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- PDB-7tau: Refined capsid structure of human adenovirus D26 at 3.4 A resolution -

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Basic information

Entry
Database: PDB / ID: 7tau
TitleRefined capsid structure of human adenovirus D26 at 3.4 A resolution
Components
  • Fiber
  • Hexon protein
  • PIX
  • PVIII
  • Penton protein
  • Pre-hexon-linking protein IIIa
  • Pre-protein VI
  • Unknown fragment
KeywordsVIRUS / Human Adenovirus D26 HAdV-D26 Ad26 Hexon Penton base IX
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 / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / viral release from host cell / host cell / endocytosis involved in viral entry into host cell ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / viral release from host cell / host cell / endocytosis involved in viral entry into host cell / viral capsid / host cell cytoplasm / cell adhesion / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Adenovirus Pll, hexon, subdomain 3 / 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 / Adenovirus Pll, hexon, subdomain 2 / Minor capsid protein VI ...Adenovirus Pll, hexon, subdomain 3 / 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 / Adenovirus Pll, hexon, subdomain 2 / 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 / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
Hexon-interlacing protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-protein VI / Pre-hexon-linking protein VIII / Fiber / Hexon protein
Similarity search - Component
Biological speciesHuman adenovirus 26
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsReddy, V.S. / Yu, X. / Barry, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI146644 United States
Citation
Journal: Viruses / Year: 2022
Title: Refined Capsid Structure of Human Adenovirus D26 at 3.4 Å Resolution.
Authors: Vijay S Reddy / Xiaodi Yu / Michael A Barry /
Abstract: Various adenoviruses are being used as viral vectors for the generation of vaccines against chronic and emerging diseases (e.g., AIDS, COVID-19). Here, we report the improved capsid structure for one ...Various adenoviruses are being used as viral vectors for the generation of vaccines against chronic and emerging diseases (e.g., AIDS, COVID-19). Here, we report the improved capsid structure for one of these vectors, human adenovirus D26 (HAdV-D26), at 3.4 Å resolution, by reprocessing the previous cryo-electron microscopy dataset and obtaining a refined model. In addition to overall improvements in the model, the highlights of the structure include (1) locating a segment of the processed peptide of VIII that was previously believed to be released from the mature virions, (2) reorientation of the helical appendage domain (APD) of IIIa situated underneath the vertex region relative to its counterpart observed in the cleavage defective () mutant of HAdV-C5 that resulted in the loss of interactions between the APD and hexon bases, and (3) the revised conformation of the cleaved N-terminal segments of pre-protein VI (pVIn), located in the hexon cavities, is highly conserved, with notable stacking interactions between the conserved His13 and Phe18 residues. Taken together, the improved model of HAdV-D26 capsid provides a better understanding of protein-protein interactions in HAdV capsids and facilitates the efforts to modify and/or design adenoviral vectors with altered properties. Last but not least, we provide some insights into clotting factors (e.g., FX and PF4) binding to AdV vectors.
#1: Journal: Sci Adv / Year: 2017
Title: Cryo-EM structure of human adenovirus D26 reveals the conservation of structural organization among human adenoviruses.
Authors: Xiaodi Yu / David Veesler / Melody G Campbell / Mary E Barry / Francisco J Asturias / Michael A Barry / Vijay S Reddy /
Abstract: Human adenoviruses (HAdVs) cause acute respiratory, ocular, and gastroenteric diseases and are also frequently used as gene and vaccine delivery vectors. Unlike the archetype human adenovirus C5 ...Human adenoviruses (HAdVs) cause acute respiratory, ocular, and gastroenteric diseases and are also frequently used as gene and vaccine delivery vectors. Unlike the archetype human adenovirus C5 (HAdV-C5), human adenovirus D26 (HAdV-D26) belongs to species-D HAdVs, which target different cellular receptors, and is differentially recognized by immune surveillance mechanisms. HAdV-D26 is being championed as a lower seroprevalent vaccine and oncolytic vector in preclinical and human clinical studies. To understand the molecular basis for their distinct biological properties and independently validate the structures of minor proteins, we determined the first structure of species-D HAdV at 3.7 Å resolution by cryo-electron microscopy. All the hexon hypervariable regions (HVRs), including HVR1, have been identified and exhibit a distinct organization compared to those of HAdV-C5. Despite the differences in the arrangement of helices in the coiled-coil structures, protein IX molecules form a continuous hexagonal network on the capsid exterior. In addition to the structurally conserved region (3 to 300) of IIIa, we identified an extra helical domain comprising residues 314 to 390 that further stabilizes the vertex region. Multiple (two to three) copies of the cleaved amino-terminal fragment of protein VI (pVIn) are observed in each hexon cavity, suggesting that there could be ≥480 copies of VI present in HAdV-D26. In addition, a localized asymmetric reconstruction of the vertex region provides new details of the three-pronged "claw hold" of the trimeric fiber and its interactions with the penton base. These observations resolve the previous conflicting assignments of the minor proteins and suggest the likely conservation of their organization across different HAdVs.
History
DepositionDec 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-25786
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  • Superimposition on EM map
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Structure viewerMolecule:
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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
N: Penton protein
O: Fiber
M: Pre-hexon-linking protein IIIa
P: PIX
Q: PIX
R: PIX
S: PIX
U: PVIII
V: PVIII
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
X: Unknown fragment


Theoretical massNumber of molelcules
Total (without water)1,784,19131
Polymers1,784,19131
Non-polymers00
Water0
1
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
N: Penton protein
O: Fiber
M: Pre-hexon-linking protein IIIa
P: PIX
Q: PIX
R: PIX
S: PIX
U: PVIII
V: PVIII
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
X: Unknown fragment
x 60


Theoretical massNumber of molelcules
Total (without water)107,051,4511860
Polymers107,051,4511860
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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
N: Penton protein
O: Fiber
M: Pre-hexon-linking protein IIIa
P: PIX
Q: PIX
R: PIX
S: PIX
U: PVIII
V: PVIII
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
X: Unknown fragment
x 5


  • icosahedral pentamer
  • 8.92 MDa, 155 polymers
Theoretical massNumber of molelcules
Total (without water)8,920,954155
Polymers8,920,954155
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
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
N: Penton protein
O: Fiber
M: Pre-hexon-linking protein IIIa
P: PIX
Q: PIX
R: PIX
S: PIX
U: PVIII
V: PVIII
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
X: Unknown fragment
x 6


  • icosahedral 23 hexamer
  • 10.7 MDa, 186 polymers
Theoretical massNumber of molelcules
Total (without water)10,705,145186
Polymers10,705,145186
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 7 types, 30 molecules ABCDEFGHIJKLNOMPQRSUV123456789

#1: Protein
Hexon protein / / CP-H / Protein II


Mass: 107218.703 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: Q3S8B3
#2: Protein Penton protein / / CP-P / Penton base protein / Protein III


Mass: 58647.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKL2
#3: Protein Fiber /


Mass: 41039.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKM1
#4: Protein Pre-hexon-linking protein IIIa / Capsid vertex-specific component IIIa / CVSC / Protein IIIa / pIIIa


Mass: 62201.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKL1
#5: Protein
PIX / Protein IX


Mass: 13800.377 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKK7
#6: Protein PVIII / Protein VIII


Mass: 24633.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKM0
#7: Protein
Pre-protein VI / pVI


Mass: 25546.086 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKL5

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Protein/peptide , 1 types, 1 molecules X

#8: Protein/peptide Unknown fragment


Mass: 1294.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26

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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 26Adenoviridae / Type: TISSUE / Details: Adenovirus / Entity ID: all / Source: NATURAL
Source (natural)Organism: Human adenovirus 26
Buffer solutionpH: 8.1 / Details: 40 mM Tris pH 8.1 300 mM NaCl 10 mM CaCl2
Buffer componentConc.: 40 mM / Name: Tris / Formula: Tris
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Gradient purified virus
Specimen supportGrid material: COPPER / Grid type: C-flat-1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K / Details: Blot for 3 seconds before plunging

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 53 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2000
Image scansMovie frames/image: 38

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9cisTEMinitial Euler assignment
11cisTEMclassification
12cisTEM3D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 37026
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30834 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 150 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 5TX1

5tx1


Accession code: 5TX1 / Source name: PDB / Type: experimental model

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