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- PDB-9npr: RAVV glycoprotein in complex with hNPC1-C -

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Basic information

Entry
Database: PDB / ID: 9npr
TitleRAVV glycoprotein in complex with hNPC1-C
Components
  • Envelope glycoprotein RAVV GP1
  • Envelope glycoprotein RAVV GP2
  • NPC intracellular cholesterol transporter 1
KeywordsVIRAL PROTEIN / Ravn / 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 / cholesterol transfer activity ...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 / cholesterol transfer activity / cholesterol transport / programmed cell death / bile acid metabolic process / establishment of protein localization to membrane / cholesterol efflux / adult walking behavior / lysosomal transport / cholesterol binding / cellular response to steroid hormone stimulus / negative regulation of macroautophagy / : / cellular response to low-density lipoprotein particle stimulus / response to cadmium ion / cholesterol metabolic process / neurogenesis / negative regulation of TORC1 signaling / cholesterol homeostasis / macroautophagy / liver development / autophagy / endocytosis / late endosome membrane / transmembrane signaling receptor activity / nuclear envelope / signaling receptor activity / virus receptor activity / gene expression / lysosome / membrane raft / response to xenobiotic stimulus / lysosomal membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / perinuclear region of cytoplasm / host cell plasma membrane / virion membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
TLV/ENV coat polyprotein / NPC1-like / Niemann-Pick C1, N-terminal / : / Niemann-Pick C1 N terminus / NPC1, middle luminal domain / : / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein ...TLV/ENV coat polyprotein / 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)
Ravn virus - Ravn
Kenya
1987
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsYe, G. / Bu, F. / 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: To Be Published
Title: Cryo-EM structure of Ravn marburgvirus glycoprotein complexed with its human endosomal receptor NPC1
Authors: Bu, F. / Ye, G. / Liu, B. / Li, F.
History
DepositionMar 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: NPC intracellular cholesterol transporter 1
H: NPC intracellular cholesterol transporter 1
I: NPC intracellular cholesterol transporter 1
A: Envelope glycoprotein RAVV GP1
D: Envelope glycoprotein RAVV GP2
B: Envelope glycoprotein RAVV GP1
E: Envelope glycoprotein RAVV GP2
C: Envelope glycoprotein RAVV GP1
F: Envelope glycoprotein RAVV GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,44018
Polymers265,2159
Non-polymers7,2259
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.: 3
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 RAVV GP1 / GP1 / 2 / GP / Virion spike glycoprotein


Mass: 28417.133 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ravn virus - Ravn, Kenya, 1987 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q1PDC7
#3: Protein Envelope glycoprotein RAVV GP2 / GP1 / 2 / GP / Virion spike glycoprotein


Mass: 28195.475 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ravn virus - Ravn, Kenya, 1987 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q1PDC7
#4: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
Has ligand of interestN
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: RAVV GPcl in complexed with human NPC1-C / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Ravn virus - Ravn, Kenya, 1987
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 50 e/Å2 / Film or detector model: GATAN K3 (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: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116624 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411273
ELECTRON MICROSCOPYf_angle_d0.80615319
ELECTRON MICROSCOPYf_dihedral_angle_d14.5054410
ELECTRON MICROSCOPYf_chiral_restr0.0511814
ELECTRON MICROSCOPYf_plane_restr0.0051902

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