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- PDB-7rd1: The Capsid Structure of the ChAdOx1 viral vector/chimpanzee adeno... -

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Basic information

Entry
Database: PDB / ID: 7rd1
TitleThe Capsid Structure of the ChAdOx1 viral vector/chimpanzee adenovirus Y25
Components
  • (Pre-hexon-linking protein ...) x 2
  • Hexon protein
  • Hexon-interlacing protein
  • Penton protein
  • Pre-protein VI
KeywordsVIRUS / Adenovirus / simian adenovirus / chimpanzee adenovirus / vaccine vector / DNA virus / AdV / ChAdV-Y25 / adenovirus Y25 / Y25 / viral vector / ChAdOx1 / chimp Ad / dsDNA virus / icosahedral / chimpanzee adenovirus Y25 / Y-25 / Y 25 / ChAdV
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 / viral release from host cell / endocytosis involved in viral entry into host cell / viral capsid / host cell cytoplasm ...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 / viral release from host cell / endocytosis involved in viral entry into host cell / viral capsid / host cell cytoplasm / 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 / Minor capsid protein VI / 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 / 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-interlacing protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-protein VI / Hexon protein / Pre-hexon-linking protein VIII
Similarity search - Component
Biological speciesChimpanzee adenovirus Y25
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsBaker, A.T. / Boyd, R.J. / Sarkar, D. / Vermaas, J.V. / Williams, D. / Singharoy, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1531991 United States
Citation
Journal: Sci Adv / Year: 2021
Title: ChAdOx1 interacts with CAR and PF4 with implications for thrombosis with thrombocytopenia syndrome.
Authors: Alexander T Baker / Ryan J Boyd / Daipayan Sarkar / Alicia Teijeira-Crespo / Chun Kit Chan / Emily Bates / Kasim Waraich / John Vant / Eric Wilson / Chloe D Truong / Magdalena Lipka-Lloyd / ...Authors: Alexander T Baker / Ryan J Boyd / Daipayan Sarkar / Alicia Teijeira-Crespo / Chun Kit Chan / Emily Bates / Kasim Waraich / John Vant / Eric Wilson / Chloe D Truong / Magdalena Lipka-Lloyd / Petra Fromme / Josh Vermaas / Dewight Williams / LeeAnn Machiesky / Meike Heurich / Bolni M Nagalo / Lynda Coughlan / Scott Umlauf / Po-Lin Chiu / Pierre J Rizkallah / Taylor S Cohen / Alan L Parker / Abhishek Singharoy / Mitesh J Borad /
Abstract: Vaccines derived from chimpanzee adenovirus Y25 (ChAdOx1), human adenovirus type 26 (HAdV-D26), and human adenovirus type 5 (HAdV-C5) are critical in combatting the severe acute respiratory ...Vaccines derived from chimpanzee adenovirus Y25 (ChAdOx1), human adenovirus type 26 (HAdV-D26), and human adenovirus type 5 (HAdV-C5) are critical in combatting the severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic. As part of the largest vaccination campaign in history, ultrarare side effects not seen in phase 3 trials, including thrombosis with thrombocytopenia syndrome (TTS), a rare condition resembling heparin-induced thrombocytopenia (HIT), have been observed. This study demonstrates that all three adenoviruses deployed as vaccination vectors versus SARS-CoV-2 bind to platelet factor 4 (PF4), a protein implicated in the pathogenesis of HIT. We have determined the structure of the ChAdOx1 viral vector and used it in state-of-the-art computational simulations to demonstrate an electrostatic interaction mechanism with PF4, which was confirmed experimentally by surface plasmon resonance. These data confirm that PF4 is capable of forming stable complexes with clinically relevant adenoviruses, an important step in unraveling the mechanisms underlying TTS.
#1: Journal: Biorxiv / Year: 2021
Title: The Structure of ChAdOx1/AZD-1222 Reveals Interactions with CAR and PF4 with Implications for Vaccine-induced Immune Thrombotic Thrombocytopenia
Authors: Baker, A.T. / Boyd, R.J. / Sarkar, D. / Vant, J. / Crespo, A.T. / Waraich, K. / Truong, C.D. / Bates, E. / Wilson, E. / Chan, C.K. / Lipka-Lloyd, M. / Fromme, P. / Nagalo, M.B. / Heurich, M. ...Authors: Baker, A.T. / Boyd, R.J. / Sarkar, D. / Vant, J. / Crespo, A.T. / Waraich, K. / Truong, C.D. / Bates, E. / Wilson, E. / Chan, C.K. / Lipka-Lloyd, M. / Fromme, P. / Nagalo, M.B. / Heurich, M. / Williams, D. / Chiu, P.L. / Rizkallah, P.J. / Parker, A.L. / Singharoy, A. / Borad, M.J.
History
DepositionJul 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release

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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
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
0: Pre-protein VI
U: Pre-protein VI
1: Pre-protein VI
V: Pre-protein VI
2: Pre-protein VI
W: Pre-protein VI
3: Pre-protein VI
X: Pre-protein VI
4: Pre-protein VI
Y: Pre-protein VI
8: Pre-protein VI
Z: 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: Hexon-interlacing protein
O: Hexon-interlacing protein
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Pre-hexon-linking protein IIIa
S: Pre-hexon-linking protein VIII
T: Pre-hexon-linking protein VIII


Theoretical massNumber of molelcules
Total (without water)1,821,97032
Polymers1,821,97032
Non-polymers00
Water0
1
0: Pre-protein VI
U: Pre-protein VI
1: Pre-protein VI
V: Pre-protein VI
2: Pre-protein VI
W: Pre-protein VI
3: Pre-protein VI
X: Pre-protein VI
4: Pre-protein VI
Y: Pre-protein VI
8: Pre-protein VI
Z: 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: Hexon-interlacing protein
O: Hexon-interlacing protein
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Pre-hexon-linking protein IIIa
S: Pre-hexon-linking protein VIII
T: Pre-hexon-linking protein VIII
x 60


Theoretical massNumber of molelcules
Total (without water)109,318,1971920
Polymers109,318,1971920
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
0: Pre-protein VI
U: Pre-protein VI
1: Pre-protein VI
V: Pre-protein VI
2: Pre-protein VI
W: Pre-protein VI
3: Pre-protein VI
X: Pre-protein VI
4: Pre-protein VI
Y: Pre-protein VI
8: Pre-protein VI
Z: 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: Hexon-interlacing protein
O: Hexon-interlacing protein
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Pre-hexon-linking protein IIIa
S: Pre-hexon-linking protein VIII
T: Pre-hexon-linking protein VIII
x 5


  • icosahedral pentamer
  • 9.11 MDa, 160 polymers
Theoretical massNumber of molelcules
Total (without water)9,109,850160
Polymers9,109,850160
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
0: Pre-protein VI
U: Pre-protein VI
1: Pre-protein VI
V: Pre-protein VI
2: Pre-protein VI
W: Pre-protein VI
3: Pre-protein VI
X: Pre-protein VI
4: Pre-protein VI
Y: Pre-protein VI
8: Pre-protein VI
Z: 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: Hexon-interlacing protein
O: Hexon-interlacing protein
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Pre-hexon-linking protein IIIa
S: Pre-hexon-linking protein VIII
T: Pre-hexon-linking protein VIII
x 6


  • icosahedral 23 hexamer
  • 10.9 MDa, 192 polymers
Theoretical massNumber of molelcules
Total (without water)10,931,820192
Polymers10,931,820192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 4 types, 29 molecules 0U1V2W3X4Y8ZABCDEFGHIJKLMNOPQ

#1: Protein
Pre-protein VI / pVI


Mass: 26299.689 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chimpanzee adenovirus Y25 / Gene: L3 / Production host: Homo sapiens (human) / References: UniProt: G9G853
#2: Protein
Hexon protein / / CP-H / Protein II


Mass: 106121.141 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chimpanzee adenovirus Y25 / Gene: L3 / Production host: Homo sapiens (human) / References: UniProt: G9G854
#3: Protein Penton protein / / CP-P / Penton base protein / Protein III


Mass: 59533.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chimpanzee adenovirus Y25 / Gene: L2 / Production host: Homo sapiens (human) / References: UniProt: G9G849
#4: Protein
Hexon-interlacing protein / Protein IX


Mass: 14468.118 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chimpanzee adenovirus Y25 / Gene: IX / Production host: Homo sapiens (human) / References: UniProt: G9G843

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

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


Mass: 65954.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chimpanzee adenovirus Y25 / Production host: Homo sapiens (human) / References: UniProt: G9G848
#6: Protein Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 24779.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chimpanzee adenovirus Y25 / Gene: L4 / Production host: Homo sapiens (human) / References: UniProt: G9G860

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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: Chimpanzee adenovirus Y25 / Type: VIRUS
Details: Rescued from a bacterial artificial chromosome containing the ChAdOx1 genome and propagated in HEK293 T-Rex cells.
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Chimpanzee adenovirus Y25 / Strain: ChAdOx1
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Pan troglodytes
Virus shellName: Icosahedral CapsidCapsid / Diameter: 500 nm / Triangulation number (T number): 25
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSaltNaClSodium chloride1
21 mMMagnesium ChlorideMgCl21
320 mMTrisC4H11NO31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Concentrated by centrifugation
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K
Details: Grid was R2/2 UltrAUFoil. Sample was applied and blotted twice before plunging.

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 1.1802 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2875
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2CTFFIND4.1particle selection
5RELION3.1.1CTF correction
6CTFFIND4.1CTF correction
9UCSF ChimeraXmodel fitting
14RELION3.1.13D reconstruction
15MDFFmodel refinement
16ISOLDEmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 8375
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5748 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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