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- PDB-8zdq: Cryo-EM structure of Mycobacteriophage Douge complete baseplate (... -

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Basic information

Entry
Database: PDB / ID: 8zdq
TitleCryo-EM structure of Mycobacteriophage Douge complete baseplate (gp13, gp17, gp23, gp16, gp18 and gp20)
Components
  • Baseplate Hub Protein (gp18)
  • Baseplate Upper Protein (gp23)
  • Central Fiber Protein (gp20)
  • Distal Tail Protein (gp17)
  • Tail Tube Protein (gp13)
  • Tape Measure Protein (gp16)
KeywordsVIRAL PROTEIN / Mycobacteriophage / phage structure / Icosahedral / cryo-EM / protein assembly / VIRUS
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsMaharana, J. / Wang, C.H. / Tsai, L.A. / Lowary, T.L. / Ho, M.C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Mycobacteriophage cryo-EM studies reveal the siphophage architecture at the amino acid level and its host interaction for viral genome ejection
Authors: Maharana, J. / Wang, C.H. / Tsai, L.A. / Lowary, T.L. / Ho, M.C.
History
DepositionMay 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: Tail Tube Protein (gp13)
N: Tail Tube Protein (gp13)
O: Tail Tube Protein (gp13)
P: Tail Tube Protein (gp13)
Q: Tail Tube Protein (gp13)
R: Tail Tube Protein (gp13)
S: Tape Measure Protein (gp16)
T: Tape Measure Protein (gp16)
U: Tape Measure Protein (gp16)
a: Baseplate Upper Protein (gp23)
b: Baseplate Upper Protein (gp23)
c: Baseplate Upper Protein (gp23)
d: Baseplate Upper Protein (gp23)
e: Baseplate Upper Protein (gp23)
f: Baseplate Upper Protein (gp23)
g: Baseplate Upper Protein (gp23)
h: Baseplate Upper Protein (gp23)
i: Baseplate Upper Protein (gp23)
j: Baseplate Upper Protein (gp23)
k: Baseplate Upper Protein (gp23)
l: Baseplate Upper Protein (gp23)
m: Distal Tail Protein (gp17)
n: Distal Tail Protein (gp17)
o: Distal Tail Protein (gp17)
p: Distal Tail Protein (gp17)
q: Distal Tail Protein (gp17)
r: Distal Tail Protein (gp17)
s: Baseplate Hub Protein (gp18)
t: Baseplate Hub Protein (gp18)
u: Baseplate Hub Protein (gp18)
v: Central Fiber Protein (gp20)
w: Central Fiber Protein (gp20)
x: Central Fiber Protein (gp20)


Theoretical massNumber of molelcules
Total (without water)1,801,12033
Polymers1,801,12033
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 33 molecules MNOPQRSTUabcdefghijklmnopqrstu...

#1: Protein
Tail Tube Protein (gp13)


Mass: 32112.025 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#2: Protein Tape Measure Protein (gp16)


Mass: 176109.203 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#3: Protein
Baseplate Upper Protein (gp23)


Mass: 33673.859 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#4: Protein
Distal Tail Protein (gp17)


Mass: 33771.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#5: Protein Baseplate Hub Protein (gp18)


Mass: 65026.320 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#6: Protein Central Fiber Protein (gp20)


Mass: 92774.414 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)

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Details

Has protein modificationN

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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: Mycolicibacterium smegmatis MC2 155 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 430 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31169 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00392709
ELECTRON MICROSCOPYf_angle_d0.517126702
ELECTRON MICROSCOPYf_dihedral_angle_d12.85632625
ELECTRON MICROSCOPYf_chiral_restr0.04314187
ELECTRON MICROSCOPYf_plane_restr0.00416377

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