[English] 日本語
Yorodumi
- EMDB-28544: Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like envi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28544
TitleStructure of SARS-CoV-1 Orf3a in late endosome/lysosome-like environment, MSP1D1 nanodisc
Map data
Sample
  • Complex: Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like environment, MSP1D1 nanodisc
    • Protein or peptide: ORF3a protein
    • Protein or peptide: Apolipoprotein A-I
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
KeywordsMembrane protein / SARS-CoV / SARS-CoV-2 / VIRAL PROTEIN
Function / homology
Function and homology information


: / Maturation of protein 3a / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption ...: / Maturation of protein 3a / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / protein oxidation / vitamin transport / cholesterol import / high-density lipoprotein particle binding / Microbial modulation of RIPK1-mediated regulated necrosis / ABC transporters in lipid homeostasis / blood vessel endothelial cell migration / negative regulation of heterotypic cell-cell adhesion / apolipoprotein receptor binding / apolipoprotein A-I receptor binding / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion molecule production / HDL assembly / peptidyl-methionine modification / negative regulation of very-low-density lipoprotein particle remodeling / phosphatidylcholine biosynthetic process / Translation of Structural Proteins / Virion Assembly and Release / glucocorticoid metabolic process / acylglycerol homeostasis / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / lipid storage / Chylomicron assembly / positive regulation of cholesterol metabolic process / high-density lipoprotein particle clearance / phospholipid homeostasis / chylomicron / high-density lipoprotein particle remodeling / phospholipid efflux / chemorepellent activity / very-low-density lipoprotein particle / reverse cholesterol transport / : / cholesterol transfer activity / high-density lipoprotein particle assembly / cholesterol transport / low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / high-density lipoprotein particle / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / inorganic cation transmembrane transport / HDL remodeling / endothelial cell proliferation / voltage-gated calcium channel complex / Scavenging by Class A Receptors / negative regulation of interleukin-1 beta production / cholesterol efflux / negative chemotaxis / adrenal gland development / positive regulation of Rho protein signal transduction / cholesterol binding / host cell Golgi membrane / cholesterol biosynthetic process / endocytic vesicle / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cholesterol efflux / Scavenging of heme from plasma / Attachment and Entry / positive regulation of substrate adhesion-dependent cell spreading / Retinoid metabolism and transport / positive regulation of phagocytosis / voltage-gated potassium channel complex / positive regulation of stress fiber assembly / endocytic vesicle lumen / heat shock protein binding / cholesterol metabolic process / integrin-mediated signaling pathway / cholesterol homeostasis / Post-translational protein phosphorylation / regulation of protein phosphorylation / Heme signaling / PPARA activates gene expression / phospholipid binding / negative regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / Platelet degranulation / protein complex oligomerization / monoatomic ion channel activity / amyloid-beta binding / cytoplasmic vesicle / secretory granule lumen / collagen-containing extracellular matrix / early endosome / protein stabilization / blood microparticle
Similarity search - Function
Protein 3a, betacoronavirus / 3a-like viroporin, transmembrane domain, alpha/betacoronavirus / 3a-like viroporin, cytosolic domain, alpha/betacoronavirus / Betacoronavirus viroporin / Coronavirus (CoV) 3a-like viroporin trans-membrane (TM) domain profile. / Coronavirus (CoV) 3a-like viroporin cytosolic (CD) domain profile. / Apolipoprotein A/E / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
Apolipoprotein A-I / ORF3a protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMiller AN / Houlihan PR / Matamala E / Cabezas-Bratesco D / Lee GY / Cristofori-Armstrong B / Dilan TL / Sanchez-Martinez S / Matthies D / Yan R ...Miller AN / Houlihan PR / Matamala E / Cabezas-Bratesco D / Lee GY / Cristofori-Armstrong B / Dilan TL / Sanchez-Martinez S / Matthies D / Yan R / Yu Z / Ren D / Brauchi SE / Clapham DE
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: bioRxiv / Year: 2022
Title: The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins.
Authors: Alexandria N Miller / Patrick R Houlihan / Ella Matamala / Deny Cabezas-Bratesco / Gi Young Lee / Ben Cristofori-Armstrong / Tanya L Dilan / Silvia Sanchez-Martinez / Doreen Matthies / Rui ...Authors: Alexandria N Miller / Patrick R Houlihan / Ella Matamala / Deny Cabezas-Bratesco / Gi Young Lee / Ben Cristofori-Armstrong / Tanya L Dilan / Silvia Sanchez-Martinez / Doreen Matthies / Rui Yan / Zhiheng Yu / Dejian Ren / Sebastian E Brauchi / David E Clapham
Abstract: The severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) and SARS-CoV-1 accessory protein Orf3a colocalizes with markers of the plasma membrane, endocytic pathway, and Golgi ...The severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) and SARS-CoV-1 accessory protein Orf3a colocalizes with markers of the plasma membrane, endocytic pathway, and Golgi apparatus. Some reports have led to annotation of both Orf3a proteins as a viroporin. Here we show that neither SARS-CoV-2 nor SARS-CoV-1 form functional ion conducting pores and that the conductances measured are common contaminants in overexpression and with high levels of protein in reconstitution studies. Cryo-EM structures of both SARS-CoV-2 and SARS-CoV-1 Orf3a display a narrow constriction and the presence of a basic aqueous vestibule, which would not favor cation permeation. We observe enrichment of the late endosomal marker Rab7 upon SARS-CoV-2 Orf3a overexpression, and co-immunoprecipitation with VPS39. Interestingly, SARS-CoV-1 Orf3a does not cause the same cellular phenotype as SARS-CoV-2 Orf3a and does not interact with VPS39. To explain this difference, we find that a divergent, unstructured loop of SARS-CoV-2 Orf3a facilitates its binding with VPS39, a HOPS complex tethering protein involved in late endosome and autophagosome fusion with lysosomes. We suggest that the added loop enhances SARS-CoV-2 Orf3a ability to co-opt host cellular trafficking mechanisms for viral exit or host immune evasion.
History
DepositionOct 9, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28544.png

Downloads & links

-
Map

FileDownload / File: emd_28544.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.844 Å
Density
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.045289513 - 0.096237026
Average (Standard dev.)0.000116909934 (±0.0018406784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.064 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_28544_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_28544_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like envi...

EntireName: Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like environment, MSP1D1 nanodisc
Components
  • Complex: Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like environment, MSP1D1 nanodisc
    • Protein or peptide: ORF3a protein
    • Protein or peptide: Apolipoprotein A-I
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

-
Supramolecule #1: Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like envi...

SupramoleculeName: Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like environment, MSP1D1 nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: ORF3a protein

MacromoleculeName: ORF3a protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 36.268219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDLFMRFFTL GSITAQPVKI DNASPASTVH ATATIPLQAS LPFGWLVIGV AFLAVFQSAT KIIALNKRWQ LALYKGFQFI CNLLLLFVT IYSHLLLVAA GMEAQFLYLY ALIYFLQCIN ACRIIMRCWL CWKCKSKNPL LYDANYFVCW HTHNYDYCIP Y NSVTDTIV ...String:
MDLFMRFFTL GSITAQPVKI DNASPASTVH ATATIPLQAS LPFGWLVIGV AFLAVFQSAT KIIALNKRWQ LALYKGFQFI CNLLLLFVT IYSHLLLVAA GMEAQFLYLY ALIYFLQCIN ACRIIMRCWL CWKCKSKNPL LYDANYFVCW HTHNYDYCIP Y NSVTDTIV VTEGDGISTP KLKEDYQIGG YSEDRHSGVK DYVVVHGYFT EVYYQLESTQ ITTDTGIENA TFFIFNKLVK DP PNVQIHT IDGSSGVANP AMDPIYDEPT TTTSVPLGGR GLEVLFQGPG SGQLVGSGGL EGGGGWSHPQ FEKGGGSGGG SGG GSWSHP QFEK

UniProtKB: ORF3a protein

-
Macromolecule #2: Apolipoprotein A-I

MacromoleculeName: Apolipoprotein A-I / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.704729 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHHHHHHHDY DIPTTENLYF QGSTFSKLRE QLGPVTQEFW DNLEKETEGL RQEMSKDLEE VKAKVQPYLD DFQKKWQEEM ELYRQKVEP LRAELQEGAR QKLHELQEKL SPLGEEMRDR ARAHVDALRT HLAPYSDELR QRLAARLEAL KENGGARLAE Y HAKATEHL ...String:
GHHHHHHHDY DIPTTENLYF QGSTFSKLRE QLGPVTQEFW DNLEKETEGL RQEMSKDLEE VKAKVQPYLD DFQKKWQEEM ELYRQKVEP LRAELQEGAR QKLHELQEKL SPLGEEMRDR ARAHVDALRT HLAPYSDELR QRLAARLEAL KENGGARLAE Y HAKATEHL STLSEKAKPA LEDLRQGLLP VLESFKVSFL SALEEYTKKL NTQ

UniProtKB: Apolipoprotein A-I

-
Macromolecule #3: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 3 / Number of copies: 2 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 13970 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7kjr

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 162607
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8eqs:
Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like environment, MSP1D1 nanodisc

+
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://pdbjlvh1.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