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- PDB-11ml: Bacteriophage Goslar Empty Capsid Asymmetric Unit -

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Basic information

Entry
Database: PDB / ID: 11ml
TitleBacteriophage Goslar Empty Capsid Asymmetric Unit
Components
  • Capsid Decorator gp77
  • Capsid Latch gp146
  • Major capsid protein
KeywordsVIRAL PROTEIN / Tail Assembly
Function / homology: / Bacteriophage PhiKZ major capsid protein gp120 / Uncharacterized protein / Major capsid protein / Uncharacterized protein
Function and homology information
Biological speciesGoslarvirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.16 Å
AuthorsBasu, D. / Gu, Y. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Emerging Pathogens Initiative United States
CitationJournal: To Be Published
Title: Bacteriophage Goslar Empty Capsid Asymmetric Unit
Authors: Basu, D. / Gu, Y. / Corbett, K.D.
History
DepositionMar 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A0: Major capsid protein
A1: Major capsid protein
A2: Major capsid protein
A3: Major capsid protein
A4: Major capsid protein
A5: Major capsid protein
A6: Major capsid protein
A7: Major capsid protein
A8: Major capsid protein
A9: Major capsid protein
Ar: Major capsid protein
As: Major capsid protein
At: Major capsid protein
Au: Major capsid protein
Av: Major capsid protein
Aw: Major capsid protein
Ax: Major capsid protein
Ay: Major capsid protein
Az: Major capsid protein
B: Capsid Latch gp146
BA: Major capsid protein
BB: Major capsid protein
BC: Major capsid protein
BD: Major capsid protein
BE: Major capsid protein
BF: Major capsid protein
BG: Major capsid protein
BH: Major capsid protein
G: Capsid Decorator gp77


Theoretical massNumber of molelcules
Total (without water)2,287,38929
Polymers2,287,38929
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Major capsid protein


Mass: 83400.391 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Source: (natural) Goslarvirus / References: UniProt: A0A482GE55
#2: Protein Capsid Latch gp146


Mass: 11689.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Goslarvirus / References: UniProt: A0A482GKM0
#3: Protein Capsid Decorator gp77


Mass: 23889.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Goslarvirus / References: UniProt: A0A482GDR9
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: Goslarvirus / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Goslarvirus
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
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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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: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4535 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 272.71 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0078129776
ELECTRON MICROSCOPYf_angle_d0.8934175701
ELECTRON MICROSCOPYf_chiral_restr0.05119702
ELECTRON MICROSCOPYf_plane_restr0.004723128
ELECTRON MICROSCOPYf_dihedral_angle_d7.393448926

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