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- PDB-11ed: C12 Portal Assembly of Bacteriophage Goslar -

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Basic information

Entry
Database: PDB / ID: 11ed
TitleC12 Portal Assembly of Bacteriophage Goslar
Components
  • Portal Assembly Protein gp233
  • Portal Protein gp36
  • Tail Adaptor Protein gp50 NTD
KeywordsVIRAL PROTEIN / Portal Assembly / Phage
Function / homology: / Family of unknown function (DUF7484) / : / : / Putative phage head-tail joining protein / Phage head to tail associated domain / Uncharacterized protein / Virion structural protein / Virion structural protein
Function and homology information
Biological speciesGoslarvirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.82 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: C12 Portal Assembly of Bacteriophage Goslar
Authors: Basu, D.
History
DepositionFeb 18, 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

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Assembly

Deposited unit
J: Portal Protein gp36
U: Portal Assembly Protein gp233
g: Tail Adaptor Protein gp50 NTD


Theoretical massNumber of molelcules
Total (without water)190,6383
Polymers190,6383
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 Portal Protein gp36


Mass: 108728.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Goslarvirus / References: UniProt: A0A482GK98
#2: Protein Portal Assembly Protein gp233


Mass: 31988.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Goslarvirus / References: UniProt: A0A482GEL4
#3: Protein Tail Adaptor Protein gp50 NTD


Mass: 49920.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Goslarvirus / References: UniProt: A0A482GGR9
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
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil
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 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64344 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 153.14 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00219411
ELECTRON MICROSCOPYf_angle_d0.427712779
ELECTRON MICROSCOPYf_chiral_restr0.03721445
ELECTRON MICROSCOPYf_plane_restr0.0031659
ELECTRON MICROSCOPYf_dihedral_angle_d10.92733475

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