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- EMDB-9774: Capsid structure of a freshwater cyanophage Siphoviridae Mic1 -

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Basic information

Entry
Database: EMDB / ID: EMD-9774
TitleCapsid structure of a freshwater cyanophage Siphoviridae Mic1
Map datathe mrc map after postprocess
SampleCyanophage != Microcystis phage Mic1

Cyanophage

  • Virus: Microcystis phage Mic1 (virus)
    • Protein or peptide: major capsid protein
    • Protein or peptide: cement protein
Keywordscyanophage / Siphoviridae / capsid / VIRUS
Function / homologyCement / Major capsid protein
Function and homology information
Biological speciesMicrocystis phage Mic1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsJin H / Jiang YL
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31630001 China
National Natural Science Foundation of China31621002 China
Ministry of Science and Technology (China)2016YFA0400900 China
Chinese Academy of Sciences China
CitationJournal: Structure / Year: 2019
Title: Capsid Structure of a Freshwater Cyanophage Siphoviridae Mic1.
Authors: Hua Jin / Yong-Liang Jiang / Feng Yang / Jun-Tao Zhang / Wei-Fang Li / Ke Zhou / Jue Ju / Yuxing Chen / Cong-Zhao Zhou /
Abstract: Cyanobacteria are the most abundant photosynthetic microorganisms, the global distribution of which is mainly regulated by the corresponding cyanophages. A systematic screening of water samples in ...Cyanobacteria are the most abundant photosynthetic microorganisms, the global distribution of which is mainly regulated by the corresponding cyanophages. A systematic screening of water samples in the Lake Chaohu enabled us to isolate a freshwater siphocyanophage that infects Microcystis wesenbergii, thus termed Mic1. Using cryoelectron microscopy, we solved the 3.5-Å structure of Mic1 capsid. The major capsid protein gp40 of an HK97-like fold forms two types of capsomers, hexons and pentons. The capsomers interact with each other via the interweaved N-terminal arms of gp40 in addition to a tail-in-mouth joint along the three-fold symmetric axis, resulting in the assembly of capsid in a mortise-and-tenon pattern. The novel-fold cement protein gp47 sticks at the two-fold symmetric axis and further fixes the capsid. These findings provide structural insights into the assembly of cyanophages, and set up a platform to explore the mechanism of specific interactions and co-evolution with cyanobacteria.
History
DepositionJan 5, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseOct 2, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6j3q
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6j3q
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9774.png

Downloads & links

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Map

FileDownload / File: emd_9774.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe mrc map after postprocess
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 800 pix.
= 1088. Å		1.36 Å/pix.
x 800 pix.
= 1088. Å		1.36 Å/pix.
x 800 pix.
= 1088. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.06584724 - 0.1399208
Average (Standard dev.)0.0011295206 (±0.006781062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1088.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z1088.0001088.0001088.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS800800800
D min/max/mean-0.0660.1400.001

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Supplemental data

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Sample components

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Entire : Cyanophage

EntireName: Cyanophage
Components
  • Virus: Microcystis phage Mic1 (virus)
    • Protein or peptide: major capsid protein
    • Protein or peptide: cement protein

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Supramolecule #1: Microcystis phage Mic1

SupramoleculeName: Microcystis phage Mic1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2587456 / Sci species name: Microcystis phage Mic1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Microcystis wesenbergii (bacteria)
Virus shellShell ID: 1 / Name: gp40 / Diameter: 880.0 Å / T number (triangulation number): 13

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Macromolecule #1: major capsid protein

MacromoleculeName: major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Microcystis phage Mic1 (virus)
Molecular weightTheoretical: 37.879035 KDa
SequenceString: MAKLNLAVLN NVFSELLTQE INRSATFLGL LSKYPERKSN IQWGVGMGGT TATGVAITGS APAASMDATL PAQLPISAAS VQSTFTLNL KEIEESKEQV TNEELRNLLE AQMRNAVEEI ATTLNKKLYD GSGAIADGGL IGLSIAASGQ DYAGISSATY P LWNVSEVD ...String:
MAKLNLAVLN NVFSELLTQE INRSATFLGL LSKYPERKSN IQWGVGMGGT TATGVAITGS APAASMDATL PAQLPISAAS VQSTFTLNL KEIEESKEQV TNEELRNLLE AQMRNAVEEI ATTLNKKLYD GSGAIADGGL IGLSIAASGQ DYAGISSATY P LWNVSEVD AWDANATGTD KRQALKTDFM LELDRKIRYR PGAYDLILTT PKVVEQYKKV FEANRSYQIM TFDGQRVPLI DL GFNVAGY MGRPIIDDVF CSRTRTAAES AITTALGTAV DEGVMYFLKK DDLRFYSTPV VGAFSANGVY TLMRQLAQTS LYV DNFVVG CIPQLQLTTR KNVGVIKNIK VG

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Macromolecule #2: cement protein

MacromoleculeName: cement protein / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Microcystis phage Mic1 (virus)
Molecular weightTheoretical: 10.199458 KDa
SequenceString:
MPLVYTPAVR GGANPASGSY LLDPQYVNSG VDILQATYGY NINGTANADQ LLQRDAILAI LEYALKDTAF VNAIQAVAAG SGVTTPASF VSACVTKLTA

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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: 7.5 / Details: 50 mM Tris-HCl pH7.5, 100 mM NaCl, 10 mM MgSO4
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1935 / Average exposure time: 5.76 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 18800
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 9702
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 2.0)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6j3q:
Capsid structure of a freshwater cyanophage Siphoviridae Mic1

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