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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
Biological speciesSYNECHOCOCCUS PHAGE SYN5 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
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 /
Abstract: Marine viruses play crucial roles in shaping the dynamics of oceanic microbial communities and in the carbon cycle on Earth. Here we report a 4.7-Å structure of a cyanobacterial virus, Syn5, by ...Marine viruses play crucial roles in shaping the dynamics of oceanic microbial communities and in the carbon cycle on Earth. Here we report a 4.7-Å structure of a cyanobacterial virus, Syn5, by electron cryo-microscopy and modelling. A Cα backbone trace of the major capsid protein (gp39) reveals a classic phage protein fold. In addition, two knob-like proteins protruding from the capsid surface are also observed. Using bioinformatics and structure analysis tools, these proteins are identified to correspond to gp55 and gp58 (each with two copies per asymmetric unit). The non 1:1 stoichiometric distribution of gp55/58 to gp39 breaks all expected local symmetries and leads to non-quasi-equivalence of the capsid subunits, suggesting a role in capsid stabilization. Such a structural arrangement has not yet been observed in any known virus structures.
History
DepositionMay 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Other
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_imaging
Item: _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min
Revision 1.4Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id
Revision 1.5Dec 23, 2020Group: Data processing / Category: em_3d_reconstruction / Item: _em_3d_reconstruction.resolution

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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
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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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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
Polymers245,7427
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
Polymers14,744,512420
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
Polymers1,228,70935
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
Polymers1,474,45142
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.309017, -0.951057), (0.951057, 0.309017), (1)
3generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)
4generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)
5generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)
6generate(0.361803, 0.262865, 0.894428), (-0.587785, 0.809017), (-0.723607, -0.525731, 0.447213)
7generate(0.361803, -0.262865, 0.894428), (0.587785, 0.809017), (-0.723607, 0.525731, 0.447213)
8generate(-0.138196, -0.425325, 0.894428), (0.951057, -0.309017), (0.276393, 0.850651, 0.447213)
9generate(-0.447213, 0.894428), (-1), (0.894428, 0.447213)
10generate(-0.138196, 0.425325, 0.894428), (-0.951057, -0.309017), (0.276393, -0.850651, 0.447213)
11generate(-0.447214, 0.850651, 0.276393), (-0.52573, -0.850651), (-0.723607, -0.525731, 0.447213)
12generate(0.67082, 0.688191, 0.276393), (-0.162459, 0.5, -0.850651), (-0.723607, 0.525731, 0.447213)
13generate(0.861803, -0.425325, 0.276393), (0.425325, 0.309016, -0.850651), (0.276393, 0.850651, 0.447213)
14generate(-0.138196, -0.951057, 0.276393), (0.425325, -0.309017, -0.850651), (0.894428, 0.447213)
15generate(-0.947214, -0.16246, 0.276393), (-0.16246, -0.499999, -0.850651), (0.276393, -0.850651, 0.447213)
16generate(-0.638196, 0.262866, -0.723607), (0.262866, -0.809017, -0.525731), (-0.723607, -0.525731, 0.447213)
17generate(0.052787, 0.688191, -0.723607), (-0.688191, -0.5, -0.525731), (-0.723607, 0.525731, 0.447213)
18generate(0.67082, 0.162459, -0.723607), (-0.688191, 0.5, -0.525731), (0.276393, 0.850651, 0.447213)
19generate(0.361803, -0.587785, -0.723607), (0.262865, 0.809017, -0.525731), (0.894428, 0.447213)
20generate(-0.447214, -0.52573, -0.723607), (0.850651, -0.525731), (0.276393, -0.850651, 0.447213)
21generate(0.052787, -0.688191, -0.723607), (0.688191, -0.5, 0.525731), (-0.723607, -0.525731, 0.447213)
22generate(-0.638196, -0.262866, -0.723607), (-0.262866, -0.809017, 0.525731), (-0.723607, 0.525731, 0.447213)
23generate(-0.447214, 0.52573, -0.723607), (-0.850651, 0.525731), (0.276393, 0.850651, 0.447213)
24generate(0.361803, 0.587785, -0.723607), (-0.262865, 0.809017, 0.525731), (0.894428, 0.447213)
25generate(0.67082, -0.162459, -0.723607), (0.688191, 0.5, 0.525731), (0.276393, -0.850651, 0.447213)
26generate(0.67082, -0.688191, 0.276393), (0.162459, 0.5, 0.850651), (-0.723607, -0.525731, 0.447213)
27generate(-0.447214, -0.850651, 0.276393), (0.52573, 0.850651), (-0.723607, 0.525731, 0.447213)
28generate(-0.947214, 0.16246, 0.276393), (0.16246, -0.499999, 0.850651), (0.276393, 0.850651, 0.447213)
29generate(-0.138196, 0.951057, 0.276393), (-0.425325, -0.309017, 0.850651), (0.894428, 0.447213)
30generate(0.861803, 0.425325, 0.276393), (-0.425325, 0.309016, 0.850651), (0.276393, -0.850651, 0.447213)
31generate(-0.361803, 0.587785, 0.723607), (0.262865, 0.809017, -0.525731), (-0.894428, -0.447213)
32generate(0.447214, 0.52573, 0.723607), (0.850651, -0.525731), (-0.276393, 0.850651, -0.447213)
33generate(0.638196, -0.262866, 0.723607), (0.262866, -0.809017, -0.525731), (0.723607, 0.525731, -0.447213)
34generate(-0.052787, -0.688191, 0.723607), (-0.688191, -0.5, -0.525731), (0.723607, -0.525731, -0.447213)
35generate(-0.67082, -0.162459, 0.723607), (-0.688191, 0.5, -0.525731), (-0.276393, -0.850651, -0.447213)
36generate(0.138196, 0.951057, -0.276393), (0.425325, -0.309017, -0.850651), (-0.894428, -0.447213)
37generate(0.947214, 0.16246, -0.276393), (-0.16246, -0.499999, -0.850651), (-0.276393, 0.850651, -0.447213)
38generate(0.447214, -0.850651, -0.276393), (-0.52573, -0.850651), (0.723607, 0.525731, -0.447213)
39generate(-0.67082, -0.688191, -0.276393), (-0.162459, 0.5, -0.850651), (0.723607, -0.525731, -0.447213)
40generate(-0.861803, 0.425325, -0.276393), (0.425325, 0.309016, -0.850651), (-0.276393, -0.850651, -0.447213)
41generate(0.447213, -0.894428), (-1), (-0.894428, -0.447213)
42generate(0.138196, -0.425325, -0.894428), (-0.951057, -0.309017), (-0.276393, 0.850651, -0.447213)
43generate(-0.361803, -0.262865, -0.894428), (-0.587785, 0.809017), (0.723607, 0.525731, -0.447213)
44generate(-0.361803, 0.262865, -0.894428), (0.587785, 0.809017), (0.723607, -0.525731, -0.447213)
45generate(0.138196, 0.425325, -0.894428), (0.951057, -0.309017), (-0.276393, -0.850651, -0.447213)
46generate(0.138196, -0.951057, -0.276393), (-0.425325, -0.309017, 0.850651), (-0.894428, -0.447213)
47generate(-0.861803, -0.425325, -0.276393), (-0.425325, 0.309016, 0.850651), (-0.276393, 0.850651, -0.447213)
48generate(-0.67082, 0.688191, -0.276393), (0.162459, 0.5, 0.850651), (0.723607, 0.525731, -0.447213)
49generate(0.447214, 0.850651, -0.276393), (0.52573, 0.850651), (0.723607, -0.525731, -0.447213)
50generate(0.947214, -0.16246, -0.276393), (0.16246, -0.499999, 0.850651), (-0.276393, -0.850651, -0.447213)
51generate(-0.361803, -0.587785, 0.723607), (-0.262865, 0.809017, 0.525731), (-0.894428, -0.447213)
52generate(-0.67082, 0.162459, 0.723607), (0.688191, 0.5, 0.525731), (-0.276393, 0.850651, -0.447213)
53generate(-0.052787, 0.688191, 0.723607), (0.688191, -0.5, 0.525731), (0.723607, 0.525731, -0.447213)
54generate(0.638196, 0.262866, 0.723607), (-0.262866, -0.809017, 0.525731), (0.723607, -0.525731, -0.447213)
55generate(0.447214, -0.52573, 0.723607), (-0.850651, 0.525731), (-0.276393, -0.850651, -0.447213)
56generate(-1), (1), (-1)
57generate(-0.309017, 0.951057), (0.951057, 0.309017), (-1)
58generate(0.809017, 0.587785), (0.587785, -0.809017), (-1)
59generate(0.809017, -0.587785), (-0.587785, -0.809017), (-1)
60generate(-0.309017, -0.951057), (-0.951057, 0.309017), (-1)

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Components

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


Mass: 35105.980 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) SYNECHOCOCCUS PHAGE SYN5 (virus) / References: UniProt: A4ZRC0

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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: 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

MicroscopyModel: 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 X / 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 scansNum. digital images: 1000

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Processing

EM softwareName: MPSA / Category: 3D reconstruction
CTF correctionDetails: INDIVIDUAL MICROGRAPHS
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 4.7 Å / Num. of particles: 9700 / Actual pixel size: 1.32 Å
Details: 1-23 RESIDUES AT THE N-TERMINUS OF EACH CHAIN ARE NOT MODELED.
Symmetry type: POINT
RefinementHighest resolution: 4.7 Å
Refinement stepCycle: LAST / Highest resolution: 4.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 0 0 2163

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