[English] 日本語
Yorodumi
- EMDB-21391: Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21391
TitleCryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike protein
Map data
Sample
  • Complex: Porcine epidemic diarrhea virus spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITOLEIC ACID
Keywordsglycoprotein / surface / receptor-binding / membrane fusion / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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 speciesPorcine epidemic diarrhea virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKirchdoerfer RN / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123498 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127521 United States
CitationJournal: Structure / Year: 2021
Title: Structure and immune recognition of the porcine epidemic diarrhea virus spike protein.
Authors: Robert N Kirchdoerfer / Mahesh Bhandari / Olnita Martini / Leigh M Sewall / Sandhya Bangaru / Kyoung-Jin Yoon / Andrew B Ward /
Abstract: Porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a ...Porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components, including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins.
History
DepositionFeb 17, 2020-
Header (metadata) releaseFeb 26, 2020-
Map releaseFeb 26, 2020-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6vv5
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21391.png

Downloads & links

-
Map

FileDownload / File: emd_21391.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 280 pix.
= 322. Å		1.15 Å/pix.
x 280 pix.
= 322. Å		1.15 Å/pix.
x 280 pix.
= 322. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.11378142 - 0.18057886
Average (Standard dev.)0.00007580524 (±0.0069649033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 322.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z322.000322.000322.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1140.1810.000

-
Supplemental data

-
Mask #1

Fileemd_21391_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: First half map

Fileemd_21391_half_map_1.map
AnnotationFirst half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Second half map

Fileemd_21391_half_map_2.map
AnnotationSecond half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Porcine epidemic diarrhea virus spike protein

EntireName: Porcine epidemic diarrhea virus spike protein
Components
  • Complex: Porcine epidemic diarrhea virus spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITOLEIC ACID

-
Supramolecule #1: Porcine epidemic diarrhea virus spike protein

SupramoleculeName: Porcine epidemic diarrhea virus spike protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Recombinantly expressed in insect cells using a baculovirus vector.
Source (natural)Organism: Porcine epidemic diarrhea virus / Strain: 13-019349
Molecular weightTheoretical: 600 KDa

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Porcine epidemic diarrhea virus
Molecular weightTheoretical: 148.463656 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LPQDVTRCSA NTNFRRFFSK FNVQAPAVVV LGGYLPIGEN QGVNSTWYCA GQHPTASGVH GIFVSHIRGG HGFEIGISQE PFDPSGYQL YLHKATNGNT NATARLRICQ FPSIKTLGPT ANNDVTTGRN CLFNKAIPAH MSEHSVVGIT WDNDRVTVFS D KIYYFYFK ...String:
LPQDVTRCSA NTNFRRFFSK FNVQAPAVVV LGGYLPIGEN QGVNSTWYCA GQHPTASGVH GIFVSHIRGG HGFEIGISQE PFDPSGYQL YLHKATNGNT NATARLRICQ FPSIKTLGPT ANNDVTTGRN CLFNKAIPAH MSEHSVVGIT WDNDRVTVFS D KIYYFYFK NDWSRVATKC YNSGGCAMQY VYEPTYYMLN VTSAGEDGIS YQPCTANCIG YAANVFATEP NGHIPEGFSF NN WFLLSND STLVHGKVVS NQPLLVNCLL AIPKIYGLGQ FFSFNQTIDG VCNGAAVQRA PEALRFNIND ISVILAEGSI VLH TALGTN FSFVCSNSSN PHLATFAIPL GATQVPYYCF LKVDTYNSTV YKFLAVLPPT VREIVITKYG DVYVNGFGYL HLGL LDAVT INFTGHGTDD DVSGFWTIAS TNFVDALIEV QGTAIQRILY CDDPVSQLKC SQVAFDLDDG FYTISSRNLL SHEQP ISFV TLPSFNDHSF VNITVSASFG GHSGANLIAS DTTINGFSSF CVDTRQFTIS LFYNVTNSYG YVSKSQDSNC PFTLQS VND YLSFSKFCVS TSLLASACTI DLFGYPEFGS GVKFTSLYFQ FTKGELITGT PKPFEGVTDV SFMTLDVCTK YTIYGFK GE GIITLTNSSF LAGVYYTSDS GQLLAFKNVT SGAVYSVTPC SFSEQAAYVD DDIVGVISSL SSSTFNSTRE LPGFFYHS N DGSNCTEPVL VYSNIGVCKS GSIGYVPSQS GQVKIAPTVT GNISIPTNFS MSIRTEYLQL YNTPVSVDCA TYVCNGNSR CKQLLTQYTA ACKTIESALQ LSARLESVEV NSMLTISDEA LQLATISSFN GDGYNFTNVL GVSVYDPASG RVVQKRSFIE DLLFNKVVT NGLGTVDEDY KRCSNGRSVA DLVCAQYYSG VMVLPGVVDA EKLHMYSASL IGGMVLGGFT SAAALPFSYA V QARLNYLA LQTDVLQRNQ QLLAESFNSA IGNITSAFES VKEAISQTSK GLNTVAHALT KVQEVVNSQG AALTQLTVQL QH NFQAISS SIDDIYSRLD ILSADAQVDR LITGRLSALN AFVAQTLTKY TEVQASRKLA QQKVNECVKS QSQRYGFCGG DGE HIFSLV QAAPQGLLFL HTVLVPSDFV DVIAIAGLCV NDEIALTLRE PGLVLFTHEL QNHTATEYFV SSRRMFEPRK PTVS DFVQI ESCVVTYVNL TRDQLPDVIP DYIDVNKTLD EILASLPNRT GPSLPLDVFN ATYLNLTGEI ADLEQRSESL RNTTE ELQS LIYNINNTLV DLEWLNRVET GSGYIPEAPR DGQAYVRKDG EWVLLSTFLE NLYFQGGHHH HHHAWSHPQF EK

UniProtKB: Spike glycoprotein

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #6: PALMITOLEIC ACID

MacromoleculeName: PALMITOLEIC ACID / type: ligand / ID: 6 / Number of copies: 6 / Formula: PAM
Molecular weightTheoretical: 254.408 Da
Chemical component information

ChemComp-PAM:
PALMITOLEIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
25.0 mMTris
150.0 mMsodium chloride
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
TemperatureMax: 100.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-64 / Number grids imaged: 1 / Average exposure time: 12.8 sec. / Average electron dose: 54.9 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm
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: 19436
Startup modelType of model: OTHER / Details: SGD initial model generation
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 19436
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5szs


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6vv5:
Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike protein

+
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