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- EMDB-77027: Cryo-EM structure of HAdV-C6 hexon trimer in complex with human c... -

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Basic information

Entry
Database: EMDB / ID: EMD-77027
TitleCryo-EM structure of HAdV-C6 hexon trimer in complex with human coagulation factor X (FX)
Map datamap of the HAdV-C6 hexon in complex with FX
Sample
  • Complex: Purified Human adenovirus type 6 hexon trimer in complex with FX
    • Protein or peptide: Hexon protein
    • Protein or peptide: Coagulation factor X
  • Ligand: CALCIUM ION
Keywordsadenovirus / hexon / coagulation factor X / virus-host interaction / cryo-EM / virus capsid / VIRAL PROTEIN
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 / 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
Hexon protein / Coagulation factor X
Similarity search - Component
Biological speciesHuman adenovirus 6 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 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: 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 OX / Reddy VS
History
DepositionMay 3, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77027.png

Downloads & links

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Map

FileReleased
Annotationmap of the HAdV-C6 hexon in complex with FX
Projections & slices

Image control

Size
Brightness
Contrast
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.01949191 - 2.0536277
Average (Standard dev.)0.005032335 (±0.05117652)
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 the HAdV-C6 hexon in complex with FX

Fileemd_77027_half_map_1.map
Annotationhalf map of the HAdV-C6 hexon in complex with FX
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of the HAdV-C6 hexon in complex with FX

Fileemd_77027_half_map_2.map
Annotationhalf map of the HAdV-C6 hexon in complex with FX
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 FX

EntireName: Purified Human adenovirus type 6 hexon trimer in complex with FX
Components
  • Complex: Purified Human adenovirus type 6 hexon trimer in complex with FX
    • Protein or peptide: Hexon protein
    • Protein or peptide: Coagulation factor X
  • Ligand: CALCIUM ION

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

SupramoleculeName: Purified Human adenovirus type 6 hexon trimer in complex with FX
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human adenovirus 6
Molecular weightTheoretical: 390 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
Recombinant expressionOrganism: Human adenovirus 6
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: Coagulation factor X

MacromoleculeName: Coagulation factor X / type: protein_or_peptide / ID: 2
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.
Number of copies: 1 / Enantiomer: LEVO / EC number: coagulation factor Xa
Source (natural)Organism: Homo sapiens (human) / Tissue: blood
Molecular weightTheoretical: 47.560695 KDa
SequenceString: MGRPLHLVLL SASLAGLLLL GESLFIRREQ ANNILARVTR ANSFL(CGU)(CGU)MKK GHL(CGU)R(CGU)CM(CGU) (CGU)TCSY(CGU)(CGU)AR(CGU) VF(CGU)DSDKTN(CGU) FWNKYDGDQC ETSPCQNQGK CKDGLGEYTC TCLEGF EGK NCELFTRKLC ...String:
MGRPLHLVLL SASLAGLLLL GESLFIRREQ ANNILARVTR ANSFL(CGU)(CGU)MKK GHL(CGU)R(CGU)CM(CGU) (CGU)TCSY(CGU)(CGU)AR(CGU) VF(CGU)DSDKTN(CGU) FWNKYDGDQC ETSPCQNQGK CKDGLGEYTC TCLEGF EGK NCELFTRKLC SLDNGDCDQF CHEEQNSVVC SCARGYTLAD NGKACIPTGP YPCGKQTLER RKRSVAQATS SSGEAPD SI TWKPYDAADL DPTENPFDLL DFNQTQPERG DNNLTRIVGG QECKDGECPW QALLINEENE GFCGGTILSE FYILTAAH C LYQAKRFKVR VGDRNTEQEE GGEAVHEVEV VIKHNRFTKE TYDFDIAVLR LKTPITFRMN VAPACLPERD WAESTLMTQ KTGIVSGFGR THEKGRQSTR LKMLEVPYVD RNSCKLSSSF IITQNMFCAG YDTKQEDACQ GDSG

UniProtKB: Coagulation factor X

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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: 3510 / 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: 280503
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER / Details: hexon trimer density map from previous study
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 68552
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot (ver. 0.9.8.92EL)
Output model

PDB-13eu:
Cryo-EM structure of HAdV-C6 hexon trimer in complex with human coagulation factor X (FX)

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