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- EMDB-63322: Local reconstruction of bovine adenovirus type 3 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-63322
TitleLocal reconstruction of bovine adenovirus type 3 capsid
Map data
Sample
  • Complex: Bovine adenovirus 3
    • Protein or peptide: Hexon protein
    • Protein or peptide: PVI
    • Protein or peptide: Pre-histone-like nucleoprotein
    • Protein or peptide: PX
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: PV
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: PIX
    • Protein or peptide: Penton protein
KeywordsComplex / VIRAL PROTEIN
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / virion component / viral penetration into host nucleus / viral capsid / host cell ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / virion component / viral penetration into host nucleus / viral capsid / host cell / viral nucleocapsid / host cell cytoplasm / endocytosis involved in viral entry into host cell / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / DNA binding / membrane
Similarity search - Function
Adenovirus late L2 mu core / Adenovirus late L2 mu core protein (Protein X) / Adenovirus core-capsid bridging protein V / Adenovirus minor core protein PV / Adenoviral core protein VII / Adenoviral core protein VII / Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal ...Adenovirus late L2 mu core / Adenovirus late L2 mu core protein (Protein X) / Adenovirus core-capsid bridging protein V / Adenovirus minor core protein PV / Adenoviral core protein VII / Adenoviral core protein VII / Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus Pll, hexon, subdomain 3 / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI / 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 / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Pre-histone-like nucleoprotein / Pre-hexon-linking protein VIII / Penton protein / Pre-hexon-linking protein IIIa / PVI / PV / PX / Hexon protein / PIX
Similarity search - Component
Biological speciesBovine adenovirus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsXiao H / Liu HR
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32371263 China
National Natural Science Foundation of China (NSFC)32401014 China
CitationJournal: J Mol Biol / Year: 2025
Title: Structural Insights into Minor and Core Proteins of Bovine Adenovirus 3: Bridging Capsid and Genomic Core.
Authors: Hao Xiao / Hao Pang / Junquan Zhou / Hao Feng / Jingdong Song / Lingpeng Cheng / Li Wang / Hongrong Liu /
Abstract: Adenoviruses are double-stranded DNA viruses with broad relevance to human and animal health and considerable potential as therapeutic vectors. Despite extensive studies, the structural details of ...Adenoviruses are double-stranded DNA viruses with broad relevance to human and animal health and considerable potential as therapeutic vectors. Despite extensive studies, the structural details of core and minor capsid proteins in adenoviruses remain poorly understood. In this study, the architecture of bovine adenovirus type 3 (BAdV-3), a member of the Mastadenovirus genus, was solved by cryo-electron microscopy. Our structure shows that BAdV-3 shares significant structural conservation with human adenoviruses. Atomic models were constructed for a previously uncharacterized region of the minor protein VI and for the core proteins V and Mu. The study revealed how core proteins bridge the genome and capsid, underscore the multifaceted roles of protein V in strengthening capsid stability and facilitating genome release.
History
DepositionJan 30, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63322.png

Downloads & links

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Map

FileDownload / File: emd_63322.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 368 pix.
= 467.36 Å		1.27 Å/pix.
x 368 pix.
= 467.36 Å		1.27 Å/pix.
x 368 pix.
= 467.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-26.989023 - 51.945709999999998
Average (Standard dev.)0.01919182 (±2.7592862)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-184-184-184
Dimensions368368368
Spacing368368368
CellA=B=C: 467.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63322_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_63322_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 : Bovine adenovirus 3

EntireName: Bovine adenovirus 3
Components
  • Complex: Bovine adenovirus 3
    • Protein or peptide: Hexon protein
    • Protein or peptide: PVI
    • Protein or peptide: Pre-histone-like nucleoprotein
    • Protein or peptide: PX
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: PV
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: PIX
    • Protein or peptide: Penton protein

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Supramolecule #1: Bovine adenovirus 3

SupramoleculeName: Bovine adenovirus 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bovine adenovirus 3

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Macromolecule #1: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Bovine adenovirus 3
Molecular weightTheoretical: 103.148008 KDa
SequenceString: MATPSMLPQW SYMHIAGQDA SEYLSPGLVQ FAQATESYFN IGNKFRNPTV APTHDVTTER SQRLQLRFVP VDREDTQYSY KTRFQLAVG DNRVLDMAST YFDIRGTLDR GASFKPYSGT AYNSFAPKSA PNNTQFRQAN NGHPAQTIAQ ASYVATIGGA N NDLQMGVD ...String:
MATPSMLPQW SYMHIAGQDA SEYLSPGLVQ FAQATESYFN IGNKFRNPTV APTHDVTTER SQRLQLRFVP VDREDTQYSY KTRFQLAVG DNRVLDMAST YFDIRGTLDR GASFKPYSGT AYNSFAPKSA PNNTQFRQAN NGHPAQTIAQ ASYVATIGGA N NDLQMGVD ERQLPVYANT TYQPEPQLGI EGWTAGSMAV IDQAGGRVLR NPTQTPCYGS YAKPTNEHGG ITKANTQVEK KY YRTGDNG NPETVFYTEE ADVLTPDTHL VHAVPAADRA KVEGLSQHAA PNRPNFIGFR DCFVGLMYYN SGGNLGVLAG QSS QLNAVV DLQDRNTELS YQMLLANTTD RSRYFSMWNQ AMDSYDPEVR VIDNVGVEDE MPNYCFPLSG VQIGNRSHEV QRNQ QQWQN VANSDNNYIG KGNLPAMEIN LAANLWRSFL YSNVALYLPD NLKFTPHNIQ LPPNTNTYEY MNGRIPVSGL IDTYV NIGT RWSPDVMDNV NPFNHHRNSG LRYRSQLLGN GRFCDFHIQV PQKFFAIRNL LLLPGTYTYE WSFRKDVNMI LQSTLG NDL RVDGATVNIT SVNLYASFFP MSHNTASTLE AMLRNDTNDQ SFNDYLSAAN MLYPIPPNAT QLPIPSRNWA AFRGWSL TR LKQRETPALG SPFDPYFTYS GTIPYLDGTF YLSHTFRKVA IQFDSSVTWP GNDRLLTPNE FEIKISVDGE GYNVAQSN M TKDWFLVQML ANYNIGYQGY HLPPDYKDRT FSFLHNFIPM CRQVPNPATE GYFGLGIVNH RTTPAYWFRF CRAPREGHP YPQLALPPHW DPRHALRDPE RKFLCDRTLW RIPFSSNFMS MGSLTDLGQN LLYANAAHAL DMTFEMDPIN EPTLLYVLFE VFDVARVHQ PHRGVIEVVY LRTPFSAGNA TT

UniProtKB: Hexon protein

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Macromolecule #2: PVI

MacromoleculeName: PVI / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Bovine adenovirus 3
Molecular weightTheoretical: 28.24935 KDa
SequenceString: MDEYNYAALA PRQGSRPMLS QWSGIGTHEM HGGRFNLGSL WSGIRNVGSA LRTGALGPGT AMRASVARPA EKDGLARKDI EGVSAGIHG AVDLGRQQLE KAIEQRLERR PTAAGVEDLP LPPGTVLEAD RLPPSYAEAV AERPPPADVL LPASSKPPVA V VTLPPKKR ...String:
MDEYNYAALA PRQGSRPMLS QWSGIGTHEM HGGRFNLGSL WSGIRNVGSA LRTGALGPGT AMRASVARPA EKDGLARKDI EGVSAGIHG AVDLGRQQLE KAIEQRLERR PTAAGVEDLP LPPGTVLEAD RLPPSYAEAV AERPPPADVL LPASSKPPVA V VTLPPKKR VSEEPVEEVV IRSSAPPSYD EVMAPQPTLV AEQGAMKAVP VIKPAQPFTP AVHETQRIVT NLPITTAVTR RR GWQGTLN DIVGLGVRTV KRRRCY

UniProtKB: PVI

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Macromolecule #3: Pre-histone-like nucleoprotein

MacromoleculeName: Pre-histone-like nucleoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bovine adenovirus 3
Molecular weightTheoretical: 19.002049 KDa
SequenceString:
MAILISPSNN TGWGLGCNKM YGGARIRSDL HPVKVRSHYR AAWGSRTGRV GRRATAALAD AVAATGDPVA DTIEAVVADA RQYRRRRRR GVRRVRRLRR SPRTALQRRV RSVRRQVARA RRVGRRAAAI AADAAMAMAA PARRRRNIYW VRDAATGARV P VTTRPTVS NTV

UniProtKB: Pre-histone-like nucleoprotein

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Macromolecule #4: PX

MacromoleculeName: PX / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine adenovirus 3
Molecular weightTheoretical: 8.514133 KDa
SequenceString:
MSPRGNLTYR LRIPVALSGR RRRRTGLRGG SAYLLGRRRR RAGGGRLRGG FLPLLAPIIA AAIGAIPGIA SVAIQAAHNK

UniProtKB: PX

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Macromolecule #5: Pre-hexon-linking protein IIIa

MacromoleculeName: Pre-hexon-linking protein IIIa / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine adenovirus 3
Molecular weightTheoretical: 63.270523 KDa
SequenceString: MSDADPRIFQ LVSRQETVAM AEAPRSLGPA PSNPSLQALF QSQPSAEQEW HGVLERVMAL NKNGDFGSQP QANRFGAILE AVVPPRSDP THEKVLAIVN ALLETQAIRR DEAGQMYTAL LQRVARYNSV NVQGNLDRLI QDVKEALAQR ERTGPGAGLG S VVALNAFL ...String:
MSDADPRIFQ LVSRQETVAM AEAPRSLGPA PSNPSLQALF QSQPSAEQEW HGVLERVMAL NKNGDFGSQP QANRFGAILE AVVPPRSDP THEKVLAIVN ALLETQAIRR DEAGQMYTAL LQRVARYNSV NVQGNLDRLI QDVKEALAQR ERTGPGAGLG S VVALNAFL STQPAVVERG QENYVAFVSA LKLMVTEAPQ SEVYQAGPSF FFQTSRHGSQ TVNLSQAFDN LRPLWGVRAP VH ERTTISS LLTPNTRLLL LLIAPFTDSV GISRDSYLGH LLTLYRETIG NTRVDETTYN EITEVSRALG AEDASNLQAT LNY LLTNKQ SKLPQEFSLS PEEERVLRYV QQSVSLFLMQ DGHTATTALD QAAANIAPSF YASHRDFINR LMDYFQRAAA MAPD YFLQA VMNPHWLPPP GFFTQEFDFP EPNEGFLWDD LDSALLRAHV KEEEDQGAVG GTPAASAPAS RAHTPPPPPG AADLF APNA FRNVQNNGVD ELIDGLSRWK TYAQERQEVV ERHRRREARR RAREARLESS DDDDSDLGPF LRGTGHLVHN QFMHLK PRG PRQFW

UniProtKB: Pre-hexon-linking protein IIIa

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Macromolecule #6: PV

MacromoleculeName: PV / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine adenovirus 3
Molecular weightTheoretical: 45.388039 KDa
SequenceString: MASSRLIKEE MLDIVAPEIY KRKRPRRERA APYAVKQEEK PLVKAERKIK RGSRKRALSG VDVPLPDDGF EDDEPHIEFV SAPRRPYQW KGRRVRRVLR PGVAVSFTPG ARSLRPSSKR VYDEVYADDD FLEAAAAREG EFAYGKRGRE AAQAQLLPAV A VPEPTYVV ...String:
MASSRLIKEE MLDIVAPEIY KRKRPRRERA APYAVKQEEK PLVKAERKIK RGSRKRALSG VDVPLPDDGF EDDEPHIEFV SAPRRPYQW KGRRVRRVLR PGVAVSFTPG ARSLRPSSKR VYDEVYADDD FLEAAAAREG EFAYGKRGRE AAQAQLLPAV A VPEPTYVV LDESNPTPSY KPVTEQKVIL SRKRGVGKVE PTIQVLASKK RRMAENEDDR GAGSVAEVQM REVKPVTAAL GI QTVDVSV PDHSTPMEVV QSLSRAAQVA QRLTQQQVRP SAKIKVEAMD LSAPVDAKPL DLKPVDVKPT PTFVLPSFRS LST QTDSLP AAVVVPRKPR VHRATRRTAR GLLPYYRLHP SITPTPGYRG SVYTSSGVRL PAVRAPPSPP YPQGDSPPQR CRGR GAAAR RALSP

UniProtKB: PV

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Macromolecule #7: Pre-hexon-linking protein VIII

MacromoleculeName: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bovine adenovirus 3
Molecular weightTheoretical: 23.746486 KDa
SequenceString: MSKEIPTPYV WTFQPQMGAA AGASQDYSTR MNWFSAGPDM IHDVNNIRDA QNRILMTQSA ITATPRNLID PRQWAAHLIK QPVVGTTHV EMPRNEVLEQ HLTSHGAQIA GGGAAGDYFK SPTSARTLIP LTASCLRPDG VFQLGGGSRS SFNPLQTDFA F HALPSRPR ...String:
MSKEIPTPYV WTFQPQMGAA AGASQDYSTR MNWFSAGPDM IHDVNNIRDA QNRILMTQSA ITATPRNLID PRQWAAHLIK QPVVGTTHV EMPRNEVLEQ HLTSHGAQIA GGGAAGDYFK SPTSARTLIP LTASCLRPDG VFQLGGGSRS SFNPLQTDFA F HALPSRPR HGGIGSRQFV EEFVPAVYLN PYSGPPDSYP DQFIRHYNVY SNSVSGYS

UniProtKB: Pre-hexon-linking protein VIII

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Macromolecule #8: PIX

MacromoleculeName: PIX / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bovine adenovirus 3
Molecular weightTheoretical: 13.719456 KDa
SequenceString:
MAEEGRIYVP YVTARLPKWS GSVQDKTGSN MLGGVVLPPN SQAHRTETVG TEATRDNLHA EGARRPEDQT PYMILVEDSL GGLKRRMDL LEESNQQLLA TLNRLRTGLA AYVQANLVGG QVNPFV

UniProtKB: PIX

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Macromolecule #9: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine adenovirus 3
Molecular weightTheoretical: 55.13532 KDa
SequenceString: MLQPELQPIP LSRRRLMRRW WLGPSRRFLF DEIHVPPRYA AASAGRNSIR YSMLPPLYDT TKIYLIDNKS SDIQTLNYQN DHSDYLTTI VQNSDFTPLE ASNHSIELDE RSRWGGNLKT ILYTNLPNIT QHMFSNSFRV KMMASKKDGV PQYEWFPLRL P EGNFSETM ...String:
MLQPELQPIP LSRRRLMRRW WLGPSRRFLF DEIHVPPRYA AASAGRNSIR YSMLPPLYDT TKIYLIDNKS SDIQTLNYQN DHSDYLTTI VQNSDFTPLE ASNHSIELDE RSRWGGNLKT ILYTNLPNIT QHMFSNSFRV KMMASKKDGV PQYEWFPLRL P EGNFSETM VIDLMNNAIV ELYLALGRQE GVKEEDIGVK IDTRNFSLGY DPQTQLVTPG VYTNEAMHAD IVLLPGCAID FT HSRLNNL LGIRKRFPYQ EGFVISYEDL KGGNIPALMD VEEFNKSKTV RALREDPKGR SYHVGEDPEA RENETAYRSW YLA YNYGDP EKGVRATTLL TTGDVTCGVE QIYWSLPDMA LDPVTFKASL KTSNYPVVGT ELLPLVPRSF YNAQAVYSQW IQEK TNQTH VFNRFPENQI LVRPPAPTIT SISENKPSLT DHGIVPLRNR LGGVQRVTLT DARRRSCPYV YKSLGIVTPQ VLSSR TF

UniProtKB: Penton 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45262
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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