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- PDB-6yba: HAdV-F41 Capsid -

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Basic information

Entry
Database: PDB / ID: 6yba
TitleHAdV-F41 Capsid
Components
  • (Pre-hexon-linking protein ...) x 2
  • Hexon protein
  • Hexon-interlacing protein
  • Penton protein
  • Pre-histone-like nucleoprotein
  • Pre-protein VI
KeywordsVIRUS / Adenovirus
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 / endocytosis involved in viral entry into host cell / viral penetration into host nucleus ...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 / endocytosis involved in viral entry into host cell / viral penetration into host nucleus / viral capsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / DNA binding
Similarity search - Function
Adenoviral core protein VII / Adenoviral core protein VII / : / Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII ...Adenoviral core protein VII / Adenoviral core protein VII / : / Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / 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 / 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 protein / Hexon-interlacing protein / Pre-histone-like nucleoprotein / Pre-protein VI / Pre-hexon-linking protein VIII / Pre-hexon-linking protein IIIa / Penton protein
Similarity search - Component
Biological speciesHuman adenovirus F serotype 41
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsPerez Illana, M. / Martinez, M. / Mangroo, C. / Brown, M. / Marabini, R. / San Martin, C.
Funding support Spain, European Union, 3items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU-2016-74868P Spain
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-76400-R Spain
European Commissioninext-1750European Union
CitationJournal: Sci Adv / Year: 2021
Title: Cryo-EM structure of enteric adenovirus HAdV-F41 highlights structural variations among human adenoviruses.
Authors: Marta Pérez-Illana / Marta Martínez / Gabriela N Condezo / Mercedes Hernando-Pérez / Casandra Mangroo / Martha Brown / Roberto Marabini / Carmen San Martín /
Abstract: Enteric adenoviruses, one of the main causes of viral gastroenteritis in the world, must withstand the harsh conditions found in the gut. This requirement suggests that capsid stability must be ...Enteric adenoviruses, one of the main causes of viral gastroenteritis in the world, must withstand the harsh conditions found in the gut. This requirement suggests that capsid stability must be different from that of other adenoviruses. We report the 4-Å-resolution structure of a human enteric adenovirus, HAdV-F41, and compare it with that of other adenoviruses with respiratory (HAdV-C5) and ocular (HAdV-D26) tropisms. While the overall structures of hexon, penton base, and internal minor coat proteins IIIa and VIII are conserved, we observe partially ordered elements reinforcing the vertex region, which suggests their role in enhancing the physicochemical capsid stability of HAdV-F41. Unexpectedly, we find an organization of the external minor coat protein IX different from all previously characterized human and nonhuman mastadenoviruses. Knowledge of the structure of enteric adenoviruses provides a starting point for the design of vectors suitable for oral delivery or intestinal targeting.
History
DepositionMar 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
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: Pre-hexon-linking protein IIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Hexon-interlacing protein
U: Pre-protein VI
V: Pre-protein VI
W: Pre-histone-like nucleoprotein
Y: Pre-protein VI
u: Pre-protein VI
w: Pre-histone-like nucleoprotein


Theoretical massNumber of molelcules
Total (without water)1,633,37726
Polymers1,633,37726
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area278800 Å2
ΔGint-1441 kcal/mol
Surface area384280 Å2
MethodPISA

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Components

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Protein , 5 types, 23 molecules ABCDEFGHIJKLMQRSTUVYuWw

#1: 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 F serotype 41 / References: UniProt: B2ZX09
#2: 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 F serotype 41 / References: UniProt: Q9QAH8
#5: 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 F serotype 41 / References: UniProt: B5SNR3
#6: Protein
Pre-protein VI / pVI


Mass: 29170.145 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Human adenovirus F serotype 41 / References: UniProt: B5SNS4
#7: Protein Pre-histone-like nucleoprotein / Pre-core protein VII / pVII


Mass: 20386.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human adenovirus F serotype 41 / References: UniProt: B5SNS1

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

#3: 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 F serotype 41 / References: UniProt: Q67716
#4: Protein Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 25358.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human adenovirus F serotype 41 / References: UniProt: B5SNS9

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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
Source (natural)Organism: Human adenovirus 41
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 840 nm
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy
Image recordingElectron dose: 42 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9926 / Symmetry type: POINT

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