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- EMDB-10002: BACTERIOPHAGE SPP1 PROCAPSID-II PROTEIN -

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Basic information

Entry
Database: EMDB / ID: EMD-10002
TitleBACTERIOPHAGE SPP1 PROCAPSID-II PROTEIN
Map dataIntemediate state of the SPP1 procapsid, prior DNA packaging
Sample
  • Virus: Bacillus phage SPP1 (virus)
    • Protein or peptide: Major capsid protein
KeywordsBacteriophage / maturation process / cryo electron microscopy / capsid protein / 3D reconstruction / VIRUS
Function / homologyMajor capsid protein 13-like / Major capsid protein 13-like / T=7 icosahedral viral capsid / viral capsid / Major capsid protein
Function and homology information
Biological speciesBacillus phage SPP1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsIgnatiou A / Brasiles S
CitationJournal: Nat Commun / Year: 2019
Title: Structural transitions during the scaffolding-driven assembly of a viral capsid.
Authors: Athanasios Ignatiou / Sandrine Brasilès / Mehdi El Sadek Fadel / Jörg Bürger / Thorsten Mielke / Maya Topf / Paulo Tavares / Elena V Orlova /
Abstract: Assembly of tailed bacteriophages and herpesviruses starts with formation of procapsids (virion precursors without DNA). Scaffolding proteins (SP) drive assembly by chaperoning the major capsid ...Assembly of tailed bacteriophages and herpesviruses starts with formation of procapsids (virion precursors without DNA). Scaffolding proteins (SP) drive assembly by chaperoning the major capsid protein (MCP) to build an icosahedral lattice. Here we report near-atomic resolution cryo-EM structures of the bacteriophage SPP1 procapsid, the intermediate expanded procapsid with partially released SPs, and the mature capsid with DNA. In the intermediate state, SPs are bound only to MCP pentons and to adjacent subunits from hexons. SP departure results in the expanded state associated with unfolding of the MCP N-terminus and straightening of E-loops. The newly formed extensive inter-capsomere bonding appears to compensate for release of SPs that clasp MCP capsomeres together. Subsequent DNA packaging instigates bending of MCP A domain loops outwards, closing the hexons central opening and creating the capsid auxiliary protein binding interface. These findings provide a molecular basis for the sequential structural rearrangements during viral capsid maturation.
History
DepositionMay 24, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseOct 23, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rtl
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rtl
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10002.png

Downloads & links

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Map

FileDownload / File: emd_10002.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIntemediate state of the SPP1 procapsid, prior DNA packaging
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 600 pix.
= 786. Å		1.31 Å/pix.
x 600 pix.
= 786. Å		1.31 Å/pix.
x 600 pix.
= 786. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum0.0 - 15.11228
Average (Standard dev.)0.16541384 (±0.8142602)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 785.99994 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z786.000786.000786.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS600600600
D min/max/mean0.00015.1120.165

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Supplemental data

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Sample components

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Entire : Bacillus phage SPP1

EntireName: Bacillus phage SPP1 (virus)
Components
  • Virus: Bacillus phage SPP1 (virus)
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Bacillus phage SPP1

SupramoleculeName: Bacillus phage SPP1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10724 / Sci species name: Bacillus phage SPP1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Bacillus subtilis (bacteria)
Virus shellShell ID: 1 / Name: procapsid II / Diameter: 600.0 Å / T number (triangulation number): 7

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage SPP1 (virus)
Molecular weightTheoretical: 35.258426 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: AYTKISDVIV PELFNPYVIN TTTQLSAFFQ SGIAATDDEL NALAKKAGGG STLNMPYWND LDGDSQVLND TDDLVPQKIN AGQDKAVLI LRGNAWSSHD LAATLSGSDP MQAIGSRVAA YWAREMQKIV FAELAGVFSN DDMKDNKLDI SGTADGIYSA E TFVDASYK ...String:
AYTKISDVIV PELFNPYVIN TTTQLSAFFQ SGIAATDDEL NALAKKAGGG STLNMPYWND LDGDSQVLND TDDLVPQKIN AGQDKAVLI LRGNAWSSHD LAATLSGSDP MQAIGSRVAA YWAREMQKIV FAELAGVFSN DDMKDNKLDI SGTADGIYSA E TFVDASYK LGDHESLLTA IGMHSATMAS AVKQDLIEFV KDSQSGIRFP TYMNKRVIVD DSMPVETLED GTKVFTSYLF GA GALGYAE GQPEVPTETA RNALGSQDIL INRKHFVLHP RGVKFTENAM AGTTPTDEEL ANGANWQRVY DPKKIRIVQF KHR LQA

UniProtKB: Major capsid protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 70.0 K / Max: 85.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3840 pixel / Digitization - Dimensions - Height: 3712 pixel / Digitization - Frames/image: 4-21 / Number grids imaged: 1 / Number real images: 7000 / Average exposure time: 5.0 sec. / Average electron dose: 1.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.9 µm / Calibrated magnification: 39000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 39000
Sample stageSpecimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 11745
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC (ver. 5) / Number images used: 8808
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 5)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 5)
Final 3D classificationAvg.num./class: 1 / Software - Name: IMAGIC (ver. 5)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6rtl:
BACTERIOPHAGE SPP1 PROCAPSID-II PROTEIN

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