[English] 日本語
Yorodumi
- EMDB-21396: Porcine epidemic diarrhea virus (PEDV) spike protein with N264D m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21396
TitlePorcine epidemic diarrhea virus (PEDV) spike protein with N264D mutation, expressed in 293F cells and negatively stained
Map data
Sample
  • Complex: Porcine epidemic diarrhea virus spike protein
    • Protein or peptide: Porcine epidemic diarrhea virus (PEDV) spike protein
Biological speciesPorcine epidemic diarrhea virus
Methodsingle particle reconstruction / negative staining / Resolution: 18.0 Å
AuthorsKirchdoerfer RN / Martini O / 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-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.25
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21396.png

Downloads & links

-
Map

FileDownload / File: emd_21396.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 192 pix.
= 393.6 Å		2.05 Å/pix.
x 192 pix.
= 393.6 Å		2.05 Å/pix.
x 192 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.25 / Movie #1: 2.25
Minimum - Maximum-0.45621946 - 3.5261643
Average (Standard dev.)0.010199576 (±0.35477495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 393.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.4563.5260.010

-
Supplemental data

-
Mask #1

Fileemd_21396_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_21396_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_21396_half_map_2.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: Porcine epidemic diarrhea virus (PEDV) spike protein

-
Supramolecule #1: Porcine epidemic diarrhea virus spike protein

SupramoleculeName: Porcine epidemic diarrhea virus spike protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Recombinantly expressed in 293F cells using transient transfection
Source (natural)Organism: Porcine epidemic diarrhea virus / Strain: 13-019349
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: 293F / Recombinant plasmid: pcDNA3.4
Molecular weightExperimental: 600 KDa

-
Macromolecule #1: Porcine epidemic diarrhea virus (PEDV) spike protein

MacromoleculeName: Porcine epidemic diarrhea virus (PEDV) spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Porcine epidemic diarrhea virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LPQDVTRCSA NTNFRRFFSK FNVQAPAVVV LGGYLPIGEN QG VNSTWYC AGQHPTASGV HGIFVSHIRG GHGFEIGISQ EPFDPSGYQL YLHKATNGNT NAT ARLRIC QFPSIKTLGP TANNDVTTGR NCLFNKAIPA HMSEHSVVGI TWDNDRVTVF SDKI YYFYF ...String:
LPQDVTRCSA NTNFRRFFSK FNVQAPAVVV LGGYLPIGEN QG VNSTWYC AGQHPTASGV HGIFVSHIRG GHGFEIGISQ EPFDPSGYQL YLHKATNGNT NAT ARLRIC QFPSIKTLGP TANNDVTTGR NCLFNKAIPA HMSEHSVVGI TWDNDRVTVF SDKI YYFYF KNDWSRVATK CYNSGGCAMQ YVYEPTYYML NVTSAGEDGI SYQPCTANCI GYAAN VFAT EPNGHIPEGF SFNNWFLLSD DSTLVHGKVV SNQPLLVNCL LAIPKIYGLG QFFSFN QTI DGVCNGAAVQ RAPEALRFNI NDISVILAEG SIVLHTALGT NFSFVCSNSS NPHLATF AI PLGATQVPYY CFLKVDTYNS TVYKFLAVLP PTVREIVITK YGDVYVNGFG YLHLGLLD A VTINFTGHGT DDDVSGFWTI ASTNFVDALI EVQGTAIQRI LYCDDPVSQL KCSQVAFDL DDGFYTISSR NLLSHEQPIS FVTLPSFNDH SFVNITVSAS FGGHSGANLI ASDTTINGFS SFCVDTRQF TISLFYNVTN SYGYVSKSQD SNCPFTLQSV NDYLSFSKFC VSTSLLASAC T IDLFGYPE FGSGVKFTSL YFQFTKGELI TGTPKPFEGV TDVSFMTLDV CTKYTIYGFK GE GIITLTN SSFLAGVYYT SDSGQLLAFK NVTSGAVYSV TPCSFSEQAA YVDDDIVGVI SSL SSSTFN STRELPGFFY HSNDGSNCTE PVLVYSNIGV CKSGSIGYVP SQSGQVKIAP TVTG NISIP TNFSMSIRTE YLQLYNTPVS VDCATYVCNG NSRCKQLLTQ YTAACKTIES ALQLS ARLE SVEVNSMLTI SDEALQLATI SSFNGDGYNF TNVLGVSVYD PASGRVVQKR SFIEDL LFN KVVTNGLGTV DEDYKRCSNG RSVADLVCAQ YYSGVMVLPG VVDAEKLHMY SASLIGG MV LGGFTSAAAL PFSYAVQARL NYLALQTDVL QRNQQLLAES FNSAIGNITS AFESVKEA I SQTSKGLNTV AHALTKVQEV VNSQGAALTQ LTVQLQHNFQ AISSSIDDIY SRLDILSAD AQVDRLITGR LSALNAFVAQ TLTKYTEVQA SRKLAQQKVN ECVKSQSQRY GFCGGDGEHI FSLVQAAPQ GLLFLHTVLV PSDFVDVIAI AGLCVNDEIA LTLREPGLVL FTHELQNHTA T EYFVSSRR MFEPRKPTVS DFVQIESCVV TYVNLTRDQL PDVIPDYIDV NKTLDEILAS LP NRTGPSL PLDVFNATYL NLTGEIADLE QRSESLRNTT EELQSLIYNI NNTLVDLEWL NRV ETGSGY IPEAPRDGQA YVRKDGEWVL LSTFLENLYF QGGHHHHHHA WSHPQFEK

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
25.0 mMTris
150.0 mMsodium chloride
StainingType: NEGATIVE / Material: Uranyl formate
GridSupport film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unspecified

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-64 / Number grids imaged: 1 / Average exposure time: 0.6 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 10698
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5szs


Details: SGD initial model generation
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.0) / Number images used: 10698
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.0)
FSC plot (resolution estimation)

+
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