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- EMDB-49632: RAVV GP in complex with Nanosota-MB1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49632
TitleRAVV GP in complex with Nanosota-MB1
Map dataunsharpened map of RAVV GP/Nanosota-MB1 complex
Sample
  • Complex: RAVV GPcl/Nanosota-MV1 complex
    • Protein or peptide: Nanosota-MB1
    • Protein or peptide: Envelope glycoprotein GP1
    • Protein or peptide: Envelope glycoprotein GP2
KeywordsRavn virus / GP / VIRAL PROTEIN / nanobody
Function / homology
Function and homology information


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 / membrane
Similarity search - Function
TLV/ENV coat polyprotein / : / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesRavn virus - Ravn, Kenya, 1987 / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 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: Structural basis of receptor recognition and nanobody neutralization of marburgvirus
Authors: Ye G / Bu F / 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

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Structure visualization

Supplemental images

emd_49632.png

Downloads & links

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Map

FileDownload / File: emd_49632.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map of RAVV GP/Nanosota-MB1 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: 0.123
Minimum - Maximum-0.2992499 - 0.61387485
Average (Standard dev.)-0.00018454577 (±0.013626559)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 283.30655 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map of RAVV GP/Nanosota-MB1 complex

Fileemd_49632_additional_1.map
Annotationsharpened map of RAVV GP/Nanosota-MB1 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 GP/Nanosota-MB1 complex

Fileemd_49632_half_map_1.map
Annotationhalf map_A of RAVV GP/Nanosota-MB1 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 GP/Nanosota-MB1 complex

Fileemd_49632_half_map_2.map
Annotationhalf map_B of RAVV GP/Nanosota-MB1 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/Nanosota-MV1 complex

EntireName: RAVV GPcl/Nanosota-MV1 complex
Components
  • Complex: RAVV GPcl/Nanosota-MV1 complex
    • Protein or peptide: Nanosota-MB1
    • Protein or peptide: Envelope glycoprotein GP1
    • Protein or peptide: Envelope glycoprotein GP2

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Supramolecule #1: RAVV GPcl/Nanosota-MV1 complex

SupramoleculeName: RAVV GPcl/Nanosota-MV1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ravn virus - Ravn, Kenya, 1987

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Macromolecule #1: Nanosota-MB1

MacromoleculeName: Nanosota-MB1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 17.52102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCTASRGTIS LYAMAWFRQA PGKEREFVAA ISRFYNDFIG YSTNYADSVR ARFTISRDNA ENTVYLLMN NLKPEDTASY YCAASTEWAS ESLQYGNWGH ESSKYANWGQ GTQVTVSSGG QHHHHHHGAY PYDVPDYAS

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Macromolecule #2: Envelope glycoprotein GP1

MacromoleculeName: Envelope glycoprotein GP1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ravn virus - Ravn, Kenya, 1987
Molecular weightTheoretical: 28.645406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RAMKTIYFLI SLILIQSIKT LPVLEIASNS QPQDVDSVCS GTLQKTEDVH LMGFTLSGQK VADSPLEASK RWAFRTGVPP KNVEYTEGE EAKTCYNISV TDPSGKSLLL DPPSNIRDYP KCKTVHHIQG QNPHAQGIAL HLWGAFFLYD RVASTTMYRG K VFTEGNIA ...String:
RAMKTIYFLI SLILIQSIKT LPVLEIASNS QPQDVDSVCS GTLQKTEDVH LMGFTLSGQK VADSPLEASK RWAFRTGVPP KNVEYTEGE EAKTCYNISV TDPSGKSLLL DPPSNIRDYP KCKTVHHIQG QNPHAQGIAL HLWGAFFLYD RVASTTMYRG K VFTEGNIA AMIVNKTVHR MIFSRQGQGY RHMNLTSTNK YWTSSNETQR NDTGCFGILQ EYNSTNNQTC PPSLKPPSLP TV TPSIHST NTQINTAKSG T

UniProtKB: Envelope glycoprotein

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Macromolecule #3: Envelope glycoprotein GP2

MacromoleculeName: Envelope glycoprotein 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: 7.4
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: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176829
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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