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- PDB-6v8i: Composite atomic model of the Staphylococcus aureus phage 80alpha... -

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Basic information

Entry
Database: PDB / ID: 6v8i
TitleComposite atomic model of the Staphylococcus aureus phage 80alpha baseplate
Components
  • Distal Tail Protein, gp58
  • Fiber Lower, gp62
  • Fiber Upper, gp68
  • Major Tail Protein, gp53
  • Receptor Binding Protein, gp61Receptor (biochemistry)
  • Tail-Associated Lysin, gp59
  • Tape Measure Protein, gp57
KeywordsVIRAL PROTEIN / phage tail / tail tip / tape measure protein
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Bacteriophage 69, Orf23, major tail protein / Prophage tail endopeptidase / Prophage endopeptidase tail / Siphovirus-type tail component / Phage tail protein RIFT-related domain / BppU, N-terminal / BppU N-terminal domain / Phage major tail protein TP901-1 / Phage tail tube protein / SGNH hydrolase-type esterase domain ...Bacteriophage 69, Orf23, major tail protein / Prophage tail endopeptidase / Prophage endopeptidase tail / Siphovirus-type tail component / Phage tail protein RIFT-related domain / BppU, N-terminal / BppU N-terminal domain / Phage major tail protein TP901-1 / Phage tail tube protein / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Armadillo-type fold
Similarity search - Domain/homology
: / Major tail protein / Tape measure protein / Uncharacterized protein / Uncharacterized protein / Minor structure protein / BppU_N domain-containing protein / Tail fiber protein
Similarity search - Component
Biological speciesStaphylococcus virus 80alpha
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKizziah, J.L. / Dokland, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI083255 United States
CitationJournal: PLoS Pathog / Year: 2020
Title: Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage.
Authors: James L Kizziah / Keith A Manning / Altaira D Dearborn / Terje Dokland /
Abstract: Staphylococcus aureus is a common cause of infections in humans. The emergence of virulent, antibiotic-resistant strains of S. aureus is a significant public health concern. Most virulence and ...Staphylococcus aureus is a common cause of infections in humans. The emergence of virulent, antibiotic-resistant strains of S. aureus is a significant public health concern. Most virulence and resistance factors in S. aureus are encoded by mobile genetic elements, and transduction by bacteriophages represents the main mechanism for horizontal gene transfer. The baseplate is a specialized structure at the tip of bacteriophage tails that plays key roles in host recognition, cell wall penetration, and DNA ejection. We have used high-resolution cryo-electron microscopy to determine the structure of the S. aureus bacteriophage 80α baseplate at 3.75 Å resolution, allowing atomic models to be built for most of the major tail and baseplate proteins, including two tail fibers, the receptor binding protein, and part of the tape measure protein. Our structure provides a structural basis for understanding host recognition, cell wall penetration and DNA ejection in viruses infecting Gram-positive bacteria. Comparison to other phages demonstrates the modular design of baseplate proteins, and the adaptations to the host that take place during the evolution of staphylococci and other pathogens.
History
DepositionDec 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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 / struct_conn
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 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
AC: Distal Tail Protein, gp58
AD: Distal Tail Protein, gp58
AE: Tail-Associated Lysin, gp59
CF: Tape Measure Protein, gp57
CC: Distal Tail Protein, gp58
CD: Distal Tail Protein, gp58
CE: Tail-Associated Lysin, gp59
BF: Tape Measure Protein, gp57
BC: Distal Tail Protein, gp58
BD: Distal Tail Protein, gp58
BE: Tail-Associated Lysin, gp59
AF: Tape Measure Protein, gp57
BJ: Fiber Lower, gp62
BK: Fiber Lower, gp62
BL: Fiber Lower, gp62
DJ: Fiber Lower, gp62
DK: Fiber Lower, gp62
DL: Fiber Lower, gp62
AJ: Fiber Lower, gp62
AK: Fiber Lower, gp62
AL: Fiber Lower, gp62
FJ: Fiber Lower, gp62
FK: Fiber Lower, gp62
FL: Fiber Lower, gp62
CJ: Fiber Lower, gp62
CK: Fiber Lower, gp62
CL: Fiber Lower, gp62
EJ: Fiber Lower, gp62
EK: Fiber Lower, gp62
EL: Fiber Lower, gp62
BN: Fiber Upper, gp68
BM: Fiber Upper, gp68
DN: Fiber Upper, gp68
DM: Fiber Upper, gp68
AN: Fiber Upper, gp68
AM: Fiber Upper, gp68
FN: Fiber Upper, gp68
FM: Fiber Upper, gp68
CN: Fiber Upper, gp68
CM: Fiber Upper, gp68
EN: Fiber Upper, gp68
EM: Fiber Upper, gp68
EB: Major Tail Protein, gp53
EA: Major Tail Protein, gp53
BB: Major Tail Protein, gp53
BA: Major Tail Protein, gp53
DB: Major Tail Protein, gp53
DA: Major Tail Protein, gp53
AB: Major Tail Protein, gp53
AA: Major Tail Protein, gp53
FB: Major Tail Protein, gp53
FA: Major Tail Protein, gp53
CB: Major Tail Protein, gp53
CA: Major Tail Protein, gp53
BH: Receptor Binding Protein, gp61
BG: Receptor Binding Protein, gp61
BI: Receptor Binding Protein, gp61
DH: Receptor Binding Protein, gp61
DG: Receptor Binding Protein, gp61
DI: Receptor Binding Protein, gp61
AH: Receptor Binding Protein, gp61
AG: Receptor Binding Protein, gp61
AI: Receptor Binding Protein, gp61
FH: Receptor Binding Protein, gp61
FG: Receptor Binding Protein, gp61
FI: Receptor Binding Protein, gp61
CH: Receptor Binding Protein, gp61
CG: Receptor Binding Protein, gp61
CI: Receptor Binding Protein, gp61
EH: Receptor Binding Protein, gp61
EG: Receptor Binding Protein, gp61
EI: Receptor Binding Protein, gp61
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,130,16078
Polymers4,129,82572
Non-polymers3356
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, Fully-formed baseplates observed via negative electron microscopy and cryo-electron microscopy attached to tails of ST247 strain 80alpha (no capsids) and wild-type 80alpha
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area476810 Å2
ΔGint-2338 kcal/mol
Surface area776630 Å2

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Components

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Protein , 7 types, 72 molecules ACADCCCDBCBDAECEBECFBFAFBJBKBLDJDKDLAJAKALFJFKFLCJCKCLEJEKEL...

#1: Protein
Distal Tail Protein, gp58


Mass: 37105.004 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus virus 80alpha / Strain: ST247 / Production host: Staphylococcus aureus (bacteria) / References: UniProt: A4ZFC4
#2: Protein Tail-Associated Lysin, gp59


Mass: 71114.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus virus 80alpha / Strain: ST247 / Production host: Staphylococcus aureus (bacteria) / References: UniProt: A4ZFC5
#3: Protein Tape Measure Protein, gp57 /


Mass: 125891.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus virus 80alpha / Strain: ST247 / Production host: Staphylococcus aureus (bacteria) / References: UniProt: A4ZFC2
#4: Protein
Fiber Lower, gp62 / BppU_N domain-containing protein


Mass: 66872.477 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus virus 80alpha / Strain: ST247 / Production host: Staphylococcus aureus (bacteria) / References: UniProt: A4ZFC8
#5: Protein
Fiber Upper, gp68 / Tail fiber protein


Mass: 43866.266 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus virus 80alpha / Strain: ST247 / Production host: Staphylococcus aureus (bacteria) / References: UniProt: A4ZFD4
#6: Protein
Major Tail Protein, gp53


Mass: 21551.746 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus virus 80alpha / Strain: ST247 / Production host: Staphylococcus aureus (bacteria) / References: UniProt: A4ZFB9
#7: Protein
Receptor Binding Protein, gp61 / Receptor (biochemistry) / Minor structure protein


Mass: 73747.445 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus virus 80alpha / Strain: ST247 / Production host: Staphylococcus aureus (bacteria) / References: UniProt: A4ZFC7

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Non-polymers , 1 types, 6 molecules

#8: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe

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Details

Has ligand of interestN

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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: Staphylococcus phage 80alpha baseplate / Type: COMPLEX
Details: 80alpha baseplate attached to fully formed tails with no capsids
Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightValue: 3.7 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus virus 80alpha / Strain: ST247
Source (recombinant)Organism: Staphylococcus aureus (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMtris(hydroxymethyl)aminomethane1
250 mMsodium chlorideNaClSodium chloride1
31 mMmagnesium sulfateMgSO41
44 mMcalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 80alpha tails (with baseplates) purified by centrifugation, polyethylene glycol precipitation, and CsCl density gradation
Specimen supportGrid material: NICKEL / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal magnification: 29000 X / Nominal defocus max: 3700 nm / Nominal defocus min: 1700 nm
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 1.156 sec. / Electron dose: 104.33 e/Å2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Num. of grids imaged: 10 / Num. of real images: 6483
Image scansMovie frames/image: 37 / Used frames/image: 1-37

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Processing

EM software
IDNameVersionCategoryDetails
1RELION2particle selection
2Leginonimage acquisition
3Appionimage acquisition
5Gctf1.06_sm_30_cu8.0_x86_64CTF correction
8UCSF Chimeramodel fitting
10RELION2initial Euler assignment
11RELION3.0-beta-2final Euler assignment
12RELION3.0-beta-2classification
13RELION3.0-beta-23D reconstruction
14PHENIXmodel refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 515106
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43601 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: correlation coefficient
Details: Initial models derived from I-TASSER predictions based on GenBank sequences of modeled proteins. Rigid body fitting in UCSF Chimera followed by manual extension in Coot.
Atomic model buildingPDB-ID: 5EFV

5efv


Accession code: 5EFV / Source name: PDB / Type: experimental model

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