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- EMDB-4461: High resolution electron cryo-microscopy structure of the bacteri... -

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Basic information

Entry
Database: EMDB / ID: EMD-4461
TitleHigh resolution electron cryo-microscopy structure of the bacteriophage PR772
Map data
Sample
  • Complex: Bacteriophage PR772
    • Protein or peptide: Major Capsid Protein (P3)
    • Protein or peptide: Minor Capsid Protein (P30)
    • Protein or peptide: Infectivity Protein (P16)
    • Protein or peptide: Spike protein
    • Protein or peptide: Penton protein
KeywordsPhage / Tectiviridae / Membrane / double-barrel / helix turn helix / helix with a kink / beta-propeller / heteropentamer / penton / VIRUS
Function / homology
Function and homology information


viral capsid / membrane
Similarity search - Function
Tectiviridae, minor capsid / Tectiviridae, minor capsid / Domain of unknown function (DUF1970) / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5 C-terminal domain superfamily / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5, spike N-terminal / Bacteriophage PRD1, P5, spike N-terminal / Bacteriophage PRD1, P3 / Bacteriophage PRD1, P3, N-terminal ...Tectiviridae, minor capsid / Tectiviridae, minor capsid / Domain of unknown function (DUF1970) / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5 C-terminal domain superfamily / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5, spike N-terminal / Bacteriophage PRD1, P5, spike N-terminal / Bacteriophage PRD1, P3 / Bacteriophage PRD1, P3, N-terminal / P3 major capsid protein / Group II dsDNA virus coat/capsid protein / Viral coat protein subunit
Similarity search - Domain/homology
Infectivity protein / Minor capsid protein / Major capsid protein / Spike / Penton
Similarity search - Component
Biological speciesEnterobacteria phage PR772 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsNarayana Reddy HK / Svenda M
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research Council628-20081109822-2010-6157, 822-2012-5260 and 828-2012-108 Sweden
Knut and Alice Wallenberg FoundationKAW-2011.081 Sweden
European Research CouncilERC-291602 Sweden
Citation
Journal: Elife / Year: 2019
Title: Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture.
Authors: Hemanth Kn Reddy / Marta Carroni / Janos Hajdu / Martin Svenda /
Abstract: Bacteriophage PR772, a member of the family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged ...Bacteriophage PR772, a member of the family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T = 25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.
#1: Journal: Biorxiv / Year: 2019
Title: Electron cryo-microscopy of Bacteriophage PR772 reveals the composition and structure of the elusive vertex complex and the capsid architecture
Authors: Narayana Reddy HK / Hajdu J / Carroni M / Svenda M
History
DepositionDec 9, 2018-
Header (metadata) releaseJun 19, 2019-
Map releaseJun 19, 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: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6q5u
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6q5u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4461.png

Downloads & links

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Map

FileDownload / File: emd_4461.map.gz / Format: CCP4 / Size: 2.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 858 pix.
= 909.48 Å		1.06 Å/pix.
x 858 pix.
= 909.48 Å		1.06 Å/pix.
x 858 pix.
= 909.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 2.5 / Movie #1: 2
Minimum - Maximum-6.6406617 - 16.194255999999999
Average (Standard dev.)-0.000000000001106 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions858858858
Spacing858858858
CellA=B=C: 909.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z858858858
origin x/y/z0.0000.0000.000
length x/y/z909.480909.480909.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ858858858
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS858858858
D min/max/mean-6.64116.194-0.000

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Supplemental data

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Sample components

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Entire : Bacteriophage PR772

EntireName: Bacteriophage PR772
Components
  • Complex: Bacteriophage PR772
    • Protein or peptide: Major Capsid Protein (P3)
    • Protein or peptide: Minor Capsid Protein (P30)
    • Protein or peptide: Infectivity Protein (P16)
    • Protein or peptide: Spike protein
    • Protein or peptide: Penton protein

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Supramolecule #1: Bacteriophage PR772

SupramoleculeName: Bacteriophage PR772 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Wild type
Source (natural)Organism: Enterobacteria phage PR772 (virus)
Molecular weightTheoretical: 86 MDa

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Macromolecule #1: Major Capsid Protein (P3)

MacromoleculeName: Major Capsid Protein (P3) / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage PR772 (virus)
Molecular weightTheoretical: 43.505492 KDa
SequenceString: MAQVQQLTPA QQAALRNQQA MAANLQARQI VLQQSYPVIQ QVETQTFDPA NRSVFDVTPA NVGIVKGFLV KVTAAIKNNH ATEAVALTD FGPANLVQRV IYYDPDNQRH TETSGWHLHF VNTAKQGAPF LSSMVTDSPI KYGDVMNVID APATIAAGAT G ELTMYYWV ...String:
MAQVQQLTPA QQAALRNQQA MAANLQARQI VLQQSYPVIQ QVETQTFDPA NRSVFDVTPA NVGIVKGFLV KVTAAIKNNH ATEAVALTD FGPANLVQRV IYYDPDNQRH TETSGWHLHF VNTAKQGAPF LSSMVTDSPI KYGDVMNVID APATIAAGAT G ELTMYYWV PLAYSETDLT GAVLANVPQS KQRLKLEFAN NNTAFAAVGA NPLEAIYQGA GAADCEFEEI SYTVYQSYLD QL PVGQNGY ILPLIDLSTL YNLENSAQAG LTPNVDFVVQ YANLYRYLST IAVFDNGGSF NAGTDINYLS QRTANFSDTR KLD PKTWAA QTRRRIATDF PKGVYYCDNR DKPIYTLQYG NVGFVVNPKT VNQNARLLMG YEYFTSRTEL VNAGTISTT

UniProtKB: Major capsid protein

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Macromolecule #2: Minor Capsid Protein (P30)

MacromoleculeName: Minor Capsid Protein (P30) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage PR772 (virus)
Molecular weightTheoretical: 9.275559 KDa
SequenceString:
MALINPQFPY AGPVPIPGPA PTETMPLLNY RVEGRIAGIQ QARQFMPFLQ GPHREVAEQT YYAIGTGIQM GQTFNQPLIN TQEG

UniProtKB: Minor capsid protein

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Macromolecule #3: Infectivity Protein (P16)

MacromoleculeName: Infectivity Protein (P16) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage PR772 (virus)
Molecular weightTheoretical: 12.616262 KDa
SequenceString:
MDKKKLLYWV GGGLVLIIIW LWFRNRPAAQ VASNWEGPPY MTYNQPQAGS VTLPVAGYTS PSLTLPNRNR SCGCNPAVSA AMAQGADLA SKLTESISSQ LNNYAESLND YLASQAGV

UniProtKB: Infectivity protein

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Macromolecule #4: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage PR772 (virus)
Molecular weightTheoretical: 34.483898 KDa
SequenceString: MANQQIGGST VTYNGAIPMG GPVAINSVIE IAGTEVLVDL KLDYATGKIS GVQTLYIDLR DFLGDVTVTM PDTGQRITAR AGTQGYYPV LSTNLMKFIV SATIDGKFPM NFINFPIALG VWPSGIKGDK GDPGAPGPAG GTVVVEDSGA SFGESLLDTT S EPGKILVK ...String:
MANQQIGGST VTYNGAIPMG GPVAINSVIE IAGTEVLVDL KLDYATGKIS GVQTLYIDLR DFLGDVTVTM PDTGQRITAR AGTQGYYPV LSTNLMKFIV SATIDGKFPM NFINFPIALG VWPSGIKGDK GDPGAPGPAG GTVVVEDSGA SFGESLLDTT S EPGKILVK RISGGSGITV TDYGDEVEIE ASGGGGGGGG VTDALSLMYS TSTGGPASIA ANALTDFDLS GALTVNTVGT GL TKSAAGI QLAAGKSGLY QITMTVKNNT VTTGNYLLRV KYGSSDFVVA CPASSLTAGG TISLLIYCDV LGVPSLDVLK FSL CNDGAA LSNYIINITA AKIN

UniProtKB: Spike

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Macromolecule #5: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage PR772 (virus)
Molecular weightTheoretical: 13.757388 KDa
SequenceString:
MNVNNPNQMT VTPVYNGCDS GEGPQSVRGY FDAVAGENVK YDLTYLADTQ GFTGVQCIYI DNAENDGAFE IDVEETGQRI KCPAGKQGY FPLLVPGRAK FVARHLGSGK KSVPLFFLNF TIAQGVW

UniProtKB: Penton

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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

Concentration7 mg/mL
BufferpH: 8
GridModel: C-flat-2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 3-40 / Number grids imaged: 1 / Number real images: 3200 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 56000
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot (ver. 0.8.9.1)
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 104.93 / Target criteria: Cross-correlation coefficient
Output model

PDB-6q5u:
High resolution electron cryo-microscopy structure of the bacteriophage PR772

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