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- PDB-8eld: Bacteriophage HRP29 Icosohedral Reconstruction -

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Basic information

Entry
Database: PDB / ID: 8eld
TitleBacteriophage HRP29 Icosohedral Reconstruction
Components
  • Gp37
  • Gp47
  • Gp48
KeywordsVIRUS / HRP29
Function / homologyUncharacterized protein / Putative capsid protein / Uncharacterized protein
Function and homology information
Biological speciesShigella phage Buco (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSubramanian, S. / Bergland Drarvik, S.M. / Parent, K.N.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
National Science Foundation (NSF, United States)1750125 United States
CitationJournal: To Be Published
Title: Structure of Shigella bacteriophage HRP29
Authors: Subramanian, S. / Bergland Drarvik, S.M. / Parent, K.N.
History
DepositionSep 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gp37
B: Gp37
C: Gp37
D: Gp37
E: Gp37
F: Gp37
G: Gp37
M: Gp47
L: Gp47
H: Gp48
I: Gp48
J: Gp48
K: Gp48


Theoretical massNumber of molelcules
Total (without water)310,12013
Polymers310,12013
Non-polymers00
Water00
1
A: Gp37
B: Gp37
C: Gp37
D: Gp37
E: Gp37
F: Gp37
G: Gp37
M: Gp47
L: Gp47
H: Gp48
I: Gp48
J: Gp48
K: Gp48
x 60


Theoretical massNumber of molelcules
Total (without water)18,607,208780
Polymers18,607,208780
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: Gp37
B: Gp37
C: Gp37
D: Gp37
E: Gp37
F: Gp37
G: Gp37
M: Gp47
L: Gp47
H: Gp48
I: Gp48
J: Gp48
K: Gp48
x 5


  • icosahedral pentamer
  • 1.55 MDa, 65 polymers
Theoretical massNumber of molelcules
Total (without water)1,550,60165
Polymers1,550,60165
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Gp37
B: Gp37
C: Gp37
D: Gp37
E: Gp37
F: Gp37
G: Gp37
M: Gp47
L: Gp47
H: Gp48
I: Gp48
J: Gp48
K: Gp48
x 6


  • icosahedral 23 hexamer
  • 1.86 MDa, 78 polymers
Theoretical massNumber of molelcules
Total (without water)1,860,72178
Polymers1,860,72178
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))

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Components

#1: Protein
Gp37


Mass: 36911.305 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Shigella phage Buco (virus) / References: UniProt: A0A482JKU4
#2: Protein Gp47


Mass: 13021.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Shigella phage Buco (virus) / References: UniProt: A0A482JKV2
#3: Protein
Gp48


Mass: 6424.381 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Shigella phage Buco (virus) / References: UniProt: A0A482JG80

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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: Shigella phage HRP29 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Shigella phage Buco (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Shigella flexneri Y
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMtris(hydroxymethyl)aminomethane1
210 mMmagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 33 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFINDCTF correction
10RELION3.1.1initial Euler assignment
11RELION3.1.1final Euler assignment
13RELION3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38666 / Symmetry type: POINT

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