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- EMDB-4717: BACTERIOPHAGE SPP1 PROCAPSID-I PROTEIN -

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Basic information

Entry
Database: EMDB / ID: EMD-4717
TitleBACTERIOPHAGE SPP1 PROCAPSID-I PROTEIN
Map datacryo-EM atomic structures of the bacteriophage SPP1 procapsid I. Procapsid I (a virion precursor without DNA) is assembled first.
Sample
  • Virus: Bacillus phage SPP1 (virus)
    • Protein or peptide: Major capsid protein
KeywordsVIRUS
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: 4.5 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
DepositionMar 19, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseOct 23, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 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-6r3b
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6r3b
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4717.png

Downloads & links

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Map

FileDownload / File: emd_4717.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM atomic structures of the bacteriophage SPP1 procapsid I. Procapsid I (a virion precursor without DNA) is assembled first.
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 - 16.831703000000001
Average (Standard dev.)0.2607685 (±1.0377659)
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/mean0.00016.8320.261

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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)
Molecular weightTheoretical: 30 MDa
Virus shellShell ID: 1 / Name: procapsid / Diameter: 550.0 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
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 R3/3 / Material: COPPER / Mesh: 400 / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 60.0 K / Max: 70.0 K
Specialist opticsChromatic aberration corrector: none
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Number real images: 7000 / Average exposure time: 5.0 sec. / Average electron dose: 25.0 e/Å2 / Details: Movie frames were aligned using MOTIONCORR-2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.9 µm / Calibrated magnification: 39000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 2.5 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: 6078
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC (ver. 5) / Number images used: 4558
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 5) / Details: ab initio reconstruction
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 5)
Final 3D classificationSoftware - Name: IMAGIC (ver. 5)

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Atomic model buiding 1

Initial modelPDB ID:

4an5


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6r3b:
BACTERIOPHAGE SPP1 PROCAPSID-I PROTEIN

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