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- EMDB-60936: CryoEM structure of Adenovirus serotype 3 premature hexon in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-60936
TitleCryoEM structure of Adenovirus serotype 3 premature hexon in complex with Adenovirus serotype 2 100K
Map data
Sample
  • Complex: Complex of Adenovirus serotype2 100K dimer and serotype3 hexon trimer
    • Complex: Adenovirus serotype2 100K dimer
      • Protein or peptide: Shutoff protein
    • Complex: Adenovirus serotype3 hexon trimer
      • Protein or peptide: Hexon protein
KeywordsComplex / VIRAL PROTEIN
Function / homology
Function and homology information


viral translational shunt / intracellular transport of viral protein in host cell / T=25 icosahedral viral capsid / symbiont-mediated suppression of host translation initiation / microtubule-dependent intracellular transport of viral material towards nucleus / host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell nucleus ...viral translational shunt / intracellular transport of viral protein in host cell / T=25 icosahedral viral capsid / symbiont-mediated suppression of host translation initiation / microtubule-dependent intracellular transport of viral material towards nucleus / host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Shutoff protein L4 / Late 100kD protein / Adenovirus Pll, hexon, subdomain 3 / 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
Shutoff protein / Hexon protein
Similarity search - Component
Biological speciesHuman adenovirus 2 / Human adenovirus B3
Methodsingle particle reconstruction / Resolution: 3.23 Å
AuthorsLiu Q / Li H / Xiang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Molecular mechanisms of the viral encoded chaperone 100K in capsid folding and assembly of adenovirus.
Authors: Haining Li / Luyuan Shao / Zhe Liu / Qi Liu / Ye Xiang /
Abstract: Adenovirus is an icosahedral, non-enveloped DNA virus that infects humans and other animals. The capsid of adenovirus is mainly assembled by the major capsid protein hexon. Folding and assembly of ...Adenovirus is an icosahedral, non-enveloped DNA virus that infects humans and other animals. The capsid of adenovirus is mainly assembled by the major capsid protein hexon. Folding and assembly of hexon require the viral encoded chaperone 100K, of which the detailed structure and chaperoning mechanism remain unknown. Here, we report the cryoEM structure of 100K in complex with a pre-mature hexon trimer. The structure shows that 100K dimers bind to the bottom double jelly-roll domains of the pre-mature hexon, mainly through a hook-like domain and a loop extruded from the dimerization domain. Additionally, a groove formed at the dimerization interface of 100K accommodates the N-terminal fragment 49-53 of an adjacent hexon protomer. Mutagenesis studies indicate that the interactions at the jelly-roll domain and the N-terminus of hexon are all essential for the proper folding and assembly of hexon. 100K binds and stabilizes the partially folded hexon, preventing premature aggregation of hexon, promoting the folding of the hexon top insertion loops, and facilitating hexon trimerization.
History
DepositionJul 24, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60936.png

Downloads & links

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Map

FileDownload / File: emd_60936.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 320 pix.
= 400. Å		1.25 Å/pix.
x 320 pix.
= 400. Å		1.25 Å/pix.
x 320 pix.
= 400. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0109
Minimum - Maximum-0.024484029 - 1.7669644
Average (Standard dev.)0.0010882805 (±0.022267876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60936_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60936_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Adenovirus serotype2 100K dimer and serotype3 hexon trimer

EntireName: Complex of Adenovirus serotype2 100K dimer and serotype3 hexon trimer
Components
  • Complex: Complex of Adenovirus serotype2 100K dimer and serotype3 hexon trimer
    • Complex: Adenovirus serotype2 100K dimer
      • Protein or peptide: Shutoff protein
    • Complex: Adenovirus serotype3 hexon trimer
      • Protein or peptide: Hexon protein

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Supramolecule #1: Complex of Adenovirus serotype2 100K dimer and serotype3 hexon trimer

SupramoleculeName: Complex of Adenovirus serotype2 100K dimer and serotype3 hexon trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1

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Supramolecule #2: Adenovirus serotype2 100K dimer

SupramoleculeName: Adenovirus serotype2 100K dimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Human adenovirus 2

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Supramolecule #3: Adenovirus serotype3 hexon trimer

SupramoleculeName: Adenovirus serotype3 hexon trimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human adenovirus B3

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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 B3
Molecular weightTheoretical: 110.205797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKLEVLFQG PGSMATPSMM PQWAYMHIAG QDASEYLSPG LVQFARATDT YFSMGNKFRN PTVAPTHDV TTDRSQRLML RFVPVDREDN TYSYKVRYTL AVGDNRVLDM ASTFFDIRGV LDRGPSFKPY SGTAYNSLAP K GAPNTSQW ...String:
MDYKDHDGDY KDHDIDYKDD DDKLEVLFQG PGSMATPSMM PQWAYMHIAG QDASEYLSPG LVQFARATDT YFSMGNKFRN PTVAPTHDV TTDRSQRLML RFVPVDREDN TYSYKVRYTL AVGDNRVLDM ASTFFDIRGV LDRGPSFKPY SGTAYNSLAP K GAPNTSQW IVTTNGDNAV TTTTNTFGIA SMKGDNITKE GLQIGKDITT TEGEEKPIYA DKTYQPEPQV GEESWTDTDG TN EKFGGRA LKPATNMKPC YGSFARPTNI KGGQAKNRKV KPTTEGGVET EEPDIDMEFF DGRDAVAGAL APEIVLYTEN VNL ETPDSH VVYKPETSNN SHANLGQQAM PNRPNYIGFR DNFVGLMYYN STGNMGVLAG QASQLNAVVD LQDRNTELSY QLLL DSLGD RTRYFSMWNQ AVDSYDPDVR IIENHGIEDE LPNYCFPLNG IGPGHTYQGI KVKTDDTNGW EKDANVAPAN EITIG NNLA MEINIQANLW RSFLYSNVAL YLPDVYKYTP PNITLPTNTN TYEYMNGRVV SPSLVDSYIN IGARWSLDPM DNVNPF NHH RNAGLRYRSM LLGNGRYVPF HIQVPQKFFA VKNLLLLPGS YTYEWNFRKD VNMVLQSSLG NDLRTDGATI SFTSINL YA TFFPMAHNTA STLEAMLRND TNDQSFNDYL SAANMLYPIP ANATNIPISI PSRNWAAFRG WSFTRLKTKE TPSLGSGF D PYFVYSGSIP YLDGTFYLNH TFKKVSIMFD SSVSWPGNDR LLSPNEFEIK RTVDGEGYNV AQCNMTKDWF LVQMLANYN IGYQGFYIPE GYKDRMYSFF RNFQPMSRQV VDEVNYTDYK AVTLPYQHNN SGFVGYLAPT MRQGEPYPAN YPYPLIGTTA VKSVTQKKF LCDRTMWRIP FSSNFMSMGA LTDLGQNMLY ANSAHALDMT FEVDPMDEPT LLYLLFEVFD VVRVHQPHRG V IEAVYLRT PFSAGNATT

UniProtKB: Hexon protein

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Macromolecule #2: Shutoff protein

MacromoleculeName: Shutoff protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 2
Molecular weightTheoretical: 94.85493 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MESVEKEDSL TAPFEFATTA STDAANAPTT FPVEAPPLEE EEVIIEQDPG FVSEDDEDRS VPTEDKKQDQ DDAEANEEQV GRGDQRHGD YLDVGDDVLL KHLQRQCAII CDALQERSDV PLAIADVSLA YERHLFSPRV PPKRQENGTC EPNPRLNFYP V FAVPEVLA ...String:
MESVEKEDSL TAPFEFATTA STDAANAPTT FPVEAPPLEE EEVIIEQDPG FVSEDDEDRS VPTEDKKQDQ DDAEANEEQV GRGDQRHGD YLDVGDDVLL KHLQRQCAII CDALQERSDV PLAIADVSLA YERHLFSPRV PPKRQENGTC EPNPRLNFYP V FAVPEVLA TYHIFFQNCK IPLSCRANRS RADKQLALRQ GAVIPDIASL DEVPKIFEGL GRDEKRAANA LQQENSENES HC GVLVELE GDNARLAVLK RSIEVTHFAY PALNLPPKVM STVMSELIVR RARPLERDAN LQEQTEEGLP AVGDEQLARW LET REPADL EERRKLMMAA VLVTVELECM QRFFADPEMQ RKLEETLHYT FRQGYVRQAC KISNVELCNL VSYLGILHEN RLGQ NVLHS TLKGEARRDY VRDCVYLFLC YTWQTAMGVW QQCLEERNLK ELQKLLKQNL KDLWTAFNER SVAAHLADII FPERL LKTL QQGLPDFTSQ SMLQNFRNFI LERSGILPAT CCALPSDFVP IKYRECPPPL WGHCYLLQLA NYLAYHSDIM EDVSGD GLL ECHCRCNLCT PHRSLVCNSQ LLSESQIIGT FELQGPSPDE KSAAPGLKLT PGLWTSAYLR KFVPEDYHAH EIRFYED QS RPPNAELTAC VITQGHILGQ LQAINKARQE FLLRKGRGVY LDPQSGEELN PIPPPPQPYQ QPRALASQDG TQKEAAAA A AATHGRGGIL GQSGRGGFGR GGGDDGRLGQ PRRSFRGRRG VRRNTVTLGR IPLAGAPEIG NRSQHRYNLR SSGAAGTAC SPTQPGSLEV LFQGPRSMGW SHPQFEKGGG ARGGSGGGSW SHPQFEKGF

UniProtKB: Shutoff protein

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 232424
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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