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- EMDB-19401: FAdV-C4 AG234 Aviadenovirus structure, strain KR5 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-19401
TitleFAdV-C4 AG234 Aviadenovirus structure, strain KR5
Map data
Sample
  • Virus: Fowl aviadenovirus C
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: PIIIa
    • Protein or peptide: Pre-hexon-linking protein VIII
Keywordsadenovirus / fowl / highly thermostable / VIRUS
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral capsid / host cell / endocytosis involved in viral entry into host cell / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
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 / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain ...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 / 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
PIIIa / Penton protein / Hexon protein / Pre-hexon-linking protein VIII
Similarity search - Component
Biological speciesFowl aviadenovirus C
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPerez-Illana MP / Schachnner A / Condezo GN / Hernando-Perez M / Martinez M / Marabini R / Hess M / San Martin C
Funding support2 items
OrganizationGrant numberCountry
Other privateLa Caixa Foundation (ID 100010434),La Caixa Foundation (ID 100010434),LCF/BQ/SO16/52270032)
Other governmentco-funded by the Spanish State Research Agency and the European Regional Development Fund, PID2022-136456NB-I00/ AEI/10.13039/501100011033/FEDER,UE
CitationJournal: To Be Published
Title: FAdV-C4 AG234 Aviadenovirus structure, strain KR5
Authors: Perez-Illana MP / Schachnner A / Condezo GN / Hernando-Perez M / Martinez M / Marabini R / Hess M / San Martin C
History
DepositionJan 12, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19401.png

Downloads & links

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Map

FileDownload / File: emd_19401.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 758 pix.
= 1042.25 Å		1.38 Å/pix.
x 758 pix.
= 1042.25 Å		1.38 Å/pix.
x 758 pix.
= 1042.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.10500151 - 0.16781294
Average (Standard dev.)0.0008913822 (±0.015192559)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-379-379-379
Dimensions758758758
Spacing758758758
CellA=B=C: 1042.25 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19401_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_19401_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 : Fowl aviadenovirus C

EntireName: Fowl aviadenovirus C
Components
  • Virus: Fowl aviadenovirus C
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: PIIIa
    • Protein or peptide: Pre-hexon-linking protein VIII

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Supramolecule #1: Fowl aviadenovirus C

SupramoleculeName: Fowl aviadenovirus C / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 190063 / Sci species name: Fowl aviadenovirus C / Sci species strain: KR5 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Gallus gallus (chicken)

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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: Fowl aviadenovirus C
Molecular weightTheoretical: 106.129789 KDa
SequenceString: MAALTPDLTT ATPRLQYFHI AGPGTREYLS EDLQQFISAT GSYFDLKNKF RQTVVAPTRN VTTEKAQRLQ IRFYPIQTDD TSTGYRVRY NINVGDGWVL DMGSTYFDIK GILDRGPSFK PYCGTAYNPL APKESMFNNW SETAPGQNVS ASGQLSNVYT N TSTTKDTT ...String:
MAALTPDLTT ATPRLQYFHI AGPGTREYLS EDLQQFISAT GSYFDLKNKF RQTVVAPTRN VTTEKAQRLQ IRFYPIQTDD TSTGYRVRY NINVGDGWVL DMGSTYFDIK GILDRGPSFK PYCGTAYNPL APKESMFNNW SETAPGQNVS ASGQLSNVYT N TSTTKDTT AAQVTKISGV FPNPNQGPGI NPLRQVENAN TGVLGRFAKS QYNYAYGAYV KPVAADGSQS LTQTPYWIMN NA GTEYLGA VAVEDYTNSL SYPDTMIVPP PEDYDDYNIG TTRALRPNYI GFRDNFINLL YHDSGVCSGT LNSERSGMNV VVE LPDRNT ELSYQYMLAD MMSRHHYFAL WNQAVDQYDP EVRVFSNDGY EEGAPSYAFN PEAVGAGEGY GPDLSQIKLY TNNT AANDK NTAVTNATTN FYFGTVPSYE IDISATQRRN FIMANIAEYL PDRYKFSISG FDATSVAPTT YEYMNKRVPL TNVVD MFTN VGARWSIDQM DNVNPFNHHR NWGLKYRSQL LGNSRYVNFH IQVPQKFFAI KNLLLLSGSY TYEWVLRKDP NMILQS SLG NDLRADGASI IYNEVNLMAN FMPMDHNTSN QLELMLRNAT NDQTFVDYLG AKNALYSVPA GSTALTINIP ARTWEGM RG WSFTRIKAAE TPQLGAQYDV NFKYSGSIAY SDGGFYLSHT FRNMSILFDT SINWPGNDRL LTPNMFEIKR SVALDTEG F TMSQCDITKD WYLIQMATNY NFVYNGYRFW PDRQYFHYDF LRNFDPMTRQ GPNFALPGLF DLVSYTPTTD NSGEQPSQE AVRNNSGFIA PRSWPVWSAH QGESWPANWP YPLCGQQAIQ PGQVLSYKKF LCDNYLWTIP FSSDFMYMGE LTDLGQNPMY TNNSHSMVI NFELDPMDDP TYVYMLYGVF DTVRVNQPER NVLAMAYFRT PFATGNAV

UniProtKB: Hexon protein

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Macromolecule #2: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fowl aviadenovirus C
Molecular weightTheoretical: 57.448238 KDa
SequenceString: MWGLQPPTSI PPPPPPTELT PSTYPAMVNG YPPPAASAQS CSSSGGQSEL YMPLQRVMAP TGGRNSIKYR DYTPCRNTTK LFYVDNKAS DIDTYNKDAN HSNFRTTVIH NQDLDADTAA TESIQLDNRS CWGGDLKTAV RTNCPNVSSF FQSNSVRVRM M WKRDPPTS ...String:
MWGLQPPTSI PPPPPPTELT PSTYPAMVNG YPPPAASAQS CSSSGGQSEL YMPLQRVMAP TGGRNSIKYR DYTPCRNTTK LFYVDNKAS DIDTYNKDAN HSNFRTTVIH NQDLDADTAA TESIQLDNRS CWGGDLKTAV RTNCPNVSSF FQSNSVRVRM M WKRDPPTS TAPPSAVGSG YSVPGAQYKW YDLTVPEGNY ALCELIDLLN EGIVQLYLSE GRQNNVQKSD IGVKFDTRNF GL LRDPVTG LVTPGTYVYK GYHPDIVLLP GCAIDFTYSR LSLLLGIGKR EPYSKGFVIT YEDLQGGDIP ALLDLDSVDV NDA DGEVIE LDNAAPLLHD SAGVSYNVIY DQVTGKPVTA YRSWMLAYNV PNSQANQTTL LTVPDMAGGI GAMYTSLPDT FIAP TGFKE DNTTNLCPVV GMNLFPTYNK IYYQAASTYV QRLENSCQSA TAAFNRFPEN EILKQAPPMN VSSVCDNQPA VVQQG VLPV KSSLPGLQRV LITDDQRRPI PYVYKSIATV QPTVLSSATL Q

UniProtKB: Penton protein

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Macromolecule #3: PIIIa

MacromoleculeName: PIIIa / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fowl aviadenovirus C
Molecular weightTheoretical: 65.326297 KDa
SequenceString: MSSTEVFGAL APVGRTEVAD ALSSHANSKD ARSLRYEPYA NRLIKLQTAM VPPKVDGTSE RVAEVVKGLA EQGAIYPDQM GAIHSDLLN RVYTWNSMGV QESIQALVND VIHGQNKVLQ DELARTREIA NASMLTRFFD SLYKTVDRGQ RNFEGFKKLL R LFVNNVPN ...String:
MSSTEVFGAL APVGRTEVAD ALSSHANSKD ARSLRYEPYA NRLIKLQTAM VPPKVDGTSE RVAEVVKGLA EQGAIYPDQM GAIHSDLLN RVYTWNSMGV QESIQALVND VIHGQNKVLQ DELARTREIA NASMLTRFFD SLYKTVDRGQ RNFEGFKKLL R LFVNNVPN AEVYSSGGSF SLQINMGGQS QNINLTNAFD NLKDIWGARW DAVNNPRIGA LLTPNTRALL FFVSTFYDYG SM EPGSYLD NLMRLYKEAI RADTDAEGDA IMELGDAGAN LNLKFNQYKD TLNYLLQNKP SVPQTGPLEM SPEQESLFKY LMR QLRRAL KDGVNSDIAI STMAQYVDPR LYTSNKVFID KLQNYLLMAS ARNPYYYKTI VLDPHWVPPA GLYTDNFVIP EMMP NFSDF ASELEYGGPS RDEYFDDSPF RPPPQKKFTE KEQADYDSLI NFFDSTLGVQ SEAGWIADHR LPQAFDGALN VSERT PYNT PLPDDAPMRS RNASVSSATD ALGQLKLSGT GGAGFFDSLK PSVGTRRSTG LAKGLAGTGQ PPCPWPASVG YASAGY GPA RGIRGSGLAR RALAARGLRQ GKRLRFY

UniProtKB: PIIIa

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Macromolecule #4: Pre-hexon-linking protein VIII

MacromoleculeName: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Fowl aviadenovirus C
Molecular weightTheoretical: 26.882158 KDa
SequenceString: MNLLNAAPTP YVWKYNPVTG KCAGAQQNYG ATIDWVLPGG NSFAYAADEI RRRFPEPAVT RAITARFEAE SDQQPYAGPH ETNIITADV VRSGPPPSAV YPFDPSGVQR VQLSGGMMGG RTEGRMQLSG GLTEGRMQLA GGAAGKLPTR ARPTLRPPRW C GTTLTGNG ...String:
MNLLNAAPTP YVWKYNPVTG KCAGAQQNYG ATIDWVLPGG NSFAYAADEI RRRFPEPAVT RAITARFEAE SDQQPYAGPH ETNIITADV VRSGPPPSAV YPFDPSGVQR VQLSGGMMGG RTEGRMQLSG GLTEGRMQLA GGAAGKLPTR ARPTLRPPRW C GTTLTGNG LPADYPEMTP DAFKYYLRVQ GPSQEVDEPG VMSQRQFMTT FLPAMVPHPF DSESPDAFPA YFSSVYKGTN AF EPVFWQG

UniProtKB: Pre-hexon-linking protein VIII

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 95890 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9466
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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