[English] 日本語
Yorodumi
- EMDB-47323: Cryo-EM structure of Sudan ebolavirus glycoprotein complexed with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47323
TitleCryo-EM structure of Sudan ebolavirus glycoprotein complexed with hNPC1-C
Map datasharpened map of SUDV GPcl/NPC1-C complex
Sample
  • Complex: SUDV GP complexed with NPC1-C
    • Protein or peptide: NPC intracellular cholesterol transporter 1
    • Protein or peptide: Envelope glycoprotein
    • Protein or peptide: Shed GP
KeywordsSUDV / hNPC1-C / glycoprotein / VIRAL PROTEIN
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 speciesSudan ebolavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsBu F / Ye G / Liu B / Li F
Funding support United States, 2 items
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, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47323.png

Downloads & links

-
Map

FileDownload / File: emd_47323.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of SUDV GPcl/NPC1-C complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 320 pix.
= 283.307 Å		0.89 Å/pix.
x 320 pix.
= 283.307 Å		0.89 Å/pix.
x 320 pix.
= 283.307 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88533 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00825
Minimum - Maximum-0.29398918 - 0.5478778
Average (Standard dev.)-0.000019989919 (±0.011310393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 283.30664 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: sharpened map of SUDV GPcl/NPC1-C complex

Fileemd_47323_additional_1.map
Annotationsharpened map of SUDV GPcl/NPC1-C complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: sharpened map of SUDV GPcl/NPC1-C complex

Fileemd_47323_half_map_1.map
Annotationsharpened map of SUDV GPcl/NPC1-C complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: sharpened map of SUDV GPcl/NPC1-C complex

Fileemd_47323_half_map_2.map
Annotationsharpened map of SUDV GPcl/NPC1-C complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SUDV GP complexed with NPC1-C

EntireName: SUDV GP complexed with NPC1-C
Components
  • Complex: SUDV GP complexed with NPC1-C
    • Protein or peptide: NPC intracellular cholesterol transporter 1
    • Protein or peptide: Envelope glycoprotein
    • Protein or peptide: Shed GP

-
Supramolecule #1: SUDV GP complexed with NPC1-C

SupramoleculeName: SUDV GP complexed with NPC1-C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sudan ebolavirus

-
Macromolecule #1: NPC intracellular cholesterol transporter 1

MacromoleculeName: NPC intracellular cholesterol transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.792486 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SASTTNPVDL WSAPSSQARL EKEYFDQHFG PFFRTEQLII RAPLTDKHIY QPYPSGADVP FGPPLDIQI LHQVLDLQIA IENITASYDN ETVTLQDICL APLSPYNTNC TILSVLNYFQ NSHSVLDHKK GDDFFVYADY H THFLYCVR ...String:
MDAMKRGLCC VLLLCGAVFV SASTTNPVDL WSAPSSQARL EKEYFDQHFG PFFRTEQLII RAPLTDKHIY QPYPSGADVP FGPPLDIQI LHQVLDLQIA IENITASYDN ETVTLQDICL APLSPYNTNC TILSVLNYFQ NSHSVLDHKK GDDFFVYADY H THFLYCVR APASLNDTSL LHDPCLGTFG GPVFPWLVLG GYDDQNYNNA TALVITFPVN NYYNDTEKLQ RAQAWEKEFI NF VKNYKNP NLTISFTAER SIEDELNRES DSDGSWSHPQ FEK

UniProtKB: NPC intracellular cholesterol transporter 1

-
Macromolecule #2: Envelope glycoprotein

MacromoleculeName: Envelope glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sudan ebolavirus
Molecular weightTheoretical: 21.546752 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGGLSLLQLP RDKFRKSSFF VWVIILFQKA FSMPLGVVTN STLEVTEIDQ LVCKDHLAST DQLKSVGLNL EGSGVSTDIP SATKRWGFR SGVPPKVVSY EAGEWAENCY NLEIKKPDGS ECLPPPPDGV RGFPRCRYVH KAQGTGPCPG DYAFHKDGAF F LYDRLAST ...String:
MGGLSLLQLP RDKFRKSSFF VWVIILFQKA FSMPLGVVTN STLEVTEIDQ LVCKDHLAST DQLKSVGLNL EGSGVSTDIP SATKRWGFR SGVPPKVVSY EAGEWAENCY NLEIKKPDGS ECLPPPPDGV RGFPRCRYVH KAQGTGPCPG DYAFHKDGAF F LYDRLAST VIYRGVNFAE GVIAFLILAK PKETFLQ

UniProtKB: Envelope glycoprotein

-
Macromolecule #3: Shed GP

MacromoleculeName: Shed GP / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sudan ebolavirus
Molecular weightTheoretical: 18.787199 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GKCNPNLHYW TAQEQHNAAG IAWIPYFGPG AEGIYTEGLM HNQNALVCGL RQLANETTQA LQLFLRATTE LRTYTILNRK AIDFLLRRW GGTCRILGPD CCIEPHDWTK NITDKINQII HDFIDNPLPN GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG H HHHHH

UniProtKB: Envelope glycoprotein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.7 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159976
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5f1b


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9dz2:
Cryo-EM structure of Sudan ebolavirus glycoprotein complexed with hNPC1-C

+
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