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- PDB-4v7q: Atomic model of an infectious rotavirus particle -

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Basic information

Entry
Database: PDB / ID: 4v7q
TitleAtomic model of an infectious rotavirus particle
Components
  • Core scaffold protein
  • Intermediate capsid protein VP6
  • Outer capsid protein VP4
  • Outer layer protein VP7
KeywordsVIRUS / Rotavirus / Triple Layered Particle / Near Atomic Resolution / VP2 / VP6 / VP4 / VP7 / Double layered particle / de novo / Infectious / DLP / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


viral intermediate capsid / host cell endoplasmic reticulum lumen / host cell rough endoplasmic reticulum / T=13 icosahedral viral capsid / permeabilization of host organelle membrane involved in viral entry into host cell / T=2 icosahedral viral capsid / viral inner capsid / host cytoskeleton / viral outer capsid / viral nucleocapsid ...viral intermediate capsid / host cell endoplasmic reticulum lumen / host cell rough endoplasmic reticulum / T=13 icosahedral viral capsid / permeabilization of host organelle membrane involved in viral entry into host cell / T=2 icosahedral viral capsid / viral inner capsid / host cytoskeleton / viral outer capsid / viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / RNA binding / metal ion binding / membrane
Similarity search - Function
Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Rotavirus VP4 helical domain ...Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Viral capsid/haemagglutinin protein / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Intermediate capsid protein VP6 / Inner capsid protein VP2 / Outer capsid protein VP4 / Outer capsid glycoprotein VP7 / Outer capsid glycoprotein VP7
Similarity search - Component
Biological speciesSimian rotavirus A
Rhesus rotavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSettembre, E.C. / Chen, J.Z. / Dormitzer, P.R. / Grigorieff, N. / Harrison, S.C.
CitationJournal: EMBO J / Year: 2011
Title: Atomic model of an infectious rotavirus particle.
Authors: Ethan C Settembre / James Z Chen / Philip R Dormitzer / Nikolaus Grigorieff / Stephen C Harrison /
Abstract: Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling ...Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling enveloped-virus fusion: membrane distortion linked to conformational changes in a viral protein. Evidence for such a mechanism comes from crystallographic analyses of fragments of VP4, the rotavirus-penetration protein, and infectivity analyses of structure-based VP4 mutants. We describe here the structure of an infectious rotavirus particle determined by electron cryomicroscopy (cryoEM) and single-particle analysis at about 4.3 Å resolution. The cryoEM image reconstruction permits a nearly complete trace of the VP4 polypeptide chain, including the positions of most side chains. It shows how the two subfragments of VP4 (VP8(*) and VP5(*)) retain their association after proteolytic cleavage, reveals multiple structural roles for the β-barrel domain of VP5(*), and specifies interactions of VP4 with other capsid proteins. The virion model allows us to integrate structural and functional information into a coherent mechanism for rotavirus entry.
History
DepositionMay 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3IYU, 3N09
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jan 24, 2018Group: Data collection / Structure summary / Category: audit_author / em_image_scans / Item: _audit_author.name
Revision 1.3Dec 18, 2019Group: Database references / Derived calculations / Other / Category: atom_sites / struct_conn / struct_ref_seq_dif
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] / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 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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Structure viewerMolecule:
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Assembly

Deposited unit
AA: Core scaffold protein
AB: Core scaffold protein
AC: Intermediate capsid protein VP6
AD: Intermediate capsid protein VP6
AE: Intermediate capsid protein VP6
AF: Intermediate capsid protein VP6
AG: Intermediate capsid protein VP6
AH: Intermediate capsid protein VP6
AI: Intermediate capsid protein VP6
AJ: Intermediate capsid protein VP6
AK: Intermediate capsid protein VP6
AL: Intermediate capsid protein VP6
AM: Intermediate capsid protein VP6
AN: Intermediate capsid protein VP6
AO: Intermediate capsid protein VP6
BA: Outer layer protein VP7
BF: Outer layer protein VP7
BG: Outer layer protein VP7
BH: Outer layer protein VP7
BI: Outer layer protein VP7
BJ: Outer layer protein VP7
BK: Outer layer protein VP7
BL: Outer layer protein VP7
BM: Outer layer protein VP7
BN: Outer layer protein VP7
BO: Outer layer protein VP7
BP: Outer layer protein VP7
BQ: Outer layer protein VP7
BX: Outer capsid protein VP4
BY: Outer capsid protein VP4
BZ: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,440,03844
Polymers1,436,51931
Non-polymers3,51913
Water00
1
AA: Core scaffold protein
AB: Core scaffold protein
AC: Intermediate capsid protein VP6
AD: Intermediate capsid protein VP6
AE: Intermediate capsid protein VP6
AF: Intermediate capsid protein VP6
AG: Intermediate capsid protein VP6
AH: Intermediate capsid protein VP6
AI: Intermediate capsid protein VP6
AJ: Intermediate capsid protein VP6
AK: Intermediate capsid protein VP6
AL: Intermediate capsid protein VP6
AM: Intermediate capsid protein VP6
AN: Intermediate capsid protein VP6
AO: Intermediate capsid protein VP6
BA: Outer layer protein VP7
BF: Outer layer protein VP7
BG: Outer layer protein VP7
BH: Outer layer protein VP7
BI: Outer layer protein VP7
BJ: Outer layer protein VP7
BK: Outer layer protein VP7
BL: Outer layer protein VP7
BM: Outer layer protein VP7
BN: Outer layer protein VP7
BO: Outer layer protein VP7
BP: Outer layer protein VP7
BQ: Outer layer protein VP7
BX: Outer capsid protein VP4
BY: Outer capsid protein VP4
BZ: Outer capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)86,402,2782640
Polymers86,191,1351860
Non-polymers211,144780
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 4 types, 31 molecules AAABACADAEAFAGAHAIAJAKALAMANAOBABFBGBHBIBJBKBLBMBNBOBPBQBXBYBZ

#1: Protein Core scaffold protein / Core shell protein VP2


Mass: 93190.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A / Strain: RRV / Gene: Rotavirus / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: B3F2X3
#2: Protein
Intermediate capsid protein VP6


Mass: 44934.766 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhesus rotavirus / Strain: RRV / Gene: Rotavirus / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: B2BN53
#3: Protein
Outer layer protein VP7


Mass: 31232.234 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A / Strain: RRV / Cell (production host): KIDNEY CELLS / Organ (production host): KIDNEY / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: C3RX25, UniProt: P12476*PLUS
#4: Protein Outer capsid protein VP4


Mass: 86655.586 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A / Strain: RRV / Cell (production host): KIDNEY CELLS / Organ (production host): KIDNEY / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: C3RX20

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Sugars , 2 types, 8 molecules

#5: 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.: 7 / Source method: obtained synthetically
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
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 5 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


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

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Details

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

Component
IDNameTypeDetailsParent-ID
1Rotavirus Triple Layered ParticleVIRUSThe sample was monodisperse0
2Rhesus Rotavirus (RRV) TLP1
Details of virusHost category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Macaca mulatta / Strain: Monkey Kidney Cells
Buffer solutionName: 20 mM Tris / pH: 7.5 / Details: 20 mM Tris
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: in normal coldroom environment, ETHANE, manual plunger, front blotting for 3s before plunging, temperature 90 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Mar 1, 2008
Details: Cut-plate film holders to reduce electron back-scattering
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 56772 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderTemperature: 90 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

CTF correctionDetails: individual particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching / Resolution: 3.8 Å / Num. of particles: 4187 / Details: icosahedral (I2) averaging / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms54043 0 5 0 54048

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