+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10768 | ||||||||||||
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Title | HAdV-F41 Capsid | ||||||||||||
Map data | cryo_EM reconstruction | ||||||||||||
Sample |
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Keywords | Adenovirus / 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 | ||||||||||||
Biological species | Human adenovirus F serotype 41 / Human adenovirus 41 | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||
Authors | Perez Illana M / Martinez M | ||||||||||||
Funding support | Spain, European Union, 3 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10768.map.gz | 1.7 GB | EMDB map data format | |
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Header (meta data) | emd-10768-v30.xml emd-10768.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
Images | emd_10768.png | 118.2 KB | ||
Filedesc metadata | emd-10768.cif.gz | 6.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10768 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10768 | HTTPS FTP |
-Related structure data
Related structure data | 6ybaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10768.map.gz / Format: CCP4 / Size: 1.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryo_EM reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human adenovirus 41
Entire | Name: Human adenovirus 41 |
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Components |
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-Supramolecule #1: Human adenovirus 41
Supramolecule | Name: 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 |
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Host (natural) | Organism: Homo sapiens (human) |
Virus shell | Shell ID: 1 / Diameter: 840.0 Å |
-Macromolecule #1: Hexon protein
Macromolecule | Name: Hexon protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus F serotype 41 |
Molecular weight | Theoretical: 104.064234 KDa |
Sequence | String: 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 |
-Macromolecule #2: Penton protein
Macromolecule | Name: Penton protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus F serotype 41 |
Molecular weight | Theoretical: 57.14216 KDa |
Sequence | String: 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 |
-Macromolecule #3: Pre-hexon-linking protein IIIa
Macromolecule | Name: Pre-hexon-linking protein IIIa / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus F serotype 41 |
Molecular weight | Theoretical: 64.825246 KDa |
Sequence | String: 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 |
-Macromolecule #4: Pre-hexon-linking protein VIII
Macromolecule | Name: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus F serotype 41 |
Molecular weight | Theoretical: 25.358287 KDa |
Sequence | String: 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 |
-Macromolecule #5: Hexon-interlacing protein
Macromolecule | Name: Hexon-interlacing protein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus F serotype 41 |
Molecular weight | Theoretical: 13.617179 KDa |
Sequence | String: MSGSMEGNAV SFKGGVFSPY LTTRLPAWAG VRQNVMGSNV DGRPVAPANS ATLTYATVGS SVDTAAAAAA SAAASTARGM AADFGLYNQ LAASRSLREE DALSVVLTRL EELSQQLQDL FAKVALLNPP ANAS UniProtKB: Hexon-interlacing protein |
-Macromolecule #6: Pre-protein VI
Macromolecule | Name: Pre-protein VI / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus F serotype 41 |
Molecular weight | Theoretical: 29.170145 KDa |
Sequence | String: 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 |
-Macromolecule #7: Pre-histone-like nucleoprotein
Macromolecule | Name: Pre-histone-like nucleoprotein / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus F serotype 41 |
Molecular weight | Theoretical: 20.386445 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Applied 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 assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |