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- EMDB-76994: HAdV-C6 Hexon trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-76994
TitleHAdV-C6 Hexon trimer
Map datamap of the HAdV-C6 hexon trimer
Sample
  • Complex: Purified Human adenovirus type 6 hexon trimer
    • Protein or peptide: Hexon protein
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 / host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity
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
Similarity search - Domain/homology
Biological speciesHuman adenovirus 6
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
DepositionApr 30, 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_76994.png

Downloads & links

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Map

FileReleased
Annotationmap of the HAdV-C6 hexon trimer
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: 0.15
Minimum - Maximum-0.020024406 - 1.9942156
Average (Standard dev.)0.005036354 (±0.05222451)
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 trimer

Fileemd_76994_half_map_1.map
Annotationhalf map of the HAdV-C6 hexon trimer
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 trimer

Fileemd_76994_half_map_2.map
Annotationhalf map of the HAdV-C6 hexon trimer
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

EntireName: Purified Human adenovirus type 6 hexon trimer
Components
  • Complex: Purified Human adenovirus type 6 hexon trimer
    • Protein or peptide: Hexon protein

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Supramolecule #1: Purified Human adenovirus type 6 hexon trimer

SupramoleculeName: Purified Human adenovirus type 6 hexon trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human adenovirus 6
Molecular weightTheoretical: 330 KDa

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Macromolecule #1: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 1 / 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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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: 38.0 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: 48088
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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