[English] 日本語
Yorodumi
- EMDB-34422: Structure of SARS-CoV-1 Spike Protein with Engineered x2 Disulfid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34422
TitleStructure of SARS-CoV-1 Spike Protein with Engineered x2 Disulfide (G400C and V969C), Locked-2 Conformation
Map data9-29
Sample
  • Complex: SARS-CoV-1 spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsPROTEIN ENGINEERING / SPIKE PROTEIN / SARS-COV-1 / SARS-COV / VIRAL PROTEIN
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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 speciesSevere acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44681 Å
AuthorsZhang X / Li Z / Liu Y / Wang J / Fu L / Wang P / He J / Xiong X
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Life Sci Alliance / Year: 2023
Title: Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes.
Authors: Xixi Zhang / Zimu Li / Yanjun Zhang / Yutong Liu / Jingjing Wang / Banghui Liu / Qiuluan Chen / Qian Wang / Lutang Fu / Peiyi Wang / Xiaolin Zhong / Liang Jin / Qihong Yan / Ling Chen / Jun ...Authors: Xixi Zhang / Zimu Li / Yanjun Zhang / Yutong Liu / Jingjing Wang / Banghui Liu / Qiuluan Chen / Qian Wang / Lutang Fu / Peiyi Wang / Xiaolin Zhong / Liang Jin / Qihong Yan / Ling Chen / Jun He / Jincun Zhao / Xiaoli Xiong /
Abstract: SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed, and open. S-trimers ...SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed, and open. S-trimers adopting locked conformations are tightly packed featuring structural elements incompatible with RBD in the "up" position. For SARS-CoV-2 S, it has been shown that the locked conformations are transient under neutral pH. Probably because of their transience, locked conformations remain largely uncharacterized for SARS-CoV-1 S. In this study, we introduced x1, x2, and x3 disulfides into SARS-CoV-1 S. Some of these disulfides have been shown to preserve rare locked conformations when introduced to SARS-CoV-2 S. Introduction of these disulfides allowed us to image a variety of locked and other rare conformations for SARS-CoV-1 S by cryo-EM. We identified bound cofactors and structural features that are associated with SARS-CoV-1 S locked conformations. We compare newly determined structures with other available spike structures of SARS-related CoVs to identify conserved features and discuss their possible functions.
History
DepositionSep 30, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_34422.png

Downloads & links

-
Map

FileDownload / File: emd_34422.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation9-29
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 240 pix.
= 324. Å		1.35 Å/pix.
x 240 pix.
= 324. Å		1.35 Å/pix.
x 240 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.65864086 - 0.99792707
Average (Standard dev.)0.00015153461 (±0.021950074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_34422_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: 9-29

Fileemd_34422_half_map_1.map
Annotation9-29
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: 9-29

Fileemd_34422_half_map_2.map
Annotation9-29
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SARS-CoV-1 spike protein

EntireName: SARS-CoV-1 spike protein
Components
  • Complex: SARS-CoV-1 spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: SARS-CoV-1 spike protein

SupramoleculeName: SARS-CoV-1 spike protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus / Strain: SARS coronavirus Tor2
Molecular weightTheoretical: 410 KDa

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 130.916188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DLDRCTTFDD VQAPNYTQHT SSMRGVYYPD EIFRSDTLYL TQDLFLPFYS NVTGFHTINH TFGNPVIPFK DGIYFAATEK SNVVRGWVF GSTMNNKSQS VIIINNSTNV VIRACNFELC DNPFFAVSKP MGTQTHTMIF DNAFNCTFEY ISDAFSLDVS E KSGNFKHL ...String:
DLDRCTTFDD VQAPNYTQHT SSMRGVYYPD EIFRSDTLYL TQDLFLPFYS NVTGFHTINH TFGNPVIPFK DGIYFAATEK SNVVRGWVF GSTMNNKSQS VIIINNSTNV VIRACNFELC DNPFFAVSKP MGTQTHTMIF DNAFNCTFEY ISDAFSLDVS E KSGNFKHL REFVFKNKDG FLYVYKGYQP IDVVRDLPSG FNTLKPIFKL PLGINITNFR AILTAFSPAQ DIWGTSAAAY FV GYLKPTT FMLKYDENGT ITDAVDCSQN PLAELKCSVK SFEIDKGIYQ TSNFRVVPSG DVVRFPNITN LCPFGEVFNA TKF PSVYAW ERKKISNCVA DYSVLYNSTF FSTFKCYGVS ATKLNDLCFS NVYADSFVVK GDDVRQIAPC QTGVIADYNY KLPD DFMGC VLAWNTRNID ATSTGNYNYK YRYLRHGKLR PFERDISNVP FSPDGKPCTP PALNCYWPLN DYGFYTTTGI GYQPY RVVV LSFELLNAPA TVCGPKLSTD LIKNQCVNFN FNGLTGTGVL TPSSKRFQPF QQFGRDVSDF TDSVRDPKTS EILDIS PCS FGGVSVITPG TNASSEVAVL YQDVNCTDVS TAIHADQLTP AWRIYSTGNN VFQTQAGCLI GAEHVDTSYE CDIPIGA GI CASYHTVSLL RSTSQKSIVA YTMSLGADSS IAYSNNTIAI PTNFSISITT EVMPVSMAKT SVDCNMYICG DSTECANL L LQYGSFCTQL NRALSGIAAE QDRNTREVFA QVKQMYKTPT LKYFGGFNFS QILPDPLKPT KRSFIEDLLF NKVTLADAG FMKQYGECLG DINARDLICA QKFNGLTVLP PLLTDDMIAA YTAALVSGTA TAGWTFGAGA ALQIPFAMQM AYRFNGIGVT QNVLYENQK QIANQFNKAI SQIQESLTTT STALGKLQDV VNQNAQALNT LVKQLSSNFG AISSVLNDIL SRLDKCEAEV Q IDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQAAPHGV VFLHVTYVPS QE RNFTTAP AICHEGKAYF PREGVFVFNG TSWFITQRNF FSPQIITTDN TFVSGNCDVV IGIINNTVYD PLQPELDSFK EEL DKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQELGKYEQ YIK

UniProtKB: Spike glycoprotein

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 39 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6.5 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
1.0588236 mMKH2PO4Potassium Phosphate monobasic
155.17241 mMNaClSodium Chloride
2.966418 mMNa2HPO4Sodium Phosphate dibasic

Details: Gibco PBS C10010
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 1.6 sec. / Average electron dose: 62.0 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: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 967643 / Details: Particles were picked by Warp v1.09
Startup modelType of model: EMDB MAP
EMDB ID:

11329

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44681 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 192457
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7xtz

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 28
Output model

PDB-8h12:
Structure of SARS-CoV-1 Spike Protein with Engineered x2 Disulfide (G400C and V969C), Locked-2 Conformation

+
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