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- PDB-9dz2: Cryo-EM structure of Sudan ebolavirus glycoprotein complexed with... -

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Basic information

Entry
Database: PDB / ID: 9dz2
TitleCryo-EM structure of Sudan ebolavirus glycoprotein complexed with hNPC1-C
Components
  • Envelope glycoprotein
  • NPC intracellular cholesterol transporter 1
  • Shed GP
KeywordsVIRAL PROTEIN / SUDV / hNPC1-C / glycoprotein
Function / homology
Function and homology information


cyclodextrin metabolic process / cholesterol storage / membrane raft organization / intracellular cholesterol transport / intracellular lipid transport / sterol transport / intestinal cholesterol absorption / LDL clearance / negative regulation of epithelial cell apoptotic process / bile acid metabolic process ...cyclodextrin metabolic process / cholesterol storage / membrane raft organization / intracellular cholesterol transport / intracellular lipid transport / sterol transport / intestinal cholesterol absorption / LDL clearance / negative regulation of epithelial cell apoptotic process / bile acid metabolic process / programmed cell death / cholesterol transfer activity / cholesterol transport / establishment of protein localization to membrane / adult walking behavior / cholesterol efflux / lysosomal transport / cholesterol binding / negative regulation of macroautophagy / cellular response to steroid hormone stimulus / protein glycosylation / cellular response to low-density lipoprotein particle stimulus / response to cadmium ion / negative regulation of TORC1 signaling / neurogenesis / cholesterol metabolic process / cholesterol homeostasis / liver development / macroautophagy / autophagy / endocytosis / late endosome membrane / transmembrane signaling receptor activity / nuclear envelope / signaling receptor activity / virus receptor activity / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / gene expression / entry receptor-mediated virion attachment to host cell / lysosome / symbiont-mediated suppression of host innate immune response / membrane raft / response to xenobiotic stimulus / symbiont entry into host cell / lysosomal membrane / fusion of virus membrane with host endosome membrane / viral envelope / perinuclear region of cytoplasm / host cell plasma membrane / virion membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
NPC1-like / Niemann-Pick C1, N-terminal / : / Niemann-Pick C1 N terminus / NPC1, middle luminal domain / : / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 ...NPC1-like / Niemann-Pick C1, N-terminal / : / Niemann-Pick C1 N terminus / NPC1, middle luminal domain / : / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
NPC intracellular cholesterol transporter 1 / Envelope glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Sudan ebolavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsBu, F. / Ye, G. / Liu, B. / Li, F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089728 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI171954 United States
CitationJournal: Commun Biol / Year: 2025
Title: Cryo-EM structure of Sudan ebolavirus glycoprotein complexed with its human endosomal receptor NPC1.
Authors: Fan Bu / Gang Ye / Hailey Turner-Hubbard / Morgan Herbst / Bin Liu / Fang Li /
Abstract: Sudan ebolavirus (SUDV), like Ebola ebolavirus (EBOV), poses a significant threat to global health and security due to its high lethality. However, unlike EBOV, there are no approved vaccines or ...Sudan ebolavirus (SUDV), like Ebola ebolavirus (EBOV), poses a significant threat to global health and security due to its high lethality. However, unlike EBOV, there are no approved vaccines or treatments for SUDV, and its structural interaction with the endosomal receptor NPC1 remains unclear. This study compares the glycoproteins of SUDV and EBOV (in their proteolytically primed forms) and their binding to human NPC1 (hNPC1). The findings reveal that the SUDV glycoprotein binds significantly more strongly to hNPC1 than the EBOV glycoprotein. Using cryo-EM, we determined the structure of the SUDV glycoprotein/hNPC1 complex, identifying four key residues in the SUDV glycoprotein that differ from those in the EBOV glycoprotein and influence hNPC1 binding: Ile79, Ala141, and Pro148 enhance binding, while Gln142 reduces it. Collectively, these residue differences account for SUDV's stronger binding affinity for hNPC1. This study provides critical insights into receptor recognition across all viruses in the ebolavirus genus, including their interactions with receptors in bats, their suspected reservoir hosts. These findings advance our understanding of ebolavirus cell entry, tissue tropism, and host range.
History
DepositionOct 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: NPC intracellular cholesterol transporter 1
I: Envelope glycoprotein
J: Shed GP
A: Envelope glycoprotein
B: Shed GP
D: NPC intracellular cholesterol transporter 1
E: Envelope glycoprotein
F: Shed GP


Theoretical massNumber of molelcules
Total (without water)184,5878
Polymers184,5878
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein NPC intracellular cholesterol transporter 1 / Niemann-Pick C1 protein


Mass: 31792.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPC1 / Production host: Homo sapiens (human) / References: UniProt: O15118
#2: Protein Envelope glycoprotein / GP1 / 2 / GP


Mass: 21546.752 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q7T9D9
#3: Protein Shed GP / GP1 / 2-delta


Mass: 18787.199 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q7T9D9
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SUDV GP complexed with NPC1-C / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Sudan ebolavirus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 53.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 159976 / Symmetry type: POINT
Atomic model buildingPDB-ID: 5f1b

5f1b


Accession code: 5f1b / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049779
ELECTRON MICROSCOPYf_angle_d0.73913326
ELECTRON MICROSCOPYf_dihedral_angle_d14.5523515
ELECTRON MICROSCOPYf_chiral_restr0.0461455
ELECTRON MICROSCOPYf_plane_restr0.0051742

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