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- PDB-13er: Cryo-EM structure of HAdV-C6 hexon trimer in complex with prothro... -

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Basic information

Entry
Database: PDB / ID: 13er
TitleCryo-EM structure of HAdV-C6 hexon trimer in complex with prothrombin (FII)
Components
  • Hexon protein
  • Prothrombin
KeywordsVIRAL PROTEIN / adenovirus / hexon / coagulation factor II / virus-host interaction / cryo-EM / virus capsid
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / : / thrombospondin receptor activity / thrombin / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / negative regulation of astrocyte differentiation / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium ...T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / : / thrombospondin receptor activity / thrombin / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / negative regulation of astrocyte differentiation / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway / Platelet Aggregation (Plug Formation) / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / negative regulation of fibrinolysis / blood coagulation, fibrin clot formation / positive regulation of blood coagulation / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / : / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / fibrinolysis / : / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / growth factor activity / positive regulation of receptor signaling pathway via JAK-STAT / lipopolysaccharide binding / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / positive regulation of insulin secretion / regulation of cell shape / antimicrobial humoral immune response mediated by antimicrobial peptide / host cell / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum lumen / receptor ligand activity / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis / : / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
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 / Group II dsDNA virus coat/capsid protein / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily ...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 / Group II dsDNA virus coat/capsid protein / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Hexon protein / Prothrombin
Similarity search - Component
Biological speciesHuman adenovirus 6
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsMa, O.X. / Reddy, V.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161367 United States
CitationJournal: To Be Published
Title: Structural requirements of blood factors binding to soluble hexon trimers with implications for adenovirus cell targeting and immune evasion
Authors: Ma, O.X. / Reddy, V.S.
History
DepositionMay 3, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexon protein
B: Hexon protein
C: Hexon protein
G: Prothrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)396,74911
Polymers396,4684
Non-polymers2817
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 108635.133 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: The modeled structure lacks the N-terminal residues 1-6, an internal region corresponding to residues 139-164, and a short segment around residues 445-452, as well as the C-terminal residues ...Details: The modeled structure lacks the N-terminal residues 1-6, an internal region corresponding to residues 139-164, and a short segment around residues 445-452, as well as the C-terminal residues 948-952. These regions were not included in the model due to the absence of well-defined cryo-EM density.
Source: (natural) Human adenovirus 6 / References: UniProt: B2ZWX4
#2: Protein Prothrombin / Coagulation factor II


Mass: 70562.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The modeled prothrombin (FII) corresponds to the N-terminal Gla domain, whereas the signal peptide, propeptide, and the remaining domains (including the kringle domains and serine protease ...Details: The modeled prothrombin (FII) corresponds to the N-terminal Gla domain, whereas the signal peptide, propeptide, and the remaining domains (including the kringle domains and serine protease domain) are not included due to lack of interpretable cryo-EM density. The modeled region contains gamma-carboxyglutamic acid (Gla) residues involved in calcium coordination.
Source: (natural) Homo sapiens (human) / Tissue: blood / References: UniProt: P00734, thrombin
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Purified Human adenovirus type 6 hexon trimer in complex with prothrombin (FII)
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.40 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus 6
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of real images: 7275
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7Cootmodel fitting
12cryoSPARC3D reconstruction
13PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 1099039
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91729 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementHighest resolution: 3.22 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00423050
ELECTRON MICROSCOPYf_angle_d0.49931354
ELECTRON MICROSCOPYf_dihedral_angle_d10.2048390
ELECTRON MICROSCOPYf_chiral_restr0.0443341
ELECTRON MICROSCOPYf_plane_restr0.0044129

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