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- EMDB-49630: RAVV glycoprotein in complex with hNPC1-C -

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Basic information

Entry
Database: EMDB / ID: EMD-49630
TitleRAVV glycoprotein in complex with hNPC1-C
Map dataUnsharpened map of RAVV GPcl/h-NPC1-C complex
Sample
  • Complex: RAVV GPcl in complexed with human NPC1-C
    • Protein or peptide: NPC intracellular cholesterol transporter 1
    • Protein or peptide: Envelope glycoprotein RAVV GP1
    • Protein or peptide: Envelope glycoprotein RAVV GP2
KeywordsRavn / hNPC1-C / glycoprotein / VIRAL PROTEIN
Function / homology
Function and homology information


membrane raft organization / cytoplasmic side of lysosomal membrane / intracellular cholesterol transport / intracellular lipid transport / lysosome to ER cholesterol transport / negative regulation of epithelial cell apoptotic process / sterol transport / intestinal cholesterol absorption / cholesterol transport / bile acid metabolic process ...membrane raft organization / cytoplasmic side of lysosomal membrane / intracellular cholesterol transport / intracellular lipid transport / lysosome to ER cholesterol transport / negative regulation of epithelial cell apoptotic process / sterol transport / intestinal cholesterol absorption / cholesterol transport / bile acid metabolic process / LDL clearance / cholesterol transfer activity / establishment of protein localization to membrane / glycoprotein biosynthetic process / cholesterol efflux / lysosomal transport / cholesterol binding / response to cadmium ion / cholesterol homeostasis / negative regulation of TORC1 signaling / gene expression / autophagy / transmembrane signaling receptor activity / nuclear envelope / late endosome membrane / signaling receptor activity / lysosome / membrane raft / lysosomal membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
NPC1-like / TLV/ENV coat polyprotein / Niemann-Pick C1, N-terminal / : / Niemann-Pick C1 N terminus / NPC1, middle luminal domain / Filoviruses glycoprotein / : / Filoviruses glycoprotein, extracellular domain / Filovirus glycoprotein ...NPC1-like / TLV/ENV coat polyprotein / Niemann-Pick C1, N-terminal / : / Niemann-Pick C1 N terminus / NPC1, middle luminal domain / Filoviruses glycoprotein / : / Filoviruses glycoprotein, extracellular domain / 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 speciesRavn virus - Ravn, Kenya, 1987 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsYe G / Bu F / 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: Nature / Year: 2026
Title: Structures of Marburgvirus glycoprotein and its complex with NPC1 receptor.
Authors: Gang Ye / Fan Bu / Hailey Turner-Hubbard / Morgan Herbst / Lanying Du / Ge Yang / Bin Liu / Fang Li /
Abstract: Marburgviruses (MBVs) cause severe haemorrhagic fever with higher fatality rates than Ebola virus (EBOV). Here we show that the MBV glycoprotein (GP) mediates viral entry more efficiently than EBOV ...Marburgviruses (MBVs) cause severe haemorrhagic fever with higher fatality rates than Ebola virus (EBOV). Here we show that the MBV glycoprotein (GP) mediates viral entry more efficiently than EBOV GP. Using cryo-EM, we determined structures of MBV GP in three states: (1) unbound; (2) bound to its endosomal receptor NPC1; and (3) complexed with a neutralizing nanobody. The glycan cap shields the receptor-binding site from NPC1 but only partially from the nanobody, enabling limited immune evasion. After glycan cap cleavage, NPC1 binds to MBV GP in a distinct orientation compared with EBOV GP, providing an additional anchor and enhancing receptor affinity. NPC1 engagement also induces substantial conformational changes in MBV GP, probably facilitating membrane fusion. Furthermore, MBV GP is susceptible to the neutralizing nanobody, which mimics NPC1 at the receptor-binding site. Together, our findings reveal MBV GP as a highly efficient entry mediator and suggest structural mechanisms that may contribute to its enhanced entry efficiency.
History
DepositionMar 11, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49630.png

Downloads & links

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Map

FileDownload / File: emd_49630.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map of RAVV GPcl/h-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: 0.078
Minimum - Maximum-0.25786117 - 0.51338845
Average (Standard dev.)0.0009756869 (±0.011241418)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Additional map: sharpened map of RAVV GPcl/h-NPC1-C complex

Fileemd_49630_additional_1.map
Annotationsharpened map of RAVV GPcl/h-NPC1-C complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B of RAVV GPcl/h-NPC1-C complex

Fileemd_49630_half_map_1.map
Annotationhalf map_B of RAVV GPcl/h-NPC1-C complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A of RAVV GPcl/h-NPC1-C complex

Fileemd_49630_half_map_2.map
Annotationhalf map_A of RAVV GPcl/h-NPC1-C complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RAVV GPcl in complexed with human NPC1-C

EntireName: RAVV GPcl in complexed with human NPC1-C
Components
  • Complex: RAVV GPcl in complexed with human NPC1-C
    • Protein or peptide: NPC intracellular cholesterol transporter 1
    • Protein or peptide: Envelope glycoprotein RAVV GP1
    • Protein or peptide: Envelope glycoprotein RAVV GP2

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Supramolecule #1: RAVV GPcl in complexed with human NPC1-C

SupramoleculeName: RAVV GPcl in complexed with human NPC1-C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ravn virus - Ravn, Kenya, 1987

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Macromolecule #1: NPC intracellular cholesterol transporter 1

MacromoleculeName: NPC intracellular cholesterol transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / 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

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Macromolecule #2: Envelope glycoprotein RAVV GP1

MacromoleculeName: Envelope glycoprotein RAVV GP1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ravn virus - Ravn, Kenya, 1987
Molecular weightTheoretical: 28.417133 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIYFLISL ILIQSIKTLP VLEIASNSQP QDVDSVCSGT LQKTEDVHLM GFTLSGQKVA DSPLEASKRW AFRTGVPPKN VEYTEGEEA KTCYNISVTD PSGKSLLLDP PSNIRDYPKC KTVHHIQGQN PHAQGIALHL WGAFFLYDRV ASTTMYRGKV F TEGNIAAM ...String:
MKTIYFLISL ILIQSIKTLP VLEIASNSQP QDVDSVCSGT LQKTEDVHLM GFTLSGQKVA DSPLEASKRW AFRTGVPPKN VEYTEGEEA KTCYNISVTD PSGKSLLLDP PSNIRDYPKC KTVHHIQGQN PHAQGIALHL WGAFFLYDRV ASTTMYRGKV F TEGNIAAM IVNKTVHRMI FSRQGQGYRH MNLTSTNKYW TSSNETQRND TGCFGILQEY NSTNNQTCPP SLKPPSLPTV TP SIHSTNT QINTAKSGT

UniProtKB: Envelope glycoprotein

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Macromolecule #3: Envelope glycoprotein RAVV GP2

MacromoleculeName: Envelope glycoprotein RAVV GP2 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ravn virus - Ravn, Kenya, 1987
Molecular weightTheoretical: 28.195475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RPPIYFRKKR SIFWKEGDIF PFLDGLINTE IDFDPIPNTE TIFDESPSFN TSTNEEQHTP PNISLTFSYF PDKNGDTAYS GENENDCDA ELRIWSVQED DLAAGLSWIP FFGPGIEGLY TAGLIKNQNN LVCRLRRLAN QTAKSLELLL RVTTEERTFS L INRIAIDF ...String:
RPPIYFRKKR SIFWKEGDIF PFLDGLINTE IDFDPIPNTE TIFDESPSFN TSTNEEQHTP PNISLTFSYF PDKNGDTAYS GENENDCDA ELRIWSVQED DLAAGLSWIP FFGPGIEGLY TAGLIKNQNN LVCRLRRLAN QTAKSLELLL RVTTEERTFS L INRIAIDF LLTRWGGTCK VLGPDCCIGI EDLSKNISEQ IDKIRKDEQK EETGSGYIPE APRDGQAYVR KDGEWVLLST FL GHHHHHH

UniProtKB: Envelope glycoprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6bp2

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116624
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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