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- PDB-5a20: Structure of bacteriophage SPP1 head-to-tail interface filled wit... -

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Basic information

Entry
Database: PDB / ID: 5a20
TitleStructure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure protein
Components
  • 15 PROTEIN
  • HEAD COMPLETION PROTEIN GP16
  • MAJOR TAIL PROTEIN GP17.1
  • PORTAL PROTEIN
  • TAIL-TO-HEAD JOINING PROTEIN GP17
KeywordsVIRAL PROTEIN / TAILED BACTERIOPHAGE / SIPHOVIRIDAE / SPP1 / VIRAL ASSEMBLY / HEAD-TO-TAIL INTERFACE / DNA GATEKEEPER / ALLOSTERIC MECHANISM / CONCERTED REORGANISATION / DIAPHRAGM GATING
Function / homology
Function and homology information


viral head-tail joining / virus tail fiber assembly / viral DNA genome packaging, headful / virus tail, tube / viral portal complex / viral procapsid / symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail / virion component / viral translational frameshifting
Similarity search - Function
Portal protein, SPP1-type / : / Phage gp6-like head-tail connector protein / : / Phage gp6-like head-tail connector protein / Portal protein / Phage portal protein, SPP1 Gp6-like / Tail completion protein / Protein of unknown function (DUF3168) / : ...Portal protein, SPP1-type / : / Phage gp6-like head-tail connector protein / : / Phage gp6-like head-tail connector protein / Portal protein / Phage portal protein, SPP1 Gp6-like / Tail completion protein / Protein of unknown function (DUF3168) / : / Bacteriophage SPP1, head-tail adaptor / Phage head-tail joining protein / Bacteriophage SPP1, head-tail adaptor superfamily / Phage major tail protein TP901-1 / Phage tail tube protein / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Head completion protein gp16 / Tail completion protein gp17 / Tail tube protein gp17.1* / Portal protein / Head completion protein gp15
Similarity search - Component
Biological speciesBACILLUS PHAGE SPP1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsChaban, Y. / Lurz, R. / Brasiles, S. / Cornilleau, C. / Karreman, M. / Zinn-Justin, S. / Tavares, P. / Orlova, E.V.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structural rearrangements in the phage head-to-tail interface during assembly and infection.
Authors: Yuriy Chaban / Rudi Lurz / Sandrine Brasilès / Charlène Cornilleau / Matthia Karreman / Sophie Zinn-Justin / Paulo Tavares / Elena V Orlova /
Abstract: Many icosahedral viruses use a specialized portal vertex to control genome encapsidation and release from the viral capsid. In tailed bacteriophages, the portal system is connected to a tail ...Many icosahedral viruses use a specialized portal vertex to control genome encapsidation and release from the viral capsid. In tailed bacteriophages, the portal system is connected to a tail structure that provides the pipeline for genome delivery to the host cell. We report the first, to our knowledge, subnanometer structures of the complete portal-phage tail interface that mimic the states before and after DNA release during phage infection. They uncover structural rearrangements associated with intimate protein-DNA interactions. The portal protein gp6 of bacteriophage SPP1 undergoes a concerted reorganization of the structural elements of its central channel during interaction with DNA. A network of protein-protein interactions primes consecutive binding of proteins gp15 and gp16 to extend and close the channel. This critical step that prevents genome leakage from the capsid is achieved by a previously unidentified allosteric mechanism: gp16 binding to two different regions of gp15 drives correct positioning and folding of an inner gp16 loop to interact with equivalent loops of the other gp16 subunits. Together, these loops build a plug that closes the channel. Gp16 then fastens the tail to yield the infectious virion. The gatekeeper system opens for viral genome exit at the beginning of infection but recloses afterward, suggesting a molecular diaphragm-like mechanism to control DNA efflux. The mechanisms described here, controlling the essential steps of phage genome movements during virus assembly and infection, are likely to be conserved among long-tailed phages, the largest group of viruses in the Biosphere.
History
DepositionMay 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-2993
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  • Imaged by UCSF Chimera
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Assembly

Deposited unit
A: PORTAL PROTEIN
B: PORTAL PROTEIN
C: 15 PROTEIN
D: 15 PROTEIN
E: HEAD COMPLETION PROTEIN GP16
F: HEAD COMPLETION PROTEIN GP16
G: TAIL-TO-HEAD JOINING PROTEIN GP17
H: MAJOR TAIL PROTEIN GP17.1


Theoretical massNumber of molelcules
Total (without water)197,4988
Polymers197,4988
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

#1: Protein PORTAL PROTEIN / GENE PRODUCT 6 / GP6 / PORTAL VERTEX PROTEIN


Mass: 57405.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BACILLUS PHAGE SPP1 (virus) / References: UniProt: P54309
#2: Protein 15 PROTEIN / HEAD COMPLETION PROTEIN / GP15


Mass: 11629.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BACILLUS PHAGE SPP1 (virus) / References: UniProt: Q38584
#3: Protein HEAD COMPLETION PROTEIN GP16


Mass: 12615.069 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BACILLUS PHAGE SPP1 (virus) / References: UniProt: O48446
#4: Protein TAIL-TO-HEAD JOINING PROTEIN GP17


Mass: 15025.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BACILLUS PHAGE SPP1 (virus) / References: UniProt: O48448
#5: Protein MAJOR TAIL PROTEIN GP17.1


Mass: 19172.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BACILLUS PHAGE SPP1 (virus) / References: UniProt: O48449

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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: BACTERIOPHAGE SPP1 HEAD- TO-TAIL INTERFACE / Type: VIRUS / Details: MICROGRAPHS SELECTED BY OPTICAL DIFFRACTION
Buffer solutionName: SEE REFERENCE FOR DETAILS / pH: 7.5 / Details: SEE REFERENCE FOR DETAILS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Oct 9, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 900 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 400

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Processing

EM software
IDNameCategoryDetails
1Flex-EMmodel fitting
2MODELLERmodel fitting
3UCSF Chimeramodel fitting
4VEDAmodel fittingUROX
5EMAN3D reconstruction
6IMAGIC3D reconstruction
7SPIDER3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionMethod: ANGULAR RECONSTITUTION / Resolution: 7.6 Å / Num. of particles: 14000 / Nominal pixel size: 1.2 Å / Actual pixel size: 1.15 Å
Magnification calibration: CROSS- -CORRELATION WITH FITTED ATOMIC COORDINATES
Details: ATOMIC COORDINATES FOR GP6, GP15, GP16, GP17 WERE OBTAINED FROM PDB FILES 2JES (LEBEDEV ET AL., EMBO J., 2007, 26, 1984), 2KBZ, 2KCA (LHUILLIER ET AL., PROC.NATL.ACAD.SCI. USA, 2009, 106, ...Details: ATOMIC COORDINATES FOR GP6, GP15, GP16, GP17 WERE OBTAINED FROM PDB FILES 2JES (LEBEDEV ET AL., EMBO J., 2007, 26, 1984), 2KBZ, 2KCA (LHUILLIER ET AL., PROC.NATL.ACAD.SCI. USA, 2009, 106, 8507), 2LFP (CHAGOT ET AL., PROTEINS, 2012, 80, 319), CORRESPONDIGLY, AND DOCKED INTO EM ELECTRON DENSITY MAP USING FLEXIBLE FIT. ATOMIC COORDINATES FOR MISSING DOMAINS OF GP6 AND GP17.1. WERE MODELLED USING I-TASSER PROTEIN STRUCTURE PREDICTION SERVER (Y ZHANG, BMC BIOINFORMATICS, 2008, 9, 40) AND DOCKED INTO EM ELECTRON DENSITY MAP USING FLEXIBLE FIT. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2993. (DEPOSITION ID: 13331). SEQUENCE N-TERMINAL RESIDUES 1-28 AND C-TERMINAL RESIDUES 468-509 WERE NOT INCLUDED IN THE ATOMIC COORDINATES USED FOR DOCKING DUE TO DIFFICULTIES TRACING CORRESPONDING DENSITIES IN THE EM MAP. ASN 365 IS SUBSTITUTED FOR LYS, SAME AS IN PDB COORDINATE FILE 2JES, WHICH WAS USED AS A STARTING POINT FOR THE FITTING. N-TERMINAL RESIDUES 1-3 ARE OMITTED FROM THE DOCKED GP15 SEQUENCE. PRO 6 IS SUBSTITUTED WITH ARG IN GP16 SEQUENCE, AS IT IS IN THE PDB COORDINATE FILE 2KCA USED FOR FITTING N-TERMINAL RESIDUE 1 IS MISSING FROM THE DOCKED GP17 SEQUENCE. N-TERMINAL RESIDUES 1-8 AND C-TERMINAL RESIDUES 170-177 ARE MISSING FROM THE DOCKED GP17.1 SEQUENCE DUE TO DIFFICULTIES TRACING CORRESPONDING DENSITIES IN THE EM MAP.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY, NMR, PREDICTION
RefinementHighest resolution: 7.6 Å
Refinement stepCycle: LAST / Highest resolution: 7.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12799 0 0 0 12799

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