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- EMDB-60935: Structure of Adenovirus serotype 2 100K -

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Basic information

Entry
Database: EMDB / ID: EMD-60935
TitleStructure of Adenovirus serotype 2 100K
Map data
Sample
  • Complex: Adenovirus serotype2 100K dimer
    • Protein or peptide: Shutoff protein
KeywordsViral encoded chaperone / VIRAL PROTEIN
Function / homology
Function and homology information


viral translational shunt / intracellular transport of viral protein in host cell / symbiont-mediated suppression of host translation initiation / host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / RNA binding
Similarity search - Function
Shutoff protein L4 / Late 100kD protein
Similarity search - Domain/homology
Biological speciesHuman adenovirus 2
Methodsingle particle reconstruction / Resolution: 3.79 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_60935.png

Downloads & links

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Map

FileDownload / File: emd_60935.map.gz / Format: CCP4 / Size: 52.7 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 240 pix.
= 300. Å		1.25 Å/pix.
x 240 pix.
= 300. Å		1.25 Å/pix.
x 240 pix.
= 300. 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: 0.0108
Minimum - Maximum-0.042188097 - 1.8016052
Average (Standard dev.)0.0011999012 (±0.025307065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60935_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_60935_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Adenovirus serotype2 100K dimer

EntireName: Adenovirus serotype2 100K dimer
Components
  • Complex: Adenovirus serotype2 100K dimer
    • Protein or peptide: Shutoff protein

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Supramolecule #1: Adenovirus serotype2 100K dimer

SupramoleculeName: Adenovirus serotype2 100K dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human adenovirus 2

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Macromolecule #1: Shutoff protein

MacromoleculeName: Shutoff protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 251682
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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