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- PDB-6z7n: The atomic structure of HAdV-F41 at pH 7.4 -

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Basic information

Entry
Database: PDB / ID: 6z7n
TitleThe atomic structure of HAdV-F41 at pH 7.4
Components
  • (Pre-hexon-linking protein ...) x 2
  • (Unknown) x 2
  • Core-capsid bridging protein
  • Fiber protein
  • Hexon protein
  • Hexon-interlacing protein
  • Penton protein
  • Pre-protein VI
KeywordsVIRUS / HAdV-F41 / virion / icosahedral
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / virion component / viral capsid ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / virion component / viral capsid / host cell / host cell cytoplasm / endocytosis involved in viral entry into host cell / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Adenovirus core-capsid bridging protein V / Adenovirus minor core protein PV / Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus Pll, hexon, subdomain 3 / Adenovirus hexon associated protein, protein VIII ...Adenovirus core-capsid bridging protein V / Adenovirus minor core protein PV / Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus Pll, hexon, subdomain 3 / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Hexon-interlacing protein / Core-capsid bridging protein / Hexon protein / Pre-hexon-linking protein VIII / Pre-protein VI / Hexon-interlacing protein / Pre-hexon-linking protein IIIa / Penton protein
Similarity search - Component
Biological speciesHuman adenovirus 41
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsCarlson, L.-A. / Rafie, K.
Funding support Sweden, 4items
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
DepositionMay 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
0: Pre-protein VI
1: Pre-protein VI
2: Pre-protein VI
3: Pre-protein VI
4: Pre-protein VI
5: Pre-protein VI
6: Pre-protein VI
7: Pre-protein VI
8: Pre-protein VI
9: Pre-protein VI
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Core-capsid bridging protein
O: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Pre-hexon-linking protein VIII
U: Pre-hexon-linking protein VIII
X: Fiber protein
W: Unknown
V: Unknown
Y: Unknown
Z: Unknown


Theoretical massNumber of molelcules
Total (without water)1,811,44836
Polymers1,811,44836
Non-polymers00
Water00
1
0: Pre-protein VI
1: Pre-protein VI
2: Pre-protein VI
3: Pre-protein VI
4: Pre-protein VI
5: Pre-protein VI
6: Pre-protein VI
7: Pre-protein VI
8: Pre-protein VI
9: Pre-protein VI
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Core-capsid bridging protein
O: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Pre-hexon-linking protein VIII
U: Pre-hexon-linking protein VIII
X: Fiber protein
W: Unknown
V: Unknown
Y: Unknown
Z: Unknown
x 60


Theoretical massNumber of molelcules
Total (without water)108,686,8522160
Polymers108,686,8522160
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation59

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Components

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Protein , 5 types, 28 molecules 0123456789ABCDEFGHIJKLMNPQRS

#1: Protein
Pre-protein VI / pVI


Mass: 29170.145 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: P16139
#2: Protein
Hexon protein / CP-H / Protein II


Mass: 104064.234 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: P11820
#3: Protein Penton protein / CP-P / Penton base protein / Protein III


Mass: 57142.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: Q9QAH8
#4: Protein Core-capsid bridging protein / Core protein V


Mass: 39843.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: B5SNS2
#6: Protein
Hexon-interlacing protein / Protein IX


Mass: 13617.179 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: B5SNR3, UniProt: P32539*PLUS

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Pre-hexon-linking protein ... , 2 types, 3 molecules OTU

#5: Protein Pre-hexon-linking protein IIIa / Capsid vertex-specific component IIIa / CVSC / Protein IIIa / pIIIa


Mass: 64825.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: Q67716
#7: Protein Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 25330.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: P11822

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Protein/peptide , 3 types, 5 molecules XWVZY

#8: Protein/peptide Fiber protein


Mass: 899.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: belongs to one of the two fibre proteins: P14267 or P16883
Source: (natural) Human adenovirus 41 / Cell line: A549
#9: Protein/peptide Unknown


Mass: 869.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549
#10: Protein/peptide Unknown


Mass: 528.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human adenovirus 41 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Human adenovirus 41
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 900 nm
Buffer solutionpH: 7.4
Details: PBS buffer made from comemrcial PBS tablets Medicargo, PBS tablets, 09-9400-100
SpecimenConc.: 4.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.03 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6929
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.18_3845: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4Gctf1.18CTF correctionicle CTF correction
7PHENIX1.18-3845model fitting
9RELION3.0-betainitial Euler assignment
10RELION3.0-betafinal Euler assignment
11RELION3.0-betaclassification
12RELION3.0-beta3D reconstruction
13PHENIX1.18-3845model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 25667
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19472 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5TX1

5tx1
PDB Unreleased entry


Accession code: 5TX1 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.77 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00696240
ELECTRON MICROSCOPYf_angle_d0.904131061
ELECTRON MICROSCOPYf_dihedral_angle_d12.82713005
ELECTRON MICROSCOPYf_chiral_restr0.07114007
ELECTRON MICROSCOPYf_plane_restr0.00617254

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