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- EMDB-77024: Cryo-EM structure of HAdV-C6 hexon trimer in complex with prothro... -

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Entry
Database: EMDB / ID: EMD-77024
TitleCryo-EM structure of HAdV-C6 hexon trimer in complex with prothrombin (FII)
Map dataHAdV-C6 hexon trimer in complex with human coagulation factor FII
Sample
  • Complex: Purified Human adenovirus type 6 hexon trimer in complex with prothrombin (FII)
    • Protein or peptide: Hexon protein
    • Protein or peptide: Prothrombin
  • Ligand: CALCIUM ION
Keywordsadenovirus / hexon / coagulation factor II / virus-host interaction / cryo-EM / virus capsid / VIRAL PROTEIN
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / negative regulation of astrocyte differentiation / : / thrombospondin receptor activity / thrombin / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / 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 / negative regulation of astrocyte differentiation / : / thrombospondin receptor activity / thrombin / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / 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 / Platelet Aggregation (Plug Formation) / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / negative regulation of fibrinolysis / positive regulation of blood coagulation / negative regulation of proteolysis / 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 / fibrinolysis / regulation of cytosolic calcium ion concentration / : / negative regulation of cytokine production involved in inflammatory response / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of receptor signaling pathway via JAK-STAT / acute-phase response / Cell surface interactions at the vascular wall / Peptide ligand-binding receptors / growth factor activity / response to wounding / lipopolysaccharide binding / platelet activation / 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 / host cell / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / Dengue Virus-Host Interactions / antimicrobial humoral immune response mediated by antimicrobial peptide / extracellular matrix / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / endoplasmic reticulum lumen / receptor ligand activity / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsMa OX / Reddy VS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161367 United States
CitationJournal: PLoS Pathog / Year: 2026
Title: Structural requirements of blood factors binding to soluble hexon trimers with implications for adenovirus cell targeting and immune evasion.
Authors: Olivia X Ma / Shao-Chia Lu / Haley E Mudrick / Mary E Barry / Jarrod B French / Michael A Barry / Vijay S Reddy /
Abstract: Human adenovirus serotype 5 (HAdV-C5) is widely used as a gene delivery vector in both experimental and clinical settings. Upon intravenous administration, HAdV-C5 exhibits strong liver tropism, ...Human adenovirus serotype 5 (HAdV-C5) is widely used as a gene delivery vector in both experimental and clinical settings. Upon intravenous administration, HAdV-C5 exhibits strong liver tropism, largely mediated by interactions between its major capsid protein, hexon (Hx), and coagulation factor X (FX). In contrast, the closely related species C adenovirus 6 (HAdV-C6) also targets the liver but shows reduced dependency on coagulation factors, whereas species D adenovirus 26 (HAdV-D26) does not bind coagulation factors altogether. To define the structural basis of this serotype-specific host factor recognition, we determined high-resolution cryo-electron microscopy structures of isolated hexon trimers from HAdV-C5 and HAdV-C6 in complex with coagulation factors FX and prothrombin (factor II, FII). The resulting atomic models reveal conserved binding interfaces involving the γ-carboxyglutamic acid (Gla) domains of both coagulation factors and the hypervariable regions HVR5 and HVR7 lining the surface cavities of HAdV-C5 and HAdV-C6 hexons. Structures of hexon complexes formed by co-incubation with both FX and FII further reveal serotype-specific binding preferences under physiologically relevant conditions, showing that HAdV-C5 hexon preferentially engages FX, whereas HAdV-C6 hexon favors FII. By contrast, HAdV-D26 hexon does not bind either factor, likely due to an insertion constrained by proline residues in the HVR5 loop that restricts the factor access to the hexon cavity. Together, these findings provide a detailed structural framework for adenovirus-coagulation factor interactions and support the rational engineering of adenovirus vectors with improved targeting and safety profiles.
History
DepositionMay 3, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77024.png

Downloads & links

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Map

FileDownload / File: emd_77024.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHAdV-C6 hexon trimer in complex with human coagulation factor FII
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.024404274 - 1.7517995
Average (Standard dev.)0.0051913173 (±0.047555916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map of HAdV-C6 hexon trimer in complex...

Fileemd_77024_half_map_1.map
Annotationhalf map of HAdV-C6 hexon trimer in complex with human coagulation factor FII
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of HAdV-C6 hexon trimer in complex...

Fileemd_77024_half_map_2.map
Annotationhalf map of HAdV-C6 hexon trimer in complex with human coagulation factor FII
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Purified Human adenovirus type 6 hexon trimer in complex with pro...

EntireName: Purified Human adenovirus type 6 hexon trimer in complex with prothrombin (FII)
Components
  • Complex: Purified Human adenovirus type 6 hexon trimer in complex with prothrombin (FII)
    • Protein or peptide: Hexon protein
    • Protein or peptide: Prothrombin
  • Ligand: CALCIUM ION

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Supramolecule #1: Purified Human adenovirus type 6 hexon trimer in complex with pro...

SupramoleculeName: Purified Human adenovirus type 6 hexon trimer in complex with prothrombin (FII)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human adenovirus 6
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 1
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.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 6
Molecular weightTheoretical: 108.635133 KDa
SequenceString: MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNSCEWEQNE TAQVDAQELD EEENEANEAQ A REQEQAKK ...String:
MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNSCEWEQNE TAQVDAQELD EEENEANEAQ A REQEQAKK THVYAQAPLS GIKITKEGLQ IGTADATVAG AGKEIFADKT FQPEPQVGES QWNEADATAA GGRVLKKTTP MK PCYGSYA RPTNSNGGQG VMVEQNGKLE SQVEMQFFST STNATNEVNN IQPTVVLYSE DVNMETPDTH LSYKPKMGDK NAK VMLGQQ AMPNRPNYIA FRDNFIGLMY YNSTGNMGVL AGQASQLNAV VDLQDRNTEL SYQLLLDSIG DRTRYFSMWN QAVD SYDPD VRIIENHGTE DELPNYCFPL GGIGITDTFQ AVKTTAANGD QGNTTWQKDS TFAERNEIGV GNNFAMEINL NANLW RNFL YSNIALYLPD KLKYNPTNVE ISDNPNTYDY MNKRVVAPGL VDCYINLGAR WSLEYMDNVN PFNHHRNAGL RYRSML LGN GRYVPFHIQV PQKFFAIKNL LLLPGSYTYE WNFRKDVNMV LQSSLGNDLR VDGASIKFDS ICLYATFFPM AHNTAST LE AMLRNDTNDQ SFNDYLSAAN MLYPIPANAT NVPISIPSRN WAAFRGWAFT RLKTKETPSL GSGYDPYYTY SGSIPYLD G TFYLNHTFKK VAITFDSSVS WPGNDRLLTP NEFEIKRSVD GEGYNVAQCN MTKDWFLVQM LANYNIGYQG FYIPESYKD RMYSFFRNFQ PMSRQVVDDT KYKDYQQVGI IHQHNNSGFV GYLAPTMREG QAYPANVPYP LIGKTAVDSI TQKKFLCDRT LWRIPFSSN FMSMGALTDL GQNLLYANSA HALDMTFEVD PMDEPTLLYV LFEVFDVVRV HQPHRGVIET VYLRTPFSAG N ATT

UniProtKB: Hexon protein

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Macromolecule #2: Prothrombin

MacromoleculeName: Prothrombin / type: protein_or_peptide / ID: 2
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.
Number of copies: 1 / Enantiomer: LEVO / EC number: thrombin
Source (natural)Organism: Homo sapiens (human) / Tissue: blood
Molecular weightTheoretical: 70.56293 KDa
SequenceString: MAHVRGLQLP GCLALAALCS LVHSQHVFLA PQQARSLLQR VRRANTFL(CGU)(CGU) VRKGNL(CGU)R(CGU)C V (CGU)(CGU)TCSY(CGU)(CGU) AF(CGU)AL(CGU)SSTA TDVFWAKYTA CETARTPRDK LAACLEGNCA EGLGTNYR G HVNITRSGIE ...String:
MAHVRGLQLP GCLALAALCS LVHSQHVFLA PQQARSLLQR VRRANTFL(CGU)(CGU) VRKGNL(CGU)R(CGU)C V (CGU)(CGU)TCSY(CGU)(CGU) AF(CGU)AL(CGU)SSTA TDVFWAKYTA CETARTPRDK LAACLEGNCA EGLGTNYR G HVNITRSGIE CQLWRSRYPH KPEINSTTHP GADLQENFCR NPDSSTTGPW CYTTDPTVRR QECSIPVCGQ DQVTVAMTP RSEGSSVNLS PPLEQCVPDR GQQYQGRLAV TTHGLPCLAW ASAQAKALSK HQDFNSAVQL VENFCRNPDG DEEGVWCYVA GKPGDFGYC DLNYCEEAVE EETGDGLDED SDRAIEGRTA TSEYQTFFNP RTFGSGEADC GLRPLFEKKS LEDKTERELL E SYIDGRIV EGSDAEIGMS PWQVMLFRKS PQELLCGASL ISDRWVLTAA HCLLYPPWDK NFTENDLLVR IGKHSRTRYE RN IEKISML EKIYIHPRYN WRENLDRDIA LMKLKKPVAF SDYIHPVCLP DRETAASLLQ AGYKGRVTGW GNLKETWTAN VGK GQPSVL QVVNLPIVER PVCKDSTRIR ITDNMFCAGY KPDEGKRGDA CEGDSGGPFV MKSPFNNRWY QMGIVSWGEG CDRD GKYGF YTHVFRLKKW IQKVIDQFGE

UniProtKB: Prothrombin

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 7 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 7275 / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1099039
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER / Details: hexon trimer density map from previous study
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 91729
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-13er:
Cryo-EM structure of HAdV-C6 hexon trimer in complex with prothrombin (FII)

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