[English] 日本語
Yorodumi
- EMDB-49630: RAVV glycoprotein in complex with hNPC1-C -

+
Open data


ID or keywords:

Loading...

-
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


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 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: 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, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49630.png

Downloads & links

-
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 °

-
Supplemental data

-
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)

-
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)

-
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)

-
Sample components

-
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

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

-
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

+
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)

+
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