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- PDB-3gzu: VP7 recoated rotavirus DLP -

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Basic information

Entry
Database: PDB / ID: 3gzu
TitleVP7 recoated rotavirus DLP
Components
  • Inner capsid protein VP2
  • Intermediate capsid protein VP6
KeywordsVIRUS / rotavirus / VP7 / VP6 / VP2 / 7RP / DLP / Capsid protein / Metal-binding / Virion / Zinc / Core protein / RNA-binding / Icosaderal virus
Function / homology
Function and homology information


viral intermediate capsid / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral inner capsid / viral nucleocapsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Viral capsid alpha domain / Viral capsid alpha domain / Jelly Rolls - #170 / Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein / Jelly Rolls ...Viral capsid alpha domain / Viral capsid alpha domain / Jelly Rolls - #170 / Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Inner capsid protein VP2 / Inner capsid protein VP2 / Intermediate capsid protein VP6
Similarity search - Component
Biological speciesRotavirus A
Rhesus Rotavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChen, J.Z. / Settembre, E.C. / Harrison, S.C. / Grigorieff, N.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM.
Authors: James Z Chen / Ethan C Settembre / Scott T Aoki / Xing Zhang / A Richard Bellamy / Philip R Dormitzer / Stephen C Harrison / Nikolaus Grigorieff /
Abstract: Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle ...Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle reconstruction, we have visualized a rotavirus particle comprising the inner capsid coated with the trimeric outer-layer protein, VP7, at a resolution (4 A) comparable with that of X-ray crystallography. We have traced the VP7 polypeptide chain, including parts not seen in its X-ray crystal structure. The 3 well-ordered, 30-residue, N-terminal "arms" of each VP7 trimer grip the underlying trimer of VP6, an inner-capsid protein. Structural differences between free and particle-bound VP7 and between free and VP7-coated inner capsids may regulate mRNA transcription and release. The Ca(2+)-stabilized VP7 intratrimer contact region, which presents important neutralizing epitopes, is unaltered upon capsid binding.
History
DepositionApr 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.3Nov 13, 2019Group: Data collection / Other / Category: symmetry
Item: _symmetry.Int_Tables_number / _symmetry.space_group_name_H-M
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Inner capsid protein VP2
B: Inner capsid protein VP2
C: Intermediate capsid protein VP6
D: Intermediate capsid protein VP6
E: Intermediate capsid protein VP6
F: Intermediate capsid protein VP6
G: Intermediate capsid protein VP6
H: Intermediate capsid protein VP6
I: Intermediate capsid protein VP6
J: Intermediate capsid protein VP6
K: Intermediate capsid protein VP6
L: Intermediate capsid protein VP6
M: Intermediate capsid protein VP6
N: Intermediate capsid protein VP6
O: Intermediate capsid protein VP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)770,01720
Polymers769,69015
Non-polymers3275
Water0
1
A: Inner capsid protein VP2
B: Inner capsid protein VP2
C: Intermediate capsid protein VP6
D: Intermediate capsid protein VP6
E: Intermediate capsid protein VP6
F: Intermediate capsid protein VP6
G: Intermediate capsid protein VP6
H: Intermediate capsid protein VP6
I: Intermediate capsid protein VP6
J: Intermediate capsid protein VP6
K: Intermediate capsid protein VP6
L: Intermediate capsid protein VP6
M: Intermediate capsid protein VP6
N: Intermediate capsid protein VP6
O: Intermediate capsid protein VP6
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)46,201,0351200
Polymers46,181,413900
Non-polymers19,623300
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: Inner capsid protein VP2
B: Inner capsid protein VP2
C: Intermediate capsid protein VP6
D: Intermediate capsid protein VP6
E: Intermediate capsid protein VP6
F: Intermediate capsid protein VP6
G: Intermediate capsid protein VP6
H: Intermediate capsid protein VP6
I: Intermediate capsid protein VP6
J: Intermediate capsid protein VP6
K: Intermediate capsid protein VP6
L: Intermediate capsid protein VP6
M: Intermediate capsid protein VP6
N: Intermediate capsid protein VP6
O: Intermediate capsid protein VP6
hetero molecules
x 5


  • icosahedral pentamer
  • 3.85 MDa, 75 polymers
Theoretical massNumber of molelcules
Total (without water)3,850,086100
Polymers3,848,45175
Non-polymers1,63525
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Inner capsid protein VP2
B: Inner capsid protein VP2
C: Intermediate capsid protein VP6
D: Intermediate capsid protein VP6
E: Intermediate capsid protein VP6
F: Intermediate capsid protein VP6
G: Intermediate capsid protein VP6
H: Intermediate capsid protein VP6
I: Intermediate capsid protein VP6
J: Intermediate capsid protein VP6
K: Intermediate capsid protein VP6
L: Intermediate capsid protein VP6
M: Intermediate capsid protein VP6
N: Intermediate capsid protein VP6
O: Intermediate capsid protein VP6
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 4.62 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)4,620,104120
Polymers4,618,14190
Non-polymers1,96230
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 Inner capsid protein VP2


Mass: 93127.438 Da / Num. of mol.: 2 / Fragment: VP2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B2BMF8, UniProt: B2BMD1*PLUS
#2: Protein
Intermediate capsid protein VP6


Mass: 44879.641 Da / Num. of mol.: 13 / Fragment: VP6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhesus Rotavirus / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P04509
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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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: VP7 recoated rotavirus DLP / Type: VIRUS / Details: capsid protein VP7. VP6 and VP2
Details of virusHost category: REOVIRIDAE / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Bos taurus
Buffer solutionName: 20mM TrisHCl, 50mM NaCl, 2mM CaCl2 / pH: 8 / Details: 20mM TrisHCl, 50mM NaCl, 2mM CaCl2
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: C-flat grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: manual plunging at 90K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Dec 1, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 58168 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderTemperature: 90 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GENERIC FILM / Details: Kodak ISO163

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Processing

CTF correctionDetails: individual particle CTF
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching and refinement using FEALIGN / Resolution: 3.8 Å / Num. of particles: 3780 / Nominal pixel size: 1.233 Å / Actual pixel size: 1.233 Å / Magnification calibration: 58168 / Details: projection matching by FREALIGN / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms53991 0 5 0 53996

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