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- EMDB-7473: Subparticle refinement of HSV-1 capsid vertex region. -

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Basic information

Entry
Database: EMDB / ID: 7473
TitleSubparticle refinement of HSV-1 capsid vertex region.
Map dataSubparticle refinement of HSV-1 capsid vertex region with associated tegument proteins.
SampleHuman herpesvirus 1 strain KOS:
virus / major capsid protein (MCP, VP5) / small capsid protein (SCP, VP26) / (capsid triplex subunit ...) x 2 / (tegument protein ...) x 3
Function / homologyHerpesvirus capsid shell protein 1 / Papain-like cysteine peptidase superfamily / Herpesvirus major capsid protein, upper domain superfamily / Herpesvirus capsid vertex component 1 / Herpesvirus UL35 / Herpesvirus large tegument protein, USP domain / Herpesvirus large tegument protein deneddylase / Herpesvirus UL25 family / Herpesvirus capsid protein 2 / Herpesvirus UL25 ...Herpesvirus capsid shell protein 1 / Papain-like cysteine peptidase superfamily / Herpesvirus major capsid protein, upper domain superfamily / Herpesvirus capsid vertex component 1 / Herpesvirus UL35 / Herpesvirus large tegument protein, USP domain / Herpesvirus large tegument protein deneddylase / Herpesvirus UL25 family / Herpesvirus capsid protein 2 / Herpesvirus UL25 / Herpesvirus major capsid protein / Herpesvirus VP23 like capsid protein / Herpes virus major capsid protein / Herpesvirus capsid shell protein VP19C / Large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 family / Herpesvirus UL17 protein / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / NEDD8-specific protease activity / DNA packaging / viral DNA genome replication / modulation by virus of host protein ubiquitination / viral release from host cell / viral genome packaging / thiol-dependent ubiquitinyl hydrolase activity / ubiquitinyl hydrolase 1 / Cysteine proteases / viral capsid / viral penetration into host nucleus / viral entry into host cell / host cell cytoplasm / host cell nucleus / viral process / structural molecule activity / DNA binding / Triplex capsid protein 1 / Capsid vertex component 1 / Triplex capsid protein 2 / Major capsid protein / Capsid vertex component 2 / Large tegument protein deneddylase / Small capsomere-interacting protein
Function and homology information
SourceHuman herpesvirus 1 strain KOS
Methodsingle particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsDai XH / Zhou ZH
CitationJournal: Science / Year: 2018
Title: Structure of the herpes simplex virus 1 capsid with associated tegument protein complexes.
Authors: Xinghong Dai / Z Hong Zhou
Abstract: Herpes simplex viruses (HSVs) rely on capsid-associated tegument complex (CATC) for long-range axonal transport of their genome-containing capsids between sites of infection and neuronal cell bodies. ...Herpes simplex viruses (HSVs) rely on capsid-associated tegument complex (CATC) for long-range axonal transport of their genome-containing capsids between sites of infection and neuronal cell bodies. Here we report cryo-electron microscopy structures of the HSV-1 capsid with CATC up to 3.5-angstrom resolution and atomic models of multiple conformers of capsid proteins VP5, VP19c, VP23, and VP26 and tegument proteins pUL17, pUL25, and pUL36. Crowning every capsid vertex are five copies of heteropentameric CATC, each containing a pUL17 monomer supporting the coiled-coil helix bundle of a pUL25 dimer and a pUL36 dimer, thus positioning their flexible domains for potential involvement in nuclear capsid egress and axonal capsid transport. Notwithstanding newly discovered fold conservation between triplex proteins and bacteriophage λ protein gpD and the previously recognized bacteriophage HK97 gp5-like fold in VP5, HSV-1 capsid proteins exhibit extraordinary diversity in forms of domain insertion and conformational polymorphism, not only for interactions with tegument proteins but also for encapsulation of large genomes.
DateDeposition: Feb 20, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Mar 14, 2018 / Last update: Apr 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.58
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 4.58
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7473.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.03 Å/pix.
= 395.52 Å
384 pix
1.03 Å/pix.
= 395.52 Å
384 pix
1.03 Å/pix.
= 395.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density
Contour Level:2.5 (by author), 4.58 (movie #1):
Minimum - Maximum-7.806808 - 12.466984999999999
Average (Standard dev.)-0.000000007713582 (1.0)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin0.00.00.0
Limit383.0383.0383.0
Spacing384384384
CellA=B=C: 395.52 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z395.520395.520395.520
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-7.80712.467-0.000

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Supplemental data

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Sample components

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Entire Human herpesvirus 1 strain KOS

EntireName: Human herpesvirus 1 strain KOS / Details: Cultured in Vero cells. / Number of components: 8

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Component #1: virus, Human herpesvirus 1 strain KOS

VirusName: Human herpesvirus 1 strain KOS / Class: VIRION / Details: Cultured in Vero cells. / Empty: No / Enveloped: Yes / Isolate: STRAIN
MassTheoretical: 200 MDa
SpeciesSpecies: Human herpesvirus 1 strain KOS
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: capsid / Diameter: 1300.0 Å / T number(triangulation number): 16

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Component #2: protein, major capsid protein (MCP, VP5)

ProteinName: major capsid protein (MCP, VP5) / Details: MCP forms the hexons and pentons of the capsid. / Recombinant expression: No
SourceSpecies: Human herpesvirus 1 strain KOS / Strain: KOS

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Component #3: protein, small capsid protein (SCP, VP26)

ProteinName: small capsid protein (SCP, VP26) / Details: SCP binds on top of the MCP in hexons. / Recombinant expression: No
SourceSpecies: Human herpesvirus 1 strain KOS / Strain: KOS

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Component #4: protein, capsid triplex subunit 1 (VP19C)

ProteinName: capsid triplex subunit 1 (VP19C)
Details: Complexed 1:2 with capsid triplex subunit 2 to form triplexes on the capsid shell.
Recombinant expression: No
SourceSpecies: Human herpesvirus 1 strain KOS / Strain: KOS

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Component #5: protein, capsid triplex subunit 2 (VP23)

ProteinName: capsid triplex subunit 2 (VP23)
Details: Complexed 2:1 with capsid triplex subunit 1 to form triplexes on the capsid shell.
Recombinant expression: No
SourceSpecies: Human herpesvirus 1 strain KOS / Strain: KOS

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Component #6: protein, tegument protein pUL17

ProteinName: tegument protein pUL17
Details: Component of the capsid-associated tegument complex (CATC). Each CATC contains one pUL17 subunit.
Recombinant expression: No
SourceSpecies: Human herpesvirus 1 strain KOS / Strain: KOS

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Component #7: protein, tegument protein pUL25

ProteinName: tegument protein pUL25
Details: Component of the capsid-associated tegument complex (CATC). Each CATC contains two pUL25 subunits.
Recombinant expression: No
SourceSpecies: Human herpesvirus 1 strain KOS / Strain: KOS

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Component #8: protein, tegument protein pUL36

ProteinName: tegument protein pUL36
Details: Component of the capsid-associated tegument complex (CATC). Each CATC contains two pUL36 subunits.
Recombinant expression: No
SourceSpecies: Human herpesvirus 1 strain KOS / Strain: KOS

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 298 K
Details: The sample was manually blotted and frozen with a homemade plunger..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 14000.0 X (nominal), 24271.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 79.0 - K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 7356 / Sampling size: 2.5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C5 (5 fold cyclic) / Number of projections: 545340
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Subparticles of the vertex region were boxed out from the virion images using method described in Ilca et al, Nat Commun 6, 8843 (2015). These subparticles were treated as single particles and refined locally with Relion.

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL

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