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- EMDB-33029: SFTSV 2 fold hexamer -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-33029
TitleSFTSV 2 fold hexamer
Map dataSFTSV 2 fold hexamer
Sample
  • Virus: Severe fever with thrombocytopenia syndrome virus
    • Protein or peptide: Envelopment polyprotein
    • Protein or peptide: Envelopment polyprotein
KeywordsSFTSV / Virus / Glycoproteins / assembly / VIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / 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 / Envelopment polyprotein
Similarity search - Component
Biological speciesSevere fever with thrombocytopenia syndrome virus
Methodsingle particle reconstruction / cryo EM / Resolution: 5.18 Å
AuthorsSun Z / Lou Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U20A20135 China
CitationJournal: Protein Cell / Year: 2023
Title: Architecture of severe fever with thrombocytopenia syndrome virus.
Authors: Zixian Sun / Jing Cheng / Yuan Bai / Lin Cao / Daoxin Xie / Fei Deng / Xinzheng Zhang / Zihe Rao / Zhiyong Lou /
History
DepositionMar 8, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33029.png

Downloads & links

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Map

FileDownload / File: emd_33029.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSFTSV 2 fold hexamer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.012958885 - 0.022924421
Average (Standard dev.)0.00081060064 (±0.0027374849)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33029_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_33029_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 : Severe fever with thrombocytopenia syndrome virus

EntireName: Severe fever with thrombocytopenia syndrome virus
Components
  • Virus: Severe fever with thrombocytopenia syndrome virus
    • Protein or peptide: Envelopment polyprotein
    • Protein or peptide: Envelopment polyprotein

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Supramolecule #1: Severe fever with thrombocytopenia syndrome virus

SupramoleculeName: Severe fever with thrombocytopenia syndrome virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1003835
Sci species name: Severe fever with thrombocytopenia syndrome virus
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Envelopment polyprotein

MacromoleculeName: Envelopment polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe fever with thrombocytopenia syndrome virus
Molecular weightTheoretical: 61.745293 KDa
SequenceString: MMKVIWFSSL VCLVIQCSGD SGPIICAGPI HSNKSAGIPH LLGYSEKICQ IDRLIHVSSW LRNHSQFQGY VGQRGGRSQV SYYPAENSY SRWSGLLSPC DADWLGMLVV KKAKGSDMIV PGPSYKGKVL FERPTFDGYV GWGCGSGKSR TESGELCSSD S GTSSGLLP ...String:
MMKVIWFSSL VCLVIQCSGD SGPIICAGPI HSNKSAGIPH LLGYSEKICQ IDRLIHVSSW LRNHSQFQGY VGQRGGRSQV SYYPAENSY SRWSGLLSPC DADWLGMLVV KKAKGSDMIV PGPSYKGKVL FERPTFDGYV GWGCGSGKSR TESGELCSSD S GTSSGLLP SDRVLWIGDV ACQPMTPIPE ETFLELKSFS QSEFPDICKI DGIVFNQCEG ESLPQPFDVA WMDVGHSHKI IM REHKTKW VQESSSKDFV CYKEGTGPCS ESEEKACKTS GSCRGDMQFC KVAGCEHGEE ASEAKCRCSL VHKPGEVVVS YGG MRVRPK CYGFSRMMAT MEVNPPEQRI GQCTGCHLEC INGGVRLITL TSELKSATVC ASHFCSSATS GKKSTEIHFH SGSL VGKAA IHVKGALVDG TEFTFEGSCM FPDGCNAVDC TFCREFLKNP QCYPAKKWLF IIIVILLGYA GLMLLTNVLK AIGVW GSWV IAPVKLMFAI MKKLMRTVSC LVGKLMDRGR QVIHEEIGEN GEGNQDDVRI EMARPRRVRH WMYSPVILTI LAIGLA EG

UniProtKB: Envelopment polyprotein

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Macromolecule #2: Envelopment polyprotein

MacromoleculeName: Envelopment polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe fever with thrombocytopenia syndrome virus
Molecular weightTheoretical: 54.927797 KDa
SequenceString: CDEMVHADSK LVSCRQGSGN MKECVTTGRA LLPAVNPGQE ACLHFTAPGS PDSKCLKIKV KRINLKCKKS SSYFVPDARS RCTSVRRCR WAGDCQSGCP PHFTSNSFSD DWAGKMDRAG LGFSGCSDGC GGAACGCFNA APSCIFWRKW VENPHGIIWK V SPCAAWVP ...String:
CDEMVHADSK LVSCRQGSGN MKECVTTGRA LLPAVNPGQE ACLHFTAPGS PDSKCLKIKV KRINLKCKKS SSYFVPDARS RCTSVRRCR WAGDCQSGCP PHFTSNSFSD DWAGKMDRAG LGFSGCSDGC GGAACGCFNA APSCIFWRKW VENPHGIIWK V SPCAAWVP SAVIELTMPS GEVRTFHPMS GIPTQVFKGV SVTYLGSDME VSGLTDLCEI EELKSKKLAL APCNQAGMGV VG KVGEIQC SSEESARTIK KDGCIWNADL VGIELRVDDA VCYSKITSVE AVANYSAIPT TIGGLRFERS HDSQGKISGS PLD ITAIRG SFSVNYRGLR LSLSEITATC TGEVTNVSGC YSCMTGAKVS IKLHSSKNST AHVRCKGDET AFSVLEGVHS YTVS LSFDH AVVDEQCQLN CGGHESQVTL KGNLIFLDVP KFVDGSYMQT YHSTVPTGAN IPSPTDWLNA LFGNGLSRWI LGVIG VLLG GLALFFLIMF LFKLGTKQVF RSRTKLA

UniProtKB: Envelopment polyprotein

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.38 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5y10


Details: 5y10;5g47;4hjc;3n43
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54378
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7x6w:
SFTSV 2 fold hexamer

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