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- EMDB-64093: Structure of the SFTSV Gn head protein in complex with Nb261 and Nb318 -

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Basic information

Entry
Database: EMDB / ID: EMD-64093
TitleStructure of the SFTSV Gn head protein in complex with Nb261 and Nb318
Map data
Sample
  • Complex: Gn head protein in complex with Nb261 and Nb318
    • Protein or peptide: SFTSV Gn head
    • Protein or peptide: Nb261
    • Protein or peptide: Nb318
KeywordsSFTSV / nanobodies / complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell Golgi membrane / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesSevere fever with thrombocytopenia syndrome virus / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsLiang SJ / Lou ZY / Wu XL
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structure of the SFTSV Gn head protein in complex with Nb261 and Nb318
Authors: Liang SJ
History
DepositionApr 9, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64093.png

Downloads & links

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Map

FileDownload / File: emd_64093.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 270.08 Å		1.06 Å/pix.
x 256 pix.
= 270.08 Å		1.06 Å/pix.
x 256 pix.
= 270.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-0.058650114 - 13.878676
Average (Standard dev.)-0.006264481 (±0.2929831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64093_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64093_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Gn head protein in complex with Nb261 and Nb318

EntireName: Gn head protein in complex with Nb261 and Nb318
Components
  • Complex: Gn head protein in complex with Nb261 and Nb318
    • Protein or peptide: SFTSV Gn head
    • Protein or peptide: Nb261
    • Protein or peptide: Nb318

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Supramolecule #1: Gn head protein in complex with Nb261 and Nb318

SupramoleculeName: Gn head protein in complex with Nb261 and Nb318 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe fever with thrombocytopenia syndrome virus

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Macromolecule #1: SFTSV Gn head

MacromoleculeName: SFTSV Gn head / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe fever with thrombocytopenia syndrome virus
Molecular weightTheoretical: 35.366055 KDa
Recombinant expressionOrganism: Homo (humans)
SequenceString: DSGPIICAGP IHSNKSADIP HLLGYSEKIC QIDRLIHVSS WLRNHSQFQG YVGQRGGRSQ VSYYPAENSY SRWSGLLSPC DADWLGMLV VKKAKGSDMI VPGPSYKGKV FFERPTFDGY VGWGCGSGKS RTESGELCSS DSGTSSGLLP SNRVLWIGDV A CQPMTPIP ...String:
DSGPIICAGP IHSNKSADIP HLLGYSEKIC QIDRLIHVSS WLRNHSQFQG YVGQRGGRSQ VSYYPAENSY SRWSGLLSPC DADWLGMLV VKKAKGSDMI VPGPSYKGKV FFERPTFDGY VGWGCGSGKS RTESGELCSS DSGTSSGLLP SNRVLWIGDV A CQPMTPIP EETFLELKSF SQSEFPDICK IDGIVFNQCE GESLPQPFDV AWMDVGHSHK IIMREHKTKW VQESSSKDFV CY KEGTGPC SESEEKTCKT SGSCRGDMQF CKVAGCEHGE EASEAKCRCS LVHKPGEVVV SYGGMRVRPK CYGFSRMMAT LEV N

UniProtKB: Envelopment polyprotein

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Macromolecule #2: Nb261

MacromoleculeName: Nb261 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 12.681106 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGG LVQPGGSLRL SCAASGFTIS NADMRWYRQA PGKERELVAL LLSSLGGSTE YADSVKGRFT MFRDNARNTV YLQMDNLKA EDTAVYYCNV RWTDYWGQGT QVTVSS

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Macromolecule #3: Nb318

MacromoleculeName: Nb318 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 13.363756 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGG LVQAGGSLRL SCTASGLTFS SYAMGWFRQA PGKEREFVAA ISWSGGDTYY EDSVKGRFTI SRDNAANTVY LQMNSLKPE DTAVYYCNSG GIATMKLMDQ YEYWGQGTQV TVSS

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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: DIFFRACTION / 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 333824
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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