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- PDB-7x6w: SFTSV 2 fold hexamer -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7x6w
TitleSFTSV 2 fold hexamer
Components(Envelopment polyprotein) x 2
KeywordsVIRAL PROTEIN / SFTSV / Virus / Glycoproteins / assembly
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.18 Å
AuthorsSun, Z. / Lou, Z.
Funding support China, 1items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelopment polyprotein
B: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6844
Polymers116,6732
Non-polymers1,0112
Water0
1
A: Envelopment polyprotein
B: Envelopment polyprotein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)706,10424
Polymers700,03912
Non-polymers6,06612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein Envelopment polyprotein


Mass: 61745.293 Da / Num. of mol.: 1 / Fragment: Gn / Source method: isolated from a natural source
Source: (natural) Severe fever with thrombocytopenia syndrome virus
Cell line: Vero / References: UniProt: A0A1S6XXI4
#2: Protein Envelopment polyprotein


Mass: 54927.797 Da / Num. of mol.: 1 / Fragment: Gc / Source method: isolated from a natural source
Source: (natural) Severe fever with thrombocytopenia syndrome virus
References: UniProt: A0A1S6XXK1
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
Has ligand of interestY

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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: Severe fever with thrombocytopenia syndrome virus / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Severe fever with thrombocytopenia syndrome virus
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 1.38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 5.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54378 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036690
ELECTRON MICROSCOPYf_angle_d0.7329050
ELECTRON MICROSCOPYf_dihedral_angle_d7.035965
ELECTRON MICROSCOPYf_chiral_restr0.0471017
ELECTRON MICROSCOPYf_plane_restr0.0051170

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