424.32 Å		2.21 Å/pix.
x 192 pix.
= 424.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0319
Minimum - Maximum-0.066111214 - 0.114739835
Average (Standard dev.)-0.00023492923 (±0.0071439417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 424.32 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Immune complex of W328-6H2 Fab binding the RBD...

Fileemd_35961_half_map_1.map
AnnotationImmune complex of W328-6H2 Fab binding the RBD of SARS-CoV-2 WT 6p spike protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Immune complex of W328-6H2 Fab binding the RBD...

Fileemd_35961_half_map_2.map
AnnotationImmune complex of W328-6H2 Fab binding the RBD of SARS-CoV-2 WT 6p spike protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SARS-CoV-2 WT 6p in complex with W328-6H2 Fab

EntireName: SARS-CoV-2 WT 6p in complex with W328-6H2 Fab
Components
  • Complex: SARS-CoV-2 WT 6p in complex with W328-6H2 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 2 wild-type 6p
      • Complex: W328-6H2 Fab

-
Supramolecule #1: SARS-CoV-2 WT 6p in complex with W328-6H2 Fab

SupramoleculeName: SARS-CoV-2 WT 6p in complex with W328-6H2 Fab / type: complex / ID: 1 / Parent: 0
Details: Immune complex of W328-6H2 Fab binding the RBD of SARS-CoV-2 WT 6p spike protein
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #2: Severe acute respiratory syndrome coronavirus 2 wild-type 6p

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 wild-type 6p
type: complex / ID: 2 / Parent: 1 / Details: SARS-CoV-2 WT 6p
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

-
Supramolecule #3: W328-6H2 Fab

SupramoleculeName: W328-6H2 Fab / type: complex / ID: 3 / Parent: 2 / Details: W328-6H2 Fab
Source (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.015 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate

-
Electron microscopy

MicroscopeJEOL 2100F
Image recordingFilm or detector model: OTHER / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 5090
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