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- PDB-3gzt: VP7 recoated rotavirus DLP -

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Basic information

Entry
Database: PDB / ID: 3gzt
TitleVP7 recoated rotavirus DLP
ComponentsOuter capsid glycoprotein VP7
KeywordsVIRUS / rotavirus / VP7 / VP6 / VP2 / 7RP / DLP / Icosahedral virus / Capsid protein / Disulfide bond / Endoplasmic reticulum / Glycoprotein / Membrane / Transmembrane / Virion
Function / homology
Function and homology information


host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / viral outer capsid / receptor-mediated virion attachment to host cell / metal ion binding
Similarity search - Function
Rotavirus outer-layer protein VP7, domain 2 / Glycoprotein VP7, domain 1 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich ...Rotavirus outer-layer protein VP7, domain 2 / Glycoprotein VP7, domain 1 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Outer capsid glycoprotein VP7
Similarity search - Component
Biological speciesRhesus 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: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / em_image_scans / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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
B: Outer capsid glycoprotein VP7
F: Outer capsid glycoprotein VP7
G: Outer capsid glycoprotein VP7
H: Outer capsid glycoprotein VP7
I: Outer capsid glycoprotein VP7
J: Outer capsid glycoprotein VP7
K: Outer capsid glycoprotein VP7
L: Outer capsid glycoprotein VP7
M: Outer capsid glycoprotein VP7
N: Outer capsid glycoprotein VP7
O: Outer capsid glycoprotein VP7
P: Outer capsid glycoprotein VP7
Q: Outer capsid glycoprotein VP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,34556
Polymers373,62613
Non-polymers6,72043
Water00
1
B: Outer capsid glycoprotein VP7
F: Outer capsid glycoprotein VP7
G: Outer capsid glycoprotein VP7
H: Outer capsid glycoprotein VP7
I: Outer capsid glycoprotein VP7
J: Outer capsid glycoprotein VP7
K: Outer capsid glycoprotein VP7
L: Outer capsid glycoprotein VP7
M: Outer capsid glycoprotein VP7
N: Outer capsid glycoprotein VP7
O: Outer capsid glycoprotein VP7
P: Outer capsid glycoprotein VP7
Q: Outer capsid glycoprotein VP7
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)22,820,7253360
Polymers22,417,552780
Non-polymers403,1732580
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
B: Outer capsid glycoprotein VP7
F: Outer capsid glycoprotein VP7
G: Outer capsid glycoprotein VP7
H: Outer capsid glycoprotein VP7
I: Outer capsid glycoprotein VP7
J: Outer capsid glycoprotein VP7
K: Outer capsid glycoprotein VP7
L: Outer capsid glycoprotein VP7
M: Outer capsid glycoprotein VP7
N: Outer capsid glycoprotein VP7
O: Outer capsid glycoprotein VP7
P: Outer capsid glycoprotein VP7
Q: Outer capsid glycoprotein VP7
hetero molecules
x 5


  • icosahedral pentamer
  • 1.9 MDa, 65 polymers
Theoretical massNumber of molelcules
Total (without water)1,901,727280
Polymers1,868,12965
Non-polymers33,598215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
B: Outer capsid glycoprotein VP7
F: Outer capsid glycoprotein VP7
G: Outer capsid glycoprotein VP7
H: Outer capsid glycoprotein VP7
I: Outer capsid glycoprotein VP7
J: Outer capsid glycoprotein VP7
K: Outer capsid glycoprotein VP7
L: Outer capsid glycoprotein VP7
M: Outer capsid glycoprotein VP7
N: Outer capsid glycoprotein VP7
O: Outer capsid glycoprotein VP7
P: Outer capsid glycoprotein VP7
Q: Outer capsid glycoprotein VP7
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 2.28 MDa, 78 polymers
Theoretical massNumber of molelcules
Total (without water)2,282,072336
Polymers2,241,75578
Non-polymers40,317258
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
Outer capsid glycoprotein VP7


Mass: 28740.451 Da / Num. of mol.: 13 / Fragment: VP7 (UNP residues 58 to 312) / Source method: isolated from a natural source / Source: (natural) Rhesus rotavirus / Strain: UK / References: UniProt: P12476
#2: 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.: 13
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
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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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 from a VP7 recoated rotavirus DLP / Type: VIRUS / Details: capsid protein VP7. VP6 and VP2
Details of virusHost category: VERTEBRATES / Type: VIRION
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 FIELD / 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
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching and refinement using FREALIGN / Resolution: 3.8 Å / Num. of particles: 3780 / Nominal pixel size: 1.233 Å / Actual pixel size: 1.233 Å / Magnification calibration: 58168 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms26143 0 394 0 26537

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