[English] 日本語
Yorodumi
- EMDB-30037: Cryo-EM structures of HKU2 spike glycoproteins -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30037
TitleCryo-EM structures of HKU2 spike glycoproteins
Map data
Sample
  • Complex: HKU2 glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


host cell membrane / endocytosis involved in viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. ...Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesRhinolophus bat coronavirus HKU2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsWang X / Yu J / Qiao S / Guo R
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins provide insights into coronavirus evolution.
Authors: Jinfang Yu / Shuyuan Qiao / Runyu Guo / Xinquan Wang /
Abstract: Porcine coronavirus SADS-CoV has been identified from suckling piglets with severe diarrhea in southern China in 2017. The SADS-CoV genome shares ~95% identity to that of bat α-coronavirus HKU2, ...Porcine coronavirus SADS-CoV has been identified from suckling piglets with severe diarrhea in southern China in 2017. The SADS-CoV genome shares ~95% identity to that of bat α-coronavirus HKU2, suggesting that SADS-CoV may have emerged from a natural reservoir in bats. Here we report the cryo-EM structures of HKU2 and SADS-CoV spike (S) glycoprotein trimers at 2.38 Å and 2.83 Å resolution, respectively. We systematically compare the domains of HKU2 spike with those of α-, β-, γ-, and δ-coronavirus spikes, showing that the S1 subunit N- and C-terminal domains of HKU2/SADS-CoV are ancestral domains in the evolution of coronavirus spike proteins. The connecting region after the fusion peptide in the S2 subunit of HKU2/SADS-CoV adopts a unique conformation. These results structurally demonstrate a close evolutionary relationship between HKU2/SADS-CoV and β-coronavirus spikes and provide insights into the evolution and cross-species transmission of coronaviruses.
History
DepositionFeb 24, 2020-
Header (metadata) releaseMay 27, 2020-
Map releaseMay 27, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6m15
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30037.png

Downloads & links

-
Map

FileDownload / File: emd_30037.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.616 Å		1.06 Å/pix.
x 256 pix.
= 271.616 Å		1.06 Å/pix.
x 256 pix.
= 271.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0201 / Movie #1: 0.03
Minimum - Maximum-0.1313678 - 0.25833428
Average (Standard dev.)0.00039474524 (±0.0075939964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.616 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.616271.616271.616
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1310.2580.000

-
Supplemental data

-
Sample components

-
Entire : HKU2 glycoprotein

EntireName: HKU2 glycoprotein
Components
  • Complex: HKU2 glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

-
Supramolecule #1: HKU2 glycoprotein

SupramoleculeName: HKU2 glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rhinolophus bat coronavirus HKU2

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus bat coronavirus HKU2
Molecular weightTheoretical: 124.52668 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKLFIVFVLL FRVCYCCDYV DFRLFNGIFS TSRGLSNTTT VITGAYPSTN KAKWFCPTNV GRPVGTGVGI GVYAQTAQAS YETGGSGAG GYTFSVSPKH VTNLTWSLWV HRPWGANANV TVRLCRWWQK FSFNETAHFQ PAGPSSAFEC LVNGSFPSSQ H KGYMFGVT ...String:
MKLFIVFVLL FRVCYCCDYV DFRLFNGIFS TSRGLSNTTT VITGAYPSTN KAKWFCPTNV GRPVGTGVGI GVYAQTAQAS YETGGSGAG GYTFSVSPKH VTNLTWSLWV HRPWGANANV TVRLCRWWQK FSFNETAHFQ PAGPSSAFEC LVNGSFPSSQ H KGYMFGVT WYNDFVRIIF PPTVFELQLD GLQWEYVQFT GPVNAGRMTK FNVVTEISSV LVLTDQSGAV TRYSYCADGF VN GLQCKLR LFDIPPGVYS NSEVEYPVAL YTVVHNMSVC PQRPESYCGS NYCPFKRVVF SNCVVNYTSW TSGLLRDYQH LVL PNGKFN PFTECNGLNR IVDDCVTGFV LRVGRGTAVN RTVITPYLKP NECFGWSWND YQDSIYDWWI ADFVSTGAFV CEKN PDAPR TGVCITYTIE KVTFQGVLYE SNFTFAQYYN VLYFGSQLKY VRILGKVYEV APCFEASYDV LFRSSSSFGL LYRSF DCNQ LRISASRFAE RLLPSHNGTA TALGCLFNAT YAPNDTMVNC TNPLGDGFCA DLLSNVVVRR MTFEKHDTTY VAPVTN ERF TELPLDHQLV LTEQFLQTTM PKFSISCETY ICDVSKACKN LLFRYGGFCQ KIEADIRGAG VLLDSDVSGL YSTIAAK TS SITPTTDRFN VSQFFLPKVQ SNSERFESRS VIEDLLFSKI ETTGPGFYGD YYNCKKNAIQ DLTCAQYHNG ILVIPPVM D AETLGMYGGI AAASLTLGIF GGQAGITTWS LAMAGRLNAL GVVQNALVDD VNKLANGFNQ LTASVGKLAL TTSSALQAI QAVVNQNAAQ VESLVSGITE NFGAISTNFK VISQRLDKLE ADVQMDRLIN GRMNVLQLFV TNYKLKIAEL RNTHRYVQSL INECVYAQS LRNGFCGQGL HVLSLMQNAP SGIMFFHYSL IPNNTITVKT TPGLCESDEL GSKCIVAKDG VLVSANLSYW Q WSPRNLYK PENLTFANVI AVSRGANYTT LNRTFDIPEL NSTFPIDEEF REYFQNMSSE LQALKNLTAD MSKLNISAEI QL INEIAHN VSNMRVEVEK FQRYVNYVKL EVLFQGPGGG SGGGSGYIPE APRDGQAYVR KDGEWVLLST FLGWSHPQFE K

UniProtKB: Spike glycoprotein

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 27 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 71 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.784 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 421490
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