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- PDB-1m4x: PBCV-1 virus capsid, quasi-atomic model -

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Basic information

Entry
Database: PDB / ID: 1m4x
TitlePBCV-1 virus capsid, quasi-atomic model
ComponentsPBCV-1 virus capsid
KeywordsVIRUS / icosahedral virus capsid / beta barrel / Icosahedral virus
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
: / Major capsid protein
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 28 Å
AuthorsNandhagopal, N. / Simpson, A.A. / Gurnon, J.R. / Yan, X. / Baker, T.S. / Graves, M.V. / Van Etten, J.L. / Rossmann, M.G.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2002
Title: The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus.
Authors: Narayanasamy Nandhagopal / Alan A Simpson / James R Gurnon / Xiadong Yan / Timothy S Baker / Michael V Graves / James L Van Etten / Michael G Rossmann /
Abstract: Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of ...Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-A resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified. The N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded, antiparallel beta-barrel, "jelly-roll" domains related by a pseudo-sixfold rotation. The fold of the monomer and the pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses, as well as the viral proteins VP2-VP3 of picornaviruses. The structural similarities among these diverse groups of viruses, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. The trimeric capsid protein structure was used to produce a quasi-atomic model of the 1,900-A diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus.
History
DepositionJul 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Other / Category: atom_sites / cell / 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] / _cell.Z_PDB / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.length_a / _cell.length_b / _cell.length_c / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 2019Group: Data collection / Other / Category: symmetry
Item: _symmetry.Int_Tables_number / _symmetry.space_group_name_H-M
Revision 1.6Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • 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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  • Biological unit as pentasymmetron capsid unit
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  • Biological unit as trisymmetron capsid unit
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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: PBCV-1 virus capsid
B: PBCV-1 virus capsid
C: PBCV-1 virus capsid


Theoretical massNumber of molelcules
Total (without water)137,2053
Polymers137,2053
Non-polymers00
Water0
1
A: PBCV-1 virus capsid
B: PBCV-1 virus capsid
C: PBCV-1 virus capsid
x 1680


Theoretical massNumber of molelcules
Total (without water)230,503,8515040
Polymers230,503,8515040
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
build point asymmetric unit27
2
A: PBCV-1 virus capsid
B: PBCV-1 virus capsid
C: PBCV-1 virus capsid
x 28


  • icosahedral asymmetric unit
  • 3.84 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)3,841,73184
Polymers3,841,73184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
build point asymmetric unit27
3
A: PBCV-1 virus capsid
B: PBCV-1 virus capsid
C: PBCV-1 virus capsid
x 140


  • icosahedral pentamer
  • 19.2 MDa, 420 polymers
Theoretical massNumber of molelcules
Total (without water)19,208,654420
Polymers19,208,654420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
build point asymmetric unit27
4
A: PBCV-1 virus capsid
B: PBCV-1 virus capsid
C: PBCV-1 virus capsid
x 168


  • icosahedral 23 hexamer
  • 23.1 MDa, 504 polymers
Theoretical massNumber of molelcules
Total (without water)23,050,385504
Polymers23,050,385504
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation5
build point asymmetric unit27
5
A: PBCV-1 virus capsid
B: PBCV-1 virus capsid
C: PBCV-1 virus capsid
x 30


  • pentasymmetron capsid unit
  • 4.12 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)4,116,14090
Polymers4,116,14090
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
build point asymmetric unit6
6
A: PBCV-1 virus capsid
B: PBCV-1 virus capsid
C: PBCV-1 virus capsid
x 66


  • trisymmetron capsid unit
  • 9.06 MDa, 198 polymers
Theoretical massNumber of molelcules
Total (without water)9,055,508198
Polymers9,055,508198
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation2
build point asymmetric unit21
7
A: PBCV-1 virus capsid
B: PBCV-1 virus capsid
C: PBCV-1 virus capsid
x 28


  • icosahedral asymmetric unit, std point frame
  • 3.84 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)3,841,73184
Polymers3,841,73184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to point frame1
identity operation1_555x,y,z1
build point asymmetric unit27
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein PBCV-1 virus capsid


Mass: 45734.891 Da / Num. of mol.: 3 / Fragment: virus capsid / Source method: isolated from a natural source
Details: Virus infects chlorella algae, which are symbionts with Paramecium bursaria
Source: (natural) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / References: GenBank: 323324, UniProt: P30328*PLUS

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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: PBCV-1 virus capsid / Type: VIRUS / Details: T=169d quasi-symmetric icosahedron.
Details of virusHost category: ALGAE / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: electron microscopy grid - in vitrious ice
VitrificationDetails: frozen in liquid propane
Crystal grow
*PLUS
Method: cryo electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG/ST
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1Situsmodel fitting
2OTHER3D reconstruction
CTF correctionDetails: inverse of CTF was applied to images
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: polar fourier transform. / Resolution: 28 Å / Details: used Tim Baker's programs PFT, EM3DR, etc. / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: rigid body refinement in real space against Lagrangian filtered EM density, using the program SITUS.Each molecule in the icosahedral ASU was refined separately.
Details: METHOD--6d search, separately for each symmetry related molecule in the icosahedral ASU. REFINEMENT PROTOCOL--rigid body
Atomic model building

3D fitting-ID: 1 / Details: 1J5Q or 1M3Y (not exactly as found in pdb entry) / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-ID
11J5Q

1j5q
PDB Unreleased entry

1J5Q1
21M3Y

1m3y
PDB Unreleased entry

1M3Y2
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms9693 0 0 0 9693

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