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- PDB-8jg5: Cryo-EM structure of the GI.4 Chiba VLP complexed with the CV-1A1... -

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Basic information

Entry
Database: PDB / ID: 8jg5
TitleCryo-EM structure of the GI.4 Chiba VLP complexed with the CV-1A1 Fv-clasp
Components
  • VH,SARAH
  • VL,SARAH
  • VP1
KeywordsVIRUS / NOROVIRUS / GI.4 / VIRUS LIKE PARTICLE / human monoclonal antibody / Fv-clasp
Biological speciesNorovirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsHosaka, T. / Katsura, K. / Kimura-Someya, T. / Someya, Y. / Shirouzu, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21fk0108121 Japan
Japan Agency for Medical Research and Development (AMED)JP22fk0108121 Japan
CitationJournal: To Be Published
Title: Structural analyses of the GI.4 norovirus by cryo-electron microscopy and X-ray crystallography reveal binding sites for human monoclonal antibodies
Authors: Kimura-Someya, T. / Katsura, K. / Kato-Murayama, M. / Hosaka, T. / Uchikubo-Kamo, T. / Ihara, K. / Hanada, K. / Murayama, K. / Shirouzu, M. / Someya, Y.
History
DepositionMay 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP1
C: VH,SARAH
D: VL,SARAH
E: VH,SARAH
F: VL,SARAH
G: VP1


Theoretical massNumber of molelcules
Total (without water)250,4067
Polymers250,4067
Non-polymers00
Water0
1
A: VP1
B: VP1
C: VH,SARAH
D: VL,SARAH
E: VH,SARAH
F: VL,SARAH
G: VP1
x 60


Theoretical massNumber of molelcules
Total (without water)15,024,348420
Polymers15,024,348420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP1
B: VP1
C: VH,SARAH
D: VL,SARAH
E: VH,SARAH
F: VL,SARAH
G: VP1
x 5


  • icosahedral pentamer
  • 1.25 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,252,02935
Polymers1,252,02935
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP1
C: VH,SARAH
D: VL,SARAH
E: VH,SARAH
F: VL,SARAH
G: VP1
x 6


  • icosahedral 23 hexamer
  • 1.5 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,502,43542
Polymers1,502,43542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


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

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Components

#1: Protein VP1


Mass: 58108.332 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: GenBank ID AB042808 / Source: (gene. exp.) Norovirus / Gene: ORF2 / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody VH,SARAH


Mass: 19847.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: VH-SARAH chimera of linker (residues (-6)-0), VH (residues 1-118), and SARAH (residues 119-171)
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody VL,SARAH


Mass: 18193.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: VL-SARAH chimera of linker (residues (-6)-0), VL (residues 1-112), and SARAH (residues 113-162)
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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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: Viral protein 1 with its antibody fragments / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Norovirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / 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 AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47125 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416478
ELECTRON MICROSCOPYf_angle_d0.64122486
ELECTRON MICROSCOPYf_dihedral_angle_d4.2422222
ELECTRON MICROSCOPYf_chiral_restr0.0442489
ELECTRON MICROSCOPYf_plane_restr0.0052955

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