[English] 日本語
Yorodumi
- EMDB-65717: sarbecovirus Rc-o319 S-trimer in a locked-1 conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65717
Titlesarbecovirus Rc-o319 S-trimer in a locked-1 conformation
Map data
Sample
  • Organelle or cellular component: Severe acute respiratory syndrome-related coronavirus Rc-o319
    • Protein or peptide: Spike protein
  • Ligand: BILIVERDINE IX ALPHA
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
Keywordsspike protein / VIRUS / VIRAL PROTEIN
Biological speciesSarbecovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.13 Å
AuthorsWang J / Li ZX / Li ZM / Yuan H / Xiong X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82341085 China
CitationJournal: To Be Published
Title: sarbecovirus Rc-o319 S-trimer in a locked-1 conformation
Authors: Wang J / Li ZX / Li ZM / Hang Y / Xiong X
History
DepositionAug 5, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_65717.png

Downloads & links

-
Map

FileDownload / File: emd_65717.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.33665216 - 0.9320878
Average (Standard dev.)0.0007512054 (±0.029669357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_65717_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65717_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Severe acute respiratory syndrome-related coronavirus Rc-o319

EntireName: Severe acute respiratory syndrome-related coronavirus Rc-o319
Components
  • Organelle or cellular component: Severe acute respiratory syndrome-related coronavirus Rc-o319
    • Protein or peptide: Spike protein
  • Ligand: BILIVERDINE IX ALPHA
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID

-
Supramolecule #1: Severe acute respiratory syndrome-related coronavirus Rc-o319

SupramoleculeName: Severe acute respiratory syndrome-related coronavirus Rc-o319
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sarbecovirus / Strain: Rc-o319

-
Macromolecule #1: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 1
Details: 1-1175 AA Rc-o319 along with C-terminal T4 fibritin trimerization, HRV3C cleavage site (LEVLFQGP), His-tag (HHHHHHHH) and Double Strep-Tag (WSHPQFEKGGGSGGGGSGGSAWSHPQFEK).
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sarbecovirus / Strain: Rc-o319
Molecular weightTheoretical: 138.931375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFILVLLNVL SVYGCVNITY GSHHLYVSSR TRGVYYPDDA FRSSTNVLHE GFFLPFDSNV TWYSFWNQKY SVATSPFGDG VYFSTIDKS NVVRGWVFGT TLDNDTQSVL LYNDGTHVRV EVCTFHFCPT PVFSASSPHL YSSAFNCTLN YTLASVRADF T EVDGSFKT ...String:
MFILVLLNVL SVYGCVNITY GSHHLYVSSR TRGVYYPDDA FRSSTNVLHE GFFLPFDSNV TWYSFWNQKY SVATSPFGDG VYFSTIDKS NVVRGWVFGT TLDNDTQSVL LYNDGTHVRV EVCTFHFCPT PVFSASSPHL YSSAFNCTLN YTLASVRADF T EVDGSFKT IREFVFKLQD GSLNVYYAST SYVLAIGATS QLPSGVTPLV PLWKIPIGLN ITNFKTLVYL RSDNTPLQAA YV VGHLKRR TMMFKYDENG TIVDAIDCAL DPLSETKCTL RSFIVEKGIY QTSNFRVQPQ DTVVRFPNIT NLCPFSEVFN ATT FASVYA WNRKRISNCV ADYSVLYNST SFSTFQCYGV SSTKLNDLCF TNVYADSFVV RGDEVRQIAP GQTGVIADYN YKLP DDFTG CVLAWNSRNQ DASTSGNFNY YYRIWRSEKL RPFERDIAHY DYQVGTQFKS SLKNYGFYSS AGDSHQPYRV VVLSF ELLN APATVCGPKQ STELIKNKCV NFNFNGLTGT GVLTDSNKKF QSFQQFGRDV SDFTDSVKDP KTLEVLDITP CSYGGV SVI TPGTNASTQV AVLYQDVNCT DVPTAIHAEQ LTPSWRVYST GTNMFQTQAG CLIGAEHVNN SYDCDIPIGA GICATYH TP SMLRSANNNK RIVAYVMSLG AENSVAYSNN TIAIPTNFTI SVTTEVMPVS MTKTSVDCTM YICGDSVECS TLLLQYGS F CTQLNRALTG IAVEQDKNTQ EVFAQVKQIY KTPDIKDFGG FNFSQILPDP SKPSKRSFIE DLLFNKVTLA DAGFVKQYG DCLGDIQARD LICAQKFNGL TVLPPLLTDE MIAAYTAALI SGTATAGWTF GAGAALQIPF AMQMAYRFNG IGVTQNVLYE NQKLIANQF NSAIGKIQES LTSTASALGK LQDVVNQNAQ ALNTLVKQLS SNFGAISSVL NDIISRLDKV EAEVQIDRLI T GRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQAA PHGVVFLHVT YIPSQERNFT TA PAICHEG KAHFPREGVF VSNGTHWFIT QRNFYEPQII TTDNTFVSGT CDVVIGIVNN TVYDPLQPEL ESFKDELDKY FKN HTSPDI DLGDISGINA SVVDIQKEID ILKDVAKNLN ESLINLQELG KYEQYIKWPG SGYIPEAPRD GQAYVRKDGE WVLL STFLL EVLFQGPGHH HHHHHHSAWS HPQFEKGGGS GGGGSGGSAW SHPQFEKSA

-
Macromolecule #6: BILIVERDINE IX ALPHA

MacromoleculeName: BILIVERDINE IX ALPHA / type: ligand / ID: 6 / Number of copies: 3 / Formula: BLA
Molecular weightTheoretical: 582.646 Da
Chemical component information

ChemComp-BLA:
BILIVERDINE IX ALPHA

-
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 34 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #8: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 8 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7xu2

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 436107
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