[English] 日本語
Yorodumi
- EMDB-8331: Glycan shield and epitope masking of a coronavirus spike protein ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8331
TitleGlycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy
Map dataCoronavirus spike protein
Sample
  • Complex: Human coronavirus NL63 spike glycoprotein ectodomain
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscoronavirus / viral fusion protein / vaccine / NL63 / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into 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, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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 S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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 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 speciesHuman coronavirus NL63
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWalls AC / Tortorici MA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM120553-01 United States
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy.
Authors: Alexandra C Walls / M Alejandra Tortorici / Brandon Frenz / Joost Snijder / Wentao Li / Félix A Rey / Frank DiMaio / Berend-Jan Bosch / David Veesler /
Abstract: The threat of a major coronavirus pandemic urges the development of strategies to combat these pathogens. Human coronavirus NL63 (HCoV-NL63) is an α-coronavirus that can cause severe lower- ...The threat of a major coronavirus pandemic urges the development of strategies to combat these pathogens. Human coronavirus NL63 (HCoV-NL63) is an α-coronavirus that can cause severe lower-respiratory-tract infections requiring hospitalization. We report here the 3.4-Å-resolution cryo-EM reconstruction of the HCoV-NL63 coronavirus spike glycoprotein trimer, which mediates entry into host cells and is the main target of neutralizing antibodies during infection. The map resolves the extensive glycan shield obstructing the protein surface and, in combination with mass spectrometry, provides a structural framework to understand the accessibility to antibodies. The structure reveals the complete architecture of the fusion machinery including the triggering loop and the C-terminal domains, which contribute to anchoring the trimer to the viral membrane. Our data further suggest that HCoV-NL63 and other coronaviruses use molecular trickery, based on epitope masking with glycans and activating conformational changes, to evade the immune system of infected hosts.
History
DepositionAug 30, 2016-
Header (metadata) releaseSep 14, 2016-
Map releaseSep 14, 2016-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5szs
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8331.png

Downloads & links

-
Map

FileDownload / File: emd_8331.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCoronavirus spike protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.1386069 - 0.2991194
Average (Standard dev.)0.00034242327 (±0.005515339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z435.200435.200435.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1390.2990.000

-
Supplemental data

-
Sample components

-
Entire : Human coronavirus NL63 spike glycoprotein ectodomain

EntireName: Human coronavirus NL63 spike glycoprotein ectodomain
Components
  • Complex: Human coronavirus NL63 spike glycoprotein ectodomain
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Human coronavirus NL63 spike glycoprotein ectodomain

SupramoleculeName: Human coronavirus NL63 spike glycoprotein ectodomain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human coronavirus NL63
Molecular weightTheoretical: 450 KDa

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus NL63
Molecular weightTheoretical: 146.813984 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: FFTCNSNANL SMLQLGVPDN SSTIVTGLLP THWFCANQST SVYSANGFFY IDVGNHRSAF ALHTGYYDAN QYYIYVTNEI GLNASVTLK ICKFSRNTTF DFLSNASSSF DCIVNLLFTE QLGAPLGITI SGETVRLHLY NVTRTFYVPA AYKLTKLSVK C YFNYSCVF ...String:
FFTCNSNANL SMLQLGVPDN SSTIVTGLLP THWFCANQST SVYSANGFFY IDVGNHRSAF ALHTGYYDAN QYYIYVTNEI GLNASVTLK ICKFSRNTTF DFLSNASSSF DCIVNLLFTE QLGAPLGITI SGETVRLHLY NVTRTFYVPA AYKLTKLSVK C YFNYSCVF SVVNATVTVN VTTHNGRVVN YTVCDDCNGY TDNIFSVQQD GRIPNGFPFN NWFLLTNGST LVDGVSRLYQ PL RLTCLWP VPGLKSSTGF VYFNATGSDV NCNGYQHNSV VDVMRYNLNF SANSLDNLKS GVIVFKTLQY DVLFYCSNSS SGV LDTTIP FGPSSQPYYC FINSTINTTH VSTFVGILPP TVREIVVART GQFYINGFKY FDLGFIEAVN FNVTTASATD FWTV AFATF VDVLVNVSAT NIQNLLYCDS PFEKLQCEHL QFGLQDGFYS ANFLDDNVLP ETYVALPIYY QHTDINFTAT ASFGG SCYV CKPHQVNISL NGNTSVCVRT SHFSIRYIYN RVKSGSPGDS SWHIYLKSGT CPFSFSKLNN FQKFKTICFS TVEVPG SCN FPLEATWHYT SYTIVGALYV TWSEGNSITG VPYPVSGIRE FSNLVLNNCT KYNIYDYVGT GIIRSSNQSL AGGITYV SN SGNLLGFKNV STGNIFIVTP CNQPDQVAVY QQSIIGAMTA VNESRYGLQN LLQLPNFYYV SNGGNNCTTA VMTYSNFG I CADGSLIPVR PRNSSDNGIS AIITANLSIP SNWTTSVQVE YLQITSTPIV VDCATYVCNG NPRCKNLLKQ YTSACKTIE DALRLSAHLE TNDVSSMLTF DSNAFSLANV TSFGDYNLSS VLPQRNIRSS RIAGRSALED LLFSKVVTSG LGTVDVDYKS CTKGLSIAD LACAQYYNGI MVLPGVADAE RMAMYTGSLI GGMVLGGLTS AAAIPFSLAL QARLNYVALQ TDVLQENQKI L AASFNKAI NNIVASFSSV NDAITQTAEA IHTVTIALNK IQDVVNQQGS ALNHLTSQLR HNFQAISNSI QAIYDRLDSI QA DQQVDRL ITGRLAALNA FVSQVLNKYT EVRGSRRLAQ QKINECVKSQ SNRYGFCGNG THIFSIVNSA PDGLLFLHTV LLP TDYKNV KAWSGICVDG IYGYVLRQPN LVLYSDNGVF RVTSRVMFQP RLPVLSDFVQ IYNCNVTFVN ISRVELHTVI PDYV DVNKT LQEFAQNLPK YVKPNFDLTP FNLTYLNLSS ELKQLEAKTA SLFQTTVELQ GLIDQINSTY VDLKLLNRFE NLIKR MKQI EDKIEEIESK QKKIENEIAR IKKIKLVPRG SLEWSHPQFE K

UniProtKB: Spike glycoprotein

-
Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 21 / 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

Concentration1 mg/mL
BufferpH: 7.5 / Component:
ConcentrationName
20.0 mMTris-HCl
100.0 mMNaCl
GridModel: Protochips C-flat 1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 20 mA
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Average exposure time: 10.0 sec. / Average electron dose: 48.0 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

Particle selectionNumber selected: 474000
Startup modelType of model: OTHER
Details: Common-lines generated model for the MHV spike glycoprotein
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 79667
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-5szs:
Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

+
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