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- PDB-4bml: C-alpha backbone trace of major capsid protein gp39 found in mari... -

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Entry
Database: PDB / ID: 4bml
TitleC-alpha backbone trace of major capsid protein gp39 found in marine virus Syn5.
ComponentsMAJOR CAPSID PROTEIN
KeywordsVIRUS / MARINE VIRUS / OUTER CAPSID PROTEIN / MATURATION
Function / homologyMajor capsid protein
Function and homology information
Specimen sourceSYNECHOCOCCUS PHAGE SYN5 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.7 Å resolution
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G
AuthorsGipson, P. / Baker, M.L. / Raytcheva, D. / Haase-Pettingell, C. / Piret, J. / King, J. / Chiu, W.
CitationJournal: Nat Commun / Year: 2014
Title: Protruding knob-like proteins violate local symmetries in an icosahedral marine virus.
Authors: Preeti Gipson / Matthew L Baker / Desislava Raytcheva / Cameron Haase-Pettingell / Jacqueline Piret / Jonathan A King / Wah Chiu
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 9, 2013 / Release: May 21, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 21, 2014Structure modelrepositoryInitial release
1.1May 28, 2014Structure modelOther
1.2Jul 16, 2014Structure modelDatabase references
1.3Aug 30, 2017Structure modelData collectionem_imaging_em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min
1.4Oct 3, 2018Structure modelData collectiondiffrn_radiation / diffrn_radiation_wavelength / em_software_em_software.image_processing_id

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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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: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)245,7427
Polyers245,7427
Non-polymers00
Water0
1
A: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)14,744,512420
Polyers14,744,512420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
x 5


  • icosahedral pentamer
  • 1.23 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,228,70935
Polyers1,228,70935
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
x 6


  • icosahedral 23 hexamer
  • 1.47 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,474,45142
Polyers1,474,45142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide
MAJOR CAPSID PROTEIN / SYN5 / Coordinate model: Cα atoms only


Mass: 35105.980 Da / Num. of mol.: 7 / Source: (natural) SYNECHOCOCCUS PHAGE SYN5 (bacteriophage) / References: UniProt: A4ZRC0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SYNECHOCOCCUS PHAGE SYN5 / Type: VIRUS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FSC / Date: Oct 10, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 80000 / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm / Cs: 4.1 mm
Image recordingElectron dose: 23 e/Å2 / Film or detector model: GATAN ULTRASCAN 10000 (10k x 10k)
Image scansNumber digital images: 1000

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Processing

EM softwareName: MPSA / Category: 3D reconstruction
CTF correctionDetails: INDIVIDUAL MICROGRAPHS
SymmetryPoint symmetry: I
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 5.7 Å / Number of particles: 9700 / Actual pixel size: 1.32
Details: 1-23 RESIDUES AT THE N-TERMINUS OF EACH CHAIN ARE NOT MODELED.
Symmetry type: POINT
Least-squares processHighest resolution: 4.7 Å
Refine hist #LASTHighest resolution: 4.7 Å
Number of atoms included #LASTProtein: 2163 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2163

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