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- EMDB-10768: HAdV-F41 Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-10768
TitleHAdV-F41 Capsid
Map datacryo_EM reconstruction
Sample
  • Virus: Human adenovirus 41
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: Hexon-interlacing protein
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Pre-histone-like nucleoprotein
KeywordsAdenovirus / VIRUS
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 / viral procapsid / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / endocytosis involved in viral entry into host cell / viral penetration into host nucleus ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / endocytosis involved in viral entry into host cell / viral penetration into host nucleus / viral capsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / DNA binding
Similarity search - Function
Adenoviral core protein VII / Adenoviral core protein VII / : / Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII ...Adenoviral core protein VII / Adenoviral core protein VII / : / Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / 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 / 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
Hexon protein / Hexon-interlacing protein / Pre-histone-like nucleoprotein / Pre-protein VI / Pre-hexon-linking protein VIII / Pre-hexon-linking protein IIIa / Penton protein
Similarity search - Component
Biological speciesHuman adenovirus F serotype 41 / Human adenovirus 41
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsPerez Illana M / Martinez M
Funding support Spain, European Union, 3 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU-2016-74868P Spain
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-76400-R Spain
European Commissioninext-1750European Union
CitationJournal: Sci Adv / Year: 2021
Title: Cryo-EM structure of enteric adenovirus HAdV-F41 highlights structural variations among human adenoviruses.
Authors: Marta Pérez-Illana / Marta Martínez / Gabriela N Condezo / Mercedes Hernando-Pérez / Casandra Mangroo / Martha Brown / Roberto Marabini / Carmen San Martín /
Abstract: Enteric adenoviruses, one of the main causes of viral gastroenteritis in the world, must withstand the harsh conditions found in the gut. This requirement suggests that capsid stability must be ...Enteric adenoviruses, one of the main causes of viral gastroenteritis in the world, must withstand the harsh conditions found in the gut. This requirement suggests that capsid stability must be different from that of other adenoviruses. We report the 4-Å-resolution structure of a human enteric adenovirus, HAdV-F41, and compare it with that of other adenoviruses with respiratory (HAdV-C5) and ocular (HAdV-D26) tropisms. While the overall structures of hexon, penton base, and internal minor coat proteins IIIa and VIII are conserved, we observe partially ordered elements reinforcing the vertex region, which suggests their role in enhancing the physicochemical capsid stability of HAdV-F41. Unexpectedly, we find an organization of the external minor coat protein IX different from all previously characterized human and nonhuman mastadenoviruses. Knowledge of the structure of enteric adenoviruses provides a starting point for the design of vectors suitable for oral delivery or intestinal targeting.
History
DepositionMar 16, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.07
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  • Surface view with fitted model
  • Atomic models: PDB-6yba
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yba
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10768.png

Downloads & links

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Map

FileDownload / File: emd_10768.map.gz / Format: CCP4 / Size: 1.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo_EM reconstruction
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.25254947 - 0.36396697
Average (Standard dev.)0.0013525777 (±0.027217593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-390-390-390
Dimensions780780780
Spacing780780780
CellA=B=C: 1060.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z780780780
origin x/y/z0.0000.0000.000
length x/y/z1060.8001060.8001060.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-390-390-390
NC/NR/NS780780780
D min/max/mean-0.2530.3640.001

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Supplemental data

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Sample components

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Entire : Human adenovirus 41

EntireName: Human adenovirus 41
Components
  • Virus: Human adenovirus 41
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: Hexon-interlacing protein
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Pre-histone-like nucleoprotein

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Supramolecule #1: Human adenovirus 41

SupramoleculeName: Human adenovirus 41 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10524 / Sci species name: Human adenovirus 41 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Diameter: 840.0 Å

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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: Human adenovirus F serotype 41
Molecular weightTheoretical: 104.064234 KDa
SequenceString: MATPSMMPQW SYMHIAGQDA SEYLSPGLVQ FARATDTYFS LGNKFRNPTV APTHDVTTDR SQRLTLRFVP VDREDTAYSY KVRFTLAVG DNRVLDMAST YFDIRGVLDR GPSFKPYSGT AYNSLAPKTA PNPCEWKDNN KIKVRGQAPF IGTNINKDNG I QIGTDTTN ...String:
MATPSMMPQW SYMHIAGQDA SEYLSPGLVQ FARATDTYFS LGNKFRNPTV APTHDVTTDR SQRLTLRFVP VDREDTAYSY KVRFTLAVG DNRVLDMAST YFDIRGVLDR GPSFKPYSGT AYNSLAPKTA PNPCEWKDNN KIKVRGQAPF IGTNINKDNG I QIGTDTTN QPIYADKTYQ PEPQVGQTQW NSEVGAAQKV AGRVLKDTTP MLPCYGSYAK PTNEKGGQAS LITNGTDQTL TS DVNLQFF ALPSTPNEPK AVLYAENVSI EAPDTHLVYK PDVAQGTISS ADLLTQQAAP NRPNYIGFRD NFIGLMYYNS TGN MGVLAG QASQLNAVVD LQDRNTELSY QLMLDALGDR SRYFSMWNQA VDSYDPDVRI IENHGVEDEL PNYCFPLGGS AATD TYSGI KANGQTWTAD DNYADRGAEI ESGNIFAMEI NLAANLWRSF LYSNVALYLP DSYKITPDNI TLPENKNTYA YMNGR VAVP SALDTYVNIG ARWSPDPMDN VNPFNHHRNA GLRYRSMLLG NGRYVPFHIQ VPQKFFAIKN LLLLPGSYTY EWNFRK DVN MILQSSLGND LRVDGASVRF DSINLYANFF PMAHNTASTL EAMLRNDTND QSFNDYLCAA NMLYPIPSNA TSVPISI PS RNWAAFRGWS FTRLKTKETP SLGSGFDPYF TYSGSVPYLD GTFYLNHTFK KVSIMFDSSV SWPGNDRLLT PNEFEIKR T VDGEGYNVAQ CNMTKDWFLI QMLSHYNIGY QGFYVPESYK DRMYSFFRNF QPMSRQVVNT TTYKEYQNVT LPFQHNNSG FVGYMGPTMR EGQAYPANYP YPLIGQTAVP SLTQKKFLCD RTMWRIPFSS NFMSMGALTD LGQNMLYANS AHALDMTFEV DPMDEPTLL YVLFEVFDVV RIHQPHRGVI EAVYLRTPFS AGNATT

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: Human adenovirus F serotype 41
Molecular weightTheoretical: 57.14216 KDa
SequenceString: MRRAVGVPPV MAYAEGPPPS YESVMGSADS PATLEALYVP PRYLGPTEGR NSIRYSELAP LYDTTRVYLV DNKSADIASL NYQNDHSNF QTTVVQNNDF TPAEAGTQTI NFDERSRWGA DLKTILRTNM PNINEFMSTN KFKARLMVEK KNKETGLPRY E WFEFTLPE ...String:
MRRAVGVPPV MAYAEGPPPS YESVMGSADS PATLEALYVP PRYLGPTEGR NSIRYSELAP LYDTTRVYLV DNKSADIASL NYQNDHSNF QTTVVQNNDF TPAEAGTQTI NFDERSRWGA DLKTILRTNM PNINEFMSTN KFKARLMVEK KNKETGLPRY E WFEFTLPE GNYSETMTID LMNNAIVDNY LEVGRQNGVL ESDIGVKFDT RNFRLGWDPV TKLVMPGVYT NEAFHPDIVL LP GCGVDFT QSRLSNLLGI RKRLPFQEGF QIMYEDLEGG NIPALLDVAK YEASIQKAKE EGKEIGDDTF ATRPQDLVIE PVA KDSKNR SYNLLPNDQN NTAYRSWFLA YNYGDPKKGV QSWTLLTTAD VTCGSQQVYW SLPDMMQDPV TFRPSTQVSN YPVV GVELL PVHAKSFYNE QAVYSQLIRQ STALTHVFNR FPENQILVRP PAPTITTVSE NVPALTDHGT LPLRSSISGV QRVTI TDAR RRTCPYVHKA LGIVAPKVLS SRTF

UniProtKB: Penton protein

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Macromolecule #3: Pre-hexon-linking protein IIIa

MacromoleculeName: Pre-hexon-linking protein IIIa / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus F serotype 41
Molecular weightTheoretical: 64.825246 KDa
SequenceString: MQRSTAVVDG SQQVDPAMLA ALQSQPSGVT PSDDWAAAMD RILALTTRNP EAFRQQPQAN RFSAILEAVV PSRTNPTHEK VLAIVNALT ESKAIRKDEA GLIYNALLER VARYNSTNVQ ANLDRLTTDV REAVAQRERF MHDTNLGSQV ALNAFLSTLP A NVPRGQED ...String:
MQRSTAVVDG SQQVDPAMLA ALQSQPSGVT PSDDWAAAMD RILALTTRNP EAFRQQPQAN RFSAILEAVV PSRTNPTHEK VLAIVNALT ESKAIRKDEA GLIYNALLER VARYNSTNVQ ANLDRLTTDV REAVAQRERF MHDTNLGSQV ALNAFLSTLP A NVPRGQED YVSFISALRL LVAEVPQSEV YQSGPDYFFQ TSRQGLQTVN LTQAFKNLQG MWGVRAPVGD RATISSLLTP NT RLLLLLI APFTNSSTIS RDSYLGHLIT LYREAIGQTQ VDEQTFQEIT SVSRALGQQD TGSLEATLNF LLTNRQQKIP SQF TLSTEE ERILRYVQQS VSLYLMREGM TPSSALDMTA RNMEPSLYSS NRPFINRLMD YLHRAAAMNS EYFTNAILNP HWMP PSGFY TGEFDMPEGD DGFLWDDVSD SIFVPARYRK KEGGDELPLP LVEAASRGQS PFPSLPSLVS SSNSGRVLRP RLPGE TDYL NDPLLQPVRN KNFPNNGVES LVDKMNRWKT YAQEQREWEE SQSRPLAGPF SRWRRREDDQ DDSADDNSVL DLGGTG ASS NPFAHLRPQG RLGRLY

UniProtKB: Pre-hexon-linking protein IIIa

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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: Human adenovirus F serotype 41
Molecular weightTheoretical: 25.358287 KDa
SequenceString: MSKEIPTPYM WSYQPQMGLA AGASQDYSSR MNWLSAGPHM IGRVNGIRAT RNQILLEQAA LTSTPRSQLN PPNWPAVQVY QENPAPTTV LLPRDAEAEV QMTNSGAQLA GGSRHVRFRG RSSPYSPGPI KRLIIRGRGI QLNDEVVSSL TGLRPDGVFQ L GGAGRSSF ...String:
MSKEIPTPYM WSYQPQMGLA AGASQDYSSR MNWLSAGPHM IGRVNGIRAT RNQILLEQAA LTSTPRSQLN PPNWPAVQVY QENPAPTTV LLPRDAEAEV QMTNSGAQLA GGSRHVRFRG RSSPYSPGPI KRLIIRGRGI QLNDEVVSSL TGLRPDGVFQ L GGAGRSSF TPRQAYLTLQ SSSSQPRSGG IGTLQFVEEF VPSVYFNPFS GAPGLYPDDF IPNYDAVSES VDGYD

UniProtKB: Pre-hexon-linking protein VIII

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Macromolecule #5: Hexon-interlacing protein

MacromoleculeName: Hexon-interlacing protein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus F serotype 41
Molecular weightTheoretical: 13.617179 KDa
SequenceString:
MSGSMEGNAV SFKGGVFSPY LTTRLPAWAG VRQNVMGSNV DGRPVAPANS ATLTYATVGS SVDTAAAAAA SAAASTARGM AADFGLYNQ LAASRSLREE DALSVVLTRL EELSQQLQDL FAKVALLNPP ANAS

UniProtKB: Hexon-interlacing protein

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Macromolecule #6: Pre-protein VI

MacromoleculeName: Pre-protein VI / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus F serotype 41
Molecular weightTheoretical: 29.170145 KDa
SequenceString: MEDINFASLA PRHGSRPFMG TWNEIGTSQL NGGAFSWSSL WSGIKNFGSS IKSFGNKAWN SNTGQMLRDK LKDQNFQQKV VDGLASGIN GVVDIANQAL QNQINQRLEN SRQPPVALKQ RPTPEPEEVE VEEKLPPLET APPLPSKGEK RPRPELEETL V VESREPPS ...String:
MEDINFASLA PRHGSRPFMG TWNEIGTSQL NGGAFSWSSL WSGIKNFGSS IKSFGNKAWN SNTGQMLRDK LKDQNFQQKV VDGLASGIN GVVDIANQAL QNQINQRLEN SRQPPVALKQ RPTPEPEEVE VEEKLPPLET APPLPSKGEK RPRPELEETL V VESREPPS YEQALKEGAS YPMTRPIGSM ARPVYGKEKT PVTLELPPPA PTVPPMPTPT LGTNVPRLAA PTVAVATPAR RV RGANWQS TLNSIVGLGV KSLKRRRCY

UniProtKB: Pre-protein VI

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Macromolecule #7: Pre-histone-like nucleoprotein

MacromoleculeName: Pre-histone-like nucleoprotein / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus F serotype 41
Molecular weightTheoretical: 20.386445 KDa
SequenceString:
MSILISPDNN TGWGLHSAGM YGGAKRRSSQ HPVRVRGHYR APWGAHTRGI ISGRTTVDDV IDSVVADARR YQRPTSTVDS VIDSVVADA RRYAQRKSRL RRRRRRPTTA MIAARAVLRR ARRIGRRAMR RAAAAASAGR ARRQAARQAA AAIASMAQPR R GNVYWVRD ASGVRVPVRT RPPRS

UniProtKB: Pre-histone-like nucleoprotein

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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 TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

4551

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9926
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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