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- EMDB-2550: Four levels of hierarchical organization including non-covalent c... -

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Basic information

Entry
Database: EMDB / ID: EMD-2550
TitleFour levels of hierarchical organization including non-covalent chainmail brace the mature tumor herpesvirus capsid against pressurization
Map dataCapsid reconstruction of the rhesus monkey rhadinovirus
Sample
  • Sample: Rhesus monkey rhadinovirus capsid
  • Virus: Macaca mulatta rhadinovirus
Keywordsgammaherpesvirus / virus / Rhesus monkey rhadinovirus / non-covalent chainmail
Biological speciesMacaca mulatta rhadinovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsZhou ZH / Hui W / Shah S / Jih J / O'Connor C / Sherman M / Kedes D / Schein S
CitationJournal: Structure / Year: 2014
Title: Four levels of hierarchical organization, including noncovalent chainmail, brace the mature tumor herpesvirus capsid against pressurization.
Authors: Z Hong Zhou / Wong Hoi Hui / Sanket Shah / Jonathan Jih / Christine M O'Connor / Michael B Sherman / Dean H Kedes / Stan Schein /
Abstract: Like many double-stranded DNA viruses, tumor gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus withstand high internal pressure. Bacteriophage HK97 uses covalent ...Like many double-stranded DNA viruses, tumor gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus withstand high internal pressure. Bacteriophage HK97 uses covalent chainmail for this purpose, but how this is achieved noncovalently in the much larger gammaherpesvirus capsid is unknown. Our cryoelectron microscopy structure of a gammaherpesvirus capsid reveals a hierarchy of four levels of organization: (1) Within a hexon capsomer, each monomer of the major capsid protein (MCP), 1,378 amino acids and six domains, interacts with its neighboring MCPs at four sites. (2) Neighboring capsomers are linked in pairs by MCP dimerization domains and in groups of three by heterotrimeric triplex proteins. (3) Small (∼280 amino acids) HK97-like domains in MCP monomers alternate with triplex heterotrimers to form a belt that encircles each capsomer. (4) One hundred sixty-two belts concatenate to form noncovalent chainmail. The triplex heterotrimer orchestrates all four levels and likely drives maturation to an angular capsid that can withstand pressurization.
History
DepositionJan 3, 2014-
Header (metadata) releaseFeb 5, 2014-
Map releaseOct 1, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing 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
  • Download
  • Surface view colored by radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_2550.map.gz / Format: CCP4 / Size: 953.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCapsid reconstruction of the rhesus monkey rhadinovirus
Voxel sizeX=Y=Z: 2.04 Å
Density
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-13.98461056 - 21.426439290000001
Average (Standard dev.)0.05623335 (±1.50696075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00400
Dimensions800800400
Spacing800800400
CellA: 1632.0 Å / B: 1632.0 Å / C: 816.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.042.042.04
M x/y/z800800400
origin x/y/z0.0000.0000.000
length x/y/z1632.0001632.000816.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-207-207-206
NX/NY/NZ414414414
MAP C/R/S123
start NC/NR/NS00400
NC/NR/NS800800400
D min/max/mean-13.98521.4260.056

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Supplemental data

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Sample components

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Entire : Rhesus monkey rhadinovirus capsid

EntireName: Rhesus monkey rhadinovirus capsid
Components
  • Sample: Rhesus monkey rhadinovirus capsid
  • Virus: Macaca mulatta rhadinovirus

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Supramolecule #1000: Rhesus monkey rhadinovirus capsid

SupramoleculeName: Rhesus monkey rhadinovirus capsid / type: sample / ID: 1000 / Details: The capsid has T=16 icosahedral symmetry. / Oligomeric state: icosahedral viral capsid / Number unique components: 1
Molecular weightTheoretical: 198.4 MDa / Method: theoreomatic estimation

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Supramolecule #1: Macaca mulatta rhadinovirus

SupramoleculeName: Macaca mulatta rhadinovirus / type: virus / ID: 1 / NCBI-ID: 703611 / Sci species name: Macaca mulatta rhadinovirus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Macaca mulatta (Rhesus monkey) / synonym: VERTEBRATES
Molecular weightExperimental: 198.4 MDa / Theoretical: 198.4 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 1300 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

Concentration1 mg/mL
BufferpH: 8 / Details: 20mM Tris HCl at pH 8.0, 250 mM NaCl and 1 mM EDTA
GridDetails: Quantifoil R2/1 grid
VitrificationCryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: Blot manually for about 1 second before plunging.

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 33000
Sample stageSpecimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 80 K / Max: 100 K / Average: 90 K
DateAug 30, 2004
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 320 / Average electron dose: 10 e/Å2 / Bits/pixel: 14
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: OTHER / Software - Name: IMIRS / Number images used: 14374
DetailsData processing and 3D reconstruction were carried out in Microsoft Windows XP-based HP workstations with the IMIRS package

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Atomic model buiding 1

Initial modelPDB ID:

Chain - Chain ID: A
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: fit in map function from Chimera

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