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- PDB-13es: Cryo-EM structure of HAdV-C5 hexon trimer in complex with human c... -

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Basic information

Entry
Database: PDB / ID: 13es
TitleCryo-EM structure of HAdV-C5 hexon trimer in complex with human coagulation factor X (FX)
Components
  • Coagulation factor X
  • Hexon protein
KeywordsVIRAL PROTEIN / adenovirus / HAdV-C5 / hexon / coagulation factor X / virus-host interaction / cryo-EM / virus capsid
Function / homology
Function and homology information


T=25 icosahedral viral capsid / coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / microtubule-dependent intracellular transport of viral material towards nucleus / : / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / : ...T=25 icosahedral viral capsid / coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / microtubule-dependent intracellular transport of viral material towards nucleus / : / positive regulation of TOR signaling / 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 / : / phospholipid binding / Golgi lumen / blood coagulation / viral capsid / host cell / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / external side of plasma membrane / calcium ion binding / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis / : / 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 / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla 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 / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like 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. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / 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
Coagulation factor X / Hexon protein
Similarity search - Component
Biological speciesHuman adenovirus 5
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 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

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Assembly

Deposited unit
A: Hexon protein
B: Hexon protein
C: Hexon protein
G: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)379,89011
Polymers379,6104
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: 108107.617 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: The modeled hexon sequence lacks the N-terminal residues 1-6, the poorly resolved HVR region corresponding to residues 139-164, and the C-terminal residues 948-952. These residues were ...Details: The modeled hexon sequence lacks the N-terminal residues 1-6, the poorly resolved HVR region corresponding to residues 139-164, and the C-terminal residues 948-952. These residues were omitted from the model due to insufficient or unresolved cryo-EM density.
Source: (natural) Human adenovirus 5 / References: UniProt: P04133
#2: Protein Coagulation factor X / Stuart factor / Stuart-Prower factor


Mass: 55286.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The modeled coagulation factor X (FX) corresponds to the N-terminal Gla domain, while the signal peptide, propeptide, and the remainder of the protein (including EGF-like domains and the ...Details: The modeled coagulation factor X (FX) corresponds to the N-terminal Gla domain, while the signal peptide, propeptide, and the remainder of the protein (including EGF-like domains and the protease domain) are not included in the model due to absence of interpretable cryo-EM density. The retained region contains multiple gamma-carboxyglutamic acid (Gla) residues required for calcium coordination.
Source: (natural) Homo sapiens (human) / Tissue: blood / References: UniProt: P00742, coagulation factor Xa
#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 5 hexon trimer in complex with coagulation factor X
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.39 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus 5
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
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: 5192
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
7Cootmodel fitting
12cryoSPARC4.7.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 715202
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96107 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementHighest resolution: 3.23 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00123015
ELECTRON MICROSCOPYf_angle_d0.39331298
ELECTRON MICROSCOPYf_dihedral_angle_d8.2578430
ELECTRON MICROSCOPYf_chiral_restr0.0413294
ELECTRON MICROSCOPYf_plane_restr0.0034127

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