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- EMDB-6386: The capsid of Human Herpes Simplex Virus Type 1 imaged inside int... -

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Basic information

Entry
Database: EMDB / ID: EMD-6386
TitleThe capsid of Human Herpes Simplex Virus Type 1 imaged inside intact virions
Map dataReconstruction of herpes simplex type 1 capsids imaged inside intact virions
Sample
  • Sample: Capsid of human herpes simplex type 1 imaged in intact virions
  • Virus: Human herpes simplex virus type 1 (Herpes simplex virus type 1)
KeywordsHuman herpesvirus / HSV-1 / capsid / virion / VP5 / triplex
Biological speciesHuman herpes simplex virus type 1 (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsHuet A / Makhov AM / Huffman JB / Vos M / Homa FL / Conway JF
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Extensive subunit contacts underpin herpesvirus capsid stability and interior-to-exterior allostery.
Authors: Alexis Huet / Alexander M Makhov / Jamie B Huffman / Matthijn Vos / Fred L Homa / James F Conway /
Abstract: The herpesvirus capsid is a complex protein assembly that includes hundreds of copies of four major subunits and lesser numbers of several minor proteins, all of which are essential for infectivity. ...The herpesvirus capsid is a complex protein assembly that includes hundreds of copies of four major subunits and lesser numbers of several minor proteins, all of which are essential for infectivity. Cryo-electron microscopy is uniquely suited for studying interactions that govern the assembly and function of such large functional complexes. Here we report two high-quality capsid structures, from human herpes simplex virus type 1 (HSV-1) and the animal pseudorabies virus (PRV), imaged inside intact virions at ~7-Å resolution. From these, we developed a complete model of subunit and domain organization and identified extensive networks of subunit contacts that underpin capsid stability and form a pathway that may signal the completion of DNA packaging from the capsid interior to outer surface, thereby initiating nuclear egress. Differences in the folding and orientation of subunit domains between herpesvirus capsids suggest that common elements have been modified for specific functions.
History
DepositionJul 17, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseApr 20, 2016-
UpdateApr 20, 2016-
Current statusApr 20, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4000
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6386.tif

emd_6386_1.tif

Downloads & links

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Map

FileDownload / File: emd_6386.map.gz / Format: CCP4 / Size: 782.7 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationReconstruction of herpes simplex type 1 capsids imaged inside intact virions
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.16 Å/pix.
x 749 pix.
= 1617.84 Å		2.16 Å/pix.
x 749 pix.
= 1617.84 Å		2.16 Å/pix.
x 749 pix.
= 1617.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4000.0 / Movie #1: 4000
Minimum - Maximum-16735.0 - 32443.0
Average (Standard dev.)265.372436520000008 (±2403.2573242200001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions749749749
Spacing749749749
CellA=B=C: 1617.8401 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z2.162.162.16
M x/y/z749749749
origin x/y/z0.0000.0000.000
length x/y/z1617.8401617.8401617.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ454586
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS749749749
D min/max/mean-16735.00032443.000265.372

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Supplemental data

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Sample components

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Entire : Capsid of human herpes simplex type 1 imaged in intact virions

EntireName: Capsid of human herpes simplex type 1 imaged in intact virions
Components
  • Sample: Capsid of human herpes simplex type 1 imaged in intact virions
  • Virus: Human herpes simplex virus type 1 (Herpes simplex virus type 1)

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Supramolecule #1000: Capsid of human herpes simplex type 1 imaged in intact virions

SupramoleculeName: Capsid of human herpes simplex type 1 imaged in intact virions
type: sample / ID: 1000 / Oligomeric state: Icosahedral T=16 / Number unique components: 1
Molecular weightExperimental: 200 MDa / Theoretical: 200 MDa

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Supramolecule #1: Human herpes simplex virus type 1

SupramoleculeName: Human herpes simplex virus type 1 / type: virus / ID: 1 / Details: Native KOS virions / Sci species name: Human herpes simplex virus type 1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Host systemOrganism: Chlorocebus aethiops (grivet) / Recombinant cell: green monkey kidney (Vero) cells
Molecular weightExperimental: 200 MDa / Theoretical: 200 MDa
Virus shellShell ID: 1 / Diameter: 1250 Å / T number (triangulation number): 16

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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

GridDetails: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: 6 second blot

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 75,000x magnification.
DetailsNanoprobe
DateJun 12, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 49999 / Average electron dose: 30 e/Å2 / Details: 2 second exposures; no use of movie mode
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsManual selection, processing with AUTO3DEM
CTF correctionDetails: By micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: OTHER / Software - Name: AUTO3DEM, CTFFIND3
Details: Final map calculated from 25637 images of capsids inside virions. Resolution was verified by comparing cryoEM data with band-limited renditions of the HSV VP5 upper domain fragment, PDB 1NO7.
Number images used: 25637

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Atomic model buiding 1

Initial modelPDB ID:

1no7


Chain - Chain ID: A
SoftwareName: Chimera
DetailsManual docking
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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