[English] 日本語
Yorodumi
- EMDB-9585: Trypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex, ACE... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 9585
TitleTrypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex, ACE2-bound conformation 1
Map data
SampleTrypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex
  • Trypsin-cleaved SARS-CoV spike
  • human ACE2Angiotensin-converting enzyme 2
SourceSARS coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 19.7 Å resolution
AuthorsGui M / Song W
CitationJournal: PLoS Pathog. / Year: 2018
Title: Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2.
Authors: Wenfei Song / Miao Gui / Xinquan Wang / Ye Xiang
DateDeposition: Jul 26, 2018 / Header (metadata) release: Aug 8, 2018 / Map release: Aug 8, 2018 / Last update: Aug 22, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.115
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.115
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_9585.map.gz (map file in CCP4 format, 7627 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
124 pix
2.54 Å/pix.
= 314.96 Å
124 pix
2.54 Å/pix.
= 314.96 Å
124 pix
2.54 Å/pix.
= 314.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.54 Å
Density
Contour Level:0.115 (by author), 0.115 (movie #1):
Minimum - Maximum-0.03590115 - 0.24512465
Average (Standard dev.)0.0042622467 (0.023143923)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions124124124
Origin0.0.0.
Limit123.123.123.
Spacing124124124
CellA=B=C: 314.96 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.542.542.54
M x/y/z124124124
origin x/y/z0.0000.0000.000
length x/y/z314.960314.960314.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS124124124
D min/max/mean-0.0360.2450.004

-
Supplemental data

-
Mask #1

Fileemd_9585_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

-
Sample components

-
Entire Trypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex

EntireName: Trypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex
Number of components: 3

-
Component #1: protein, Trypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex

ProteinName: Trypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex
Recombinant expression: No
MassTheoretical: 400 kDa

-
Component #2: protein, Trypsin-cleaved SARS-CoV spike

ProteinName: Trypsin-cleaved SARS-CoV spike / Recombinant expression: No
SourceSpecies: SARS coronavirus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

-
Component #3: protein, human ACE2

ProteinName: human ACE2Angiotensin-converting enzyme 2 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 26217
3D reconstructionResolution: 19.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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