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- PDB-4an5: Capsid structure and its Stability at the Late Stages of Bacterio... -

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Basic information

Entry
Database: PDB / ID: 4an5
TitleCapsid structure and its Stability at the Late Stages of Bacteriophage SPP1 Assembly
ComponentsCOAT PROTEIN
KeywordsVIRUS / BACTERIOPHAGE CAPSID SPP1
Function / homologyMajor capsid protein 13-like / Major capsid protein 13-like / T=7 icosahedral viral capsid / viral capsid / Major capsid protein
Function and homology information
Biological speciesBACILLUS PHAGE SPP1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.8 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G
AuthorsWhite, H.E. / Sherman, M.B. / Brasiles, S. / Jacquet, E. / Seavers, P. / Tavares, P. / Orlova, E.V.
CitationJournal: J Virol / Year: 2012
Title: Capsid structure and its stability at the late stages of bacteriophage SPP1 assembly.
Authors: Helen E White / Michael B Sherman / Sandrine Brasilès / Eric Jacquet / Philippa Seavers / Paulo Tavares / Elena V Orlova /
Abstract: The structure of the bacteriophage SPP1 capsid was determined at subnanometer resolution by cryo-electron microscopy and single-particle analysis. The icosahedral capsid is composed of the major ...The structure of the bacteriophage SPP1 capsid was determined at subnanometer resolution by cryo-electron microscopy and single-particle analysis. The icosahedral capsid is composed of the major capsid protein gp13 and the auxiliary protein gp12, which are organized in a T=7 lattice. DNA is arranged in layers with a distance of ~24.5 Å. gp12 forms spikes that are anchored at the center of gp13 hexamers. In a gp12-deficient mutant, the centers of hexamers are closed by loops of gp13 coming together to protect the SPP1 genome from the outside environment. The HK97-like fold was used to build a pseudoatomic model of gp13. Its structural organization remains unchanged upon tail binding and following DNA release. gp13 exhibits enhanced thermostability in the DNA-filled capsid. A remarkable convergence between the thermostability of the capsid and those of the other virion components was found, revealing that the overall architecture of the SPP1 infectious particle coevolved toward high robustness.
History
DepositionMar 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3May 8, 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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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-2049
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)247,7277
Polymers247,7277
Non-polymers00
Water00
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)14,863,641420
Polymers14,863,641420
Non-polymers00
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
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN
x 5


  • icosahedral pentamer
  • 1.24 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,238,63735
Polymers1,238,63735
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN
x 6


  • icosahedral 23 hexamer
  • 1.49 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,486,36442
Polymers1,486,36442
Non-polymers00
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))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30902, -0.80902, 0.5), (0.80902, 0.5, 0.30902), (-0.5, 0.30902, 0.80902)
3generate(-0.80902, -0.5, 0.30902), (0.5, -0.30902, 0.80902), (-0.30902, 0.80902, 0.5)
4generate(-0.80902, 0.5, -0.30902), (-0.5, -0.30902, 0.80902), (0.30902, 0.80902, 0.5)
5generate(0.30902, 0.80902, -0.5), (-0.80902, 0.5, 0.30902), (0.5, 0.30902, 0.80902)
6generate(-1), (-1), (1)
7generate(-0.30902, -0.80902, 0.5), (0.80902, -0.5, -0.30902), (0.5, 0.30902, 0.80902)
8generate(0.30902, 0.80902, 0.5), (-0.80902, 0.5, -0.30902), (-0.5, -0.30902, 0.80902)
9generate(-0.30902, 0.80902, 0.5), (-0.80902, -0.5, 0.30902), (0.5, -0.30902, 0.80902)
10generate(-0.5, 0.30902, 0.80902), (0.30902, -0.80902, 0.5), (0.80902, 0.5, 0.30902)
11generate(0.5, -0.30902, 0.80902), (-0.30902, 0.80902, 0.5), (-0.80902, -0.5, 0.30902)
12generate(0.80902, 0.5, 0.30902), (-0.5, 0.30902, 0.80902), (0.30902, -0.80902, 0.5)
13generate(0.80902, -0.5, -0.30902), (0.5, 0.30902, 0.80902), (-0.30902, -0.80902, 0.5)
14generate(0.5, 0.30902, -0.80902), (0.30902, 0.80902, 0.5), (0.80902, -0.5, 0.30902)
15generate(-0.5, -0.30902, -0.80902), (-0.30902, -0.80902, 0.5), (-0.80902, 0.5, 0.30902)
16generate(-0.30902, -0.80902, -0.5), (0.80902, -0.5, 0.30902), (-0.5, -0.30902, 0.80902)
17generate(0.30902, -0.80902, -0.5), (0.80902, 0.5, -0.30902), (0.5, -0.30902, 0.80902)
18generate(-0.30902, 0.80902, -0.5), (-0.80902, -0.5, -0.30902), (-0.5, 0.30902, 0.80902)
19generate(0.5, -0.30902, -0.80902), (-0.30902, 0.80902, -0.5), (0.80902, 0.5, 0.30902)
20generate(-0.5, 0.30902, -0.80902), (0.30902, -0.80902, -0.5), (-0.80902, -0.5, 0.30902)
21generate(-0.80902, -0.5, -0.30902), (0.5, -0.30902, -0.80902), (0.30902, -0.80902, 0.5)
22generate(0.80902, 0.5, -0.30902), (-0.5, 0.30902, -0.80902), (-0.30902, 0.80902, 0.5)
23generate(0.80902, -0.5, 0.30902), (0.5, 0.30902, -0.80902), (0.30902, 0.80902, 0.5)
24generate(-0.80902, 0.5, 0.30902), (-0.5, -0.30902, -0.80902), (-0.30902, -0.80902, 0.5)
25generate(-0.5, -0.30902, 0.80902), (-0.30902, -0.80902, -0.5), (0.80902, -0.5, 0.30902)
26generate(0.5, 0.30902, 0.80902), (0.30902, 0.80902, -0.5), (-0.80902, 0.5, 0.30902)
27generate(1), (1), (1)
28generate(1), (1), (1)
29generate(-1), (1), (-1)
30generate(-1), (-1), (1)
31generate(-1), (-1), (1)
32generate(1), (-1), (-1)
33generate(-0.80902, -0.5, 0.30902), (-0.5, 0.30902, -0.80902), (0.30902, -0.80902, -0.5)
34generate(0.80902, -0.5, -0.30902), (-0.5, -0.30902, -0.80902), (0.30902, 0.80902, -0.5)
35generate(0.5, 0.30902, -0.80902), (-0.30902, -0.80902, -0.5), (-0.80902, 0.5, -0.30902)
36generate(-0.30902, -0.80902, -0.5), (-0.80902, 0.5, -0.30902), (0.5, 0.30902, -0.80902)
37generate(-0.80902, 0.5, -0.30902), (0.5, 0.30902, -0.80902), (-0.30902, -0.80902, -0.5)
38generate(-0.5, -0.30902, -0.80902), (0.30902, 0.80902, -0.5), (0.80902, -0.5, -0.30902)
39generate(-0.5, 0.30902, -0.80902), (-0.30902, 0.80902, 0.5), (0.80902, 0.5, -0.30902)
40generate(-1), (1), (-1)
41generate(-0.80902, 0.5, 0.30902), (0.5, 0.30902, 0.80902), (0.30902, 0.80902, -0.5)
42generate(0.80902, 0.5, -0.30902), (0.5, -0.30902, 0.80902), (0.30902, -0.80902, -0.5)
43generate(-0.30902, 0.80902, -0.5), (0.80902, 0.5, 0.30902), (0.5, -0.30902, -0.80902)
44generate(0.5, -0.30902, -0.80902), (0.30902, -0.80902, 0.5), (-0.80902, -0.5, -0.30902)
45generate(-0.80902, -0.5, -0.30902), (-0.5, 0.30902, 0.80902), (-0.30902, 0.80902, -0.5)
46generate(-0.30902, -0.80902, 0.5), (-0.80902, 0.5, 0.30902), (-0.5, -0.30902, -0.80902)
47generate(-0.30902, 0.80902, 0.5), (0.80902, 0.5, -0.30902), (-0.5, 0.30902, -0.80902)
48generate(1), (-1), (-1)
49generate(0.30902, 0.80902, -0.5), (0.80902, -0.5, -0.30902), (-0.5, -0.30902, -0.80902)
50generate(0.30902, -0.80902, -0.5), (-0.80902, -0.5, 0.30902), (-0.5, 0.30902, -0.80902)
51generate(-1), (1), (-1)
52generate(0.80902, 0.5, 0.30902), (0.5, -0.30902, -0.80902), (-0.30902, 0.80902, -0.5)
53generate(0.30902, -0.80902, 0.5), (-0.80902, -0.5, -0.30902), (0.5, -0.30902, -0.80902)
54generate(-0.5, 0.30902, 0.80902), (-0.30902, 0.80902, -0.5), (-0.80902, -0.5, -0.30902)
55generate(1), (-1), (-1)
56generate(0.5, -0.30902, 0.80902), (0.30902, -0.80902, -0.5), (0.80902, 0.5, -0.30902)
57generate(0.30902, 0.80902, 0.5), (0.80902, -0.5, 0.30902), (0.5, 0.30902, -0.80902)
58generate(0.80902, -0.5, 0.30902), (-0.5, -0.30902, 0.80902), (-0.30902, -0.80902, -0.5)
59generate(-0.5, -0.30902, 0.80902), (0.30902, 0.80902, 0.5), (-0.80902, 0.5, -0.30902)
60generate(0.5, 0.30902, 0.80902), (-0.30902, -0.80902, 0.5), (0.80902, -0.5, -0.30902)

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Components

#1: Protein
COAT PROTEIN / Coordinate model: Cα atoms only


Mass: 35389.621 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS PHAGE SPP1 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q38582

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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: CAPSID OF SPP1 / Type: VIRUS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT MARK I,

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Electron microscopy imaging

MicroscopyModel: JEOL 2200FS / Date: Apr 6, 2005 / Details: LOW-DOSE IMAGING PROCEDURE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 94
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Flex-EMmodel fitting
2IMAGIC3D reconstruction
CTF correctionDetails: PHASE FLIPPING
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: ANGULAR RECONSTITUTION / Resolution: 8.8 Å / Num. of particles: 5000 / Nominal pixel size: 1.49 Å / Actual pixel size: 1.49 Å
Details: ANGULAR RECONSTITUTION. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2049. (DEPOSITION ID: 10649).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: METHOD--EACH HELIX AND EVERY BETA SHEET WERE TREATED AS RIGID BODIES.
Atomic model building

3D fitting-ID: 1 / Details: HOMOLOGY MODEL BASED ON 1OHG, 1YUE / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-ID
11OHG

1ohg

1OHG1
21YUE

1yue

1YUE2
RefinementHighest resolution: 8.8 Å
Refinement stepCycle: LAST / Highest resolution: 8.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 0 0 1631

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