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- EMDB-7034: Improved cryoEM structure of human adenovirus type 5 with atomic ... -

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Entry
Database: EMDB / ID: 7034
TitleImproved cryoEM structure of human adenovirus type 5 with atomic details of minor proteins VI and VII
Map datahuman adenovirus type 5
SampleHuman adenovirus 5Adenoviridae:
virus / Hexon protein / Penton protein / (Pre-hexon-linking protein ...) x 2 / Hexon-interlacing protein / (Pre-protein VI) x 2 / Pre-histone-like nucleoprotein
Function / homologyHexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Adenoviral core protein VII / Minor capsid protein VI / Hexon-associated protein (IIIa) / Adenovirus penton base protein / Adenovirus hexon associated protein, protein VIII / Hexon, adenovirus major coat protein, N-terminal domain / Adenovirus hexon protein / Group II dsDNA virus coat/capsid protein ...Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Adenoviral core protein VII / Minor capsid protein VI / Hexon-associated protein (IIIa) / Adenovirus penton base protein / Adenovirus hexon associated protein, protein VIII / Hexon, adenovirus major coat protein, N-terminal domain / Adenovirus hexon protein / Group II dsDNA virus coat/capsid protein / Hexon coat protein, subdomain 4 / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, N-terminal / Adenoviral core protein VII / Minor capsid protein VI / Pre-hexon-linking protein IIIa / Adenovirus penton base protein / Pre-hexon-linking protein VIII / Hexon, adenovirus major coat protein, C-terminal domain / hexon binding / viral capsid, decoration / viral procapsid / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / virion / viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / viral entry into host cell / host cell cytoplasm / virion attachment to host cell / host cell nucleus / DNA binding / Hexon-interlacing protein / Hexon protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-hexon-linking protein VIII / Pre-protein VI / Pre-histone-like nucleoprotein
Function and homology information
SourceHuman adenovirus C serotype 5 / HAdV-5 (virus)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsDai XH / Wu L / Sun R / Zhou ZH
CitationJournal: J. Virol. / Year: 2017
Title: Atomic Structures of Minor Proteins VI and VII in the Human Adenovirus.
Authors: Xinghong Dai / Lily Wu / Ren Sun / Z Hong Zhou
Abstract: Human adenoviruses (Ad) are dsDNA viruses associated with infectious diseases, yet better known as tools for gene delivery and oncolytic anti-cancer therapy. Atomic structures of Ad provide the basis ...Human adenoviruses (Ad) are dsDNA viruses associated with infectious diseases, yet better known as tools for gene delivery and oncolytic anti-cancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts towards more effective applications. Since 2010, atomic models of human Ad5 have been independently derived from photographic film cryoEM and X-ray crystallography, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII and IX. To clarify these discrepancies, here we have employed the technology of direct electron-counting to obtain a cryoEM structure of human Ad5 at 3.2 Å resolution. Our improved structure unambiguously confirmed our previous cryoEM models of proteins IIIa, VIII and IX and explained the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavities of hexons - the cleaved N-terminus of precursor protein VI (pVIn), the cleaved N-terminus of precursor protein VII (pVIIn2), and mature protein VI. The binding of pVIIn2--by extension that of genome-condensing pVII--to hexons is consistent with the previously proposed dsDNA genome-capsid co-assembly for adenoviruses, which resembles that of ssRNA viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid, as exemplified by tailed bacteriophages and herpesviruses. Adenovirus is a double-edged sword to humans - as a widespread pathogen and a bioengineering tool for anti-cancer and gene therapy. Atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models from conventional/film cryoEM and X-ray crystallography for important cement proteins IIIa, VIII, and IX have caused confusion. Using the cutting-edge cryoEM technology with electron counting, we improved the structure of human adenovirus type 5 and confirmed our previous models of cement proteins IIIa, VIII, and IX, thus clarifying the inconsistent structures. The improved structure also reveals atomic details of membrane-lytic protein VI and genome-condensing protein VII and supports the previously proposed genome-capsid co-assembly mechanism for adenoviruses.
Validation ReportPDB-ID: 6b1t

SummaryFull reportAbout validation report
DateDeposition: Sep 18, 2017 / Header (metadata) release: Sep 27, 2017 / Map release: Sep 27, 2017 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6b1t
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6b1t
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7034.map.gz (map file in CCP4 format, 8388609 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1280 pix
0.85 Å/pix.
= 1088. Å
1280 pix
0.85 Å/pix.
= 1088. Å
1280 pix
0.85 Å/pix.
= 1088. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density
Contour Level:3.0 (by author), 3 (movie #1):
Minimum - Maximum-11.581982 - 16.747876999999999
Average (Standard dev.)0.004020501 (0.87556183)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128012801280
Origin-640.-640.-640.
Limit639.639.639.
Spacing128012801280
CellA=B=C: 1088.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z128012801280
origin x/y/z0.0000.0000.000
length x/y/z1088.0001088.0001088.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-640-640-640
NC/NR/NS128012801280
D min/max/mean-11.58216.7480.004

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Supplemental data

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Sample components

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Entire Human adenovirus 5

EntireName: Human adenovirus 5 / Details: Cultured in HEK293T cells and purified from media / Number of components: 9

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Component #1: virus, Human adenovirus C serotype 5

VirusName: Human adenovirus C serotype 5 / Class: VIRION / Details: Cultured in HEK293T cells and purified from media / Empty: No / Enveloped: No / Isolate: STRAIN
MassTheoretical: 150 MDa
SpeciesSpecies: Human adenovirus C serotype 5
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: capsid / Diameter: 900.0 Å / T number(triangulation number): 25

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Component #2: protein, Hexon protein

ProteinName: Hexon protein / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 108.107617 kDa
SourceSpecies: HAdV-5 (virus)

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Component #3: protein, Penton protein

ProteinName: Penton protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 63.356602 kDa
SourceSpecies: HAdV-5 (virus)

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Component #4: protein, Pre-hexon-linking protein IIIa

ProteinName: Pre-hexon-linking protein IIIa / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.322805 kDa
SourceSpecies: HAdV-5 (virus)

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Component #5: protein, Pre-hexon-linking protein VIII

ProteinName: Pre-hexon-linking protein VIII / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.71059 kDa
SourceSpecies: HAdV-5 (virus)

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Component #6: protein, Hexon-interlacing protein

ProteinName: Hexon-interlacing protein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 14.468134 kDa
SourceSpecies: HAdV-5 (virus)

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Component #7: protein, Pre-protein VI

ProteinName: Pre-protein VI / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 3.584953 kDa
SourceSpecies: HAdV-5 (virus)

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Component #8: protein, Pre-histone-like nucleoprotein

ProteinName: Pre-histone-like nucleoprotein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.198438 kDa
SourceSpecies: HAdV-5 (virus)

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Component #9: protein, Pre-protein VI

ProteinName: Pre-protein VI / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.460559 kDa
SourceSpecies: HAdV-5 (virus)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 %

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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: 81000. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 nm / Energy filter: Gatan Image Filter / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80.0 - K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5608 / Sampling size: 2.5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 53000
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Output model

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