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- EMDB-11112: The atomic structure of the HAdVF-41 penton base in solution -

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Basic information

Entry
Database: EMDB / ID: EMD-11112
TitleThe atomic structure of the HAdVF-41 penton base in solution
Map data3D reconstruction of a recombinantely expressed human Adenovirus 41 penton base.
Sample
  • Virus: Human adenovirus 41
    • Protein or peptide: Penton protein
KeywordsHAdVF-41 / penton base / pentamer / VIRAL PROTEIN
Function / homologyAdenovirus penton base protein / Adenovirus penton base protein / T=25 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / Penton protein
Function and homology information
Biological speciesHuman adenovirus F serotype 41 / Human adenovirus 41
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsCarlson L-A / Rafie K
Funding support Sweden, 4 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)CDA00047/2017-C Sweden
Swedish Research CouncilDnr 2019-01472 Sweden
Swedish Research CouncilDnr 2017-00859 Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Sci Adv / Year: 2021
Title: The structure of enteric human adenovirus 41-A leading cause of diarrhea in children.
Authors: K Rafie / A Lenman / J Fuchs / A Rajan / N Arnberg / L-A Carlson /
Abstract: Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ notably in tissue tropism and ...Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ notably in tissue tropism and pathogenicity from respiratory and ocular adenoviruses, but the structural basis for this divergence has been unknown. Here, we present the first structure of an enteric HAdV-HAdV-F41-determined by cryo-electron microscopy to a resolution of 3.8 Å. The structure reveals extensive alterations to the virion exterior as compared to nonenteric HAdVs, including a unique arrangement of capsid protein IX. The structure also provides new insights into conserved aspects of HAdV architecture such as a proposed location of core protein V, which links the viral DNA to the capsid, and assembly-induced conformational changes in the penton base protein. Our findings provide the structural basis for adaptation of enteric HAdVs to a fundamentally different tissue tropism.
History
DepositionJun 1, 2020-
Header (metadata) releaseNov 25, 2020-
Map releaseNov 25, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z7q
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11112.png

Downloads & links

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Map

FileDownload / File: emd_11112.map.gz / Format: CCP4 / Size: 19.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of a recombinantely expressed human Adenovirus 41 penton base.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.04 Å/pix.
x 172 pix.
= 179.052 Å		1.04 Å/pix.
x 172 pix.
= 179.052 Å		1.04 Å/pix.
x 172 pix.
= 179.052 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.041 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-10.825011999999999 - 16.640995
Average (Standard dev.)0.0026715219 (±0.9745105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions172172172
Spacing172172172
CellA=B=C: 179.052 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0411.0411.041
M x/y/z172172172
origin x/y/z0.0000.0000.000
length x/y/z179.052179.052179.052
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ172172172
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS172172172
D min/max/mean-10.82516.6410.003

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Supplemental data

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Half map: Half Map 1

Fileemd_11112_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_11112_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human adenovirus 41

EntireName: Human adenovirus 41
Components
  • Virus: Human adenovirus 41
    • Protein or peptide: Penton protein

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Supramolecule #1: Human adenovirus 41

SupramoleculeName: Human adenovirus 41 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The HAdVF-41 penton base was recombinantely expressed in Sf9 cells.
NCBI-ID: 10524 / Sci species name: Human adenovirus 41 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 285 KDa

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Macromolecule #1: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus F serotype 41
Molecular weightTheoretical: 57.14216 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRRAVGVPPV MAYAEGPPPS YESVMGSADS PATLEALYVP PRYLGPTEGR NSIRYSELAP LYDTTRVYLV DNKSADIASL NYQNDHSNF QTTVVQNNDF TPAEAGTQTI NFDERSRWGA DLKTILRTNM PNINEFMSTN KFKARLMVEK KNKETGLPRY E WFEFTLPE ...String:
MRRAVGVPPV MAYAEGPPPS YESVMGSADS PATLEALYVP PRYLGPTEGR NSIRYSELAP LYDTTRVYLV DNKSADIASL NYQNDHSNF QTTVVQNNDF TPAEAGTQTI NFDERSRWGA DLKTILRTNM PNINEFMSTN KFKARLMVEK KNKETGLPRY E WFEFTLPE GNYSETMTID LMNNAIVDNY LEVGRQNGVL ESDIGVKFDT RNFRLGWDPV TKLVMPGVYT NEAFHPDIVL LP GCGVDFT QSRLSNLLGI RKRLPFQEGF QIMYEDLEGG NIPALLDVAK YEASIQKAKE EGKEIGDDTF ATRPQDLVIE PVA KDSKNR SYNLLPNDQN NTAYRSWFLA YNYGDPKKGV QSWTLLTTAD VTCGSQQVYW SLPDMMQDPV TFRPSTQVSN YPVV GVELL PVHAKSFYNE QAVYSQLIRQ STALTHVFNR FPENQILVRP PAPTITTVSE NVPALTDHGT LPLRSSISGV QRVTI TDAR RRTCPYVHKA LGIVAPKVLS SRTF

UniProtKB: Penton protein

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was monodisperse with a preferred orientation in the vitrious ice.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsData were collected at a 30 degree tilt of the specimen stage due to a preferred orientation of the sample in the vitrified ice.
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 948 / Average electron dose: 0.93 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
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: 198491
Startup modelType of model: OTHER
Details: An initial dataset of the HAdV-F41 penton base collected at no tilt of the specimen stage was used to generate a low-resolution input model.
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1-beta) / Number images used: 107110
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1-beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1-beta)
Final 3D classificationSoftware - Name: RELION (ver. 3.1-beta)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6z7q:
The atomic structure of the HAdVF-41 penton base in solution

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