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Yorodumi- EMDB-8471: Cryo-Electron microscopy structure of species-D human adenovirus 26 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8471 | |||||||||
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Title | Cryo-Electron microscopy structure of species-D human adenovirus 26 | |||||||||
Map data | species-D human adenovirus 26 | |||||||||
Sample |
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Keywords | human adenovirus 26 / hexon / penton base / minor proteins / VIRUS | |||||||||
Function / homology | Function and homology information viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / hexon binding / viral release from host cell / endocytosis involved in viral entry into host cell / host cell ...viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / hexon binding / viral release from host cell / endocytosis involved in viral entry into host cell / host cell / viral capsid / host cell cytoplasm / cell adhesion / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | Human adenovirus 26 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Reddy V / Yu X | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Sci Adv / Year: 2017 Title: Cryo-EM structure of human adenovirus D26 reveals the conservation of structural organization among human adenoviruses. Authors: Xiaodi Yu / David Veesler / Melody G Campbell / Mary E Barry / Francisco J Asturias / Michael A Barry / Vijay S Reddy / Abstract: Human adenoviruses (HAdVs) cause acute respiratory, ocular, and gastroenteric diseases and are also frequently used as gene and vaccine delivery vectors. Unlike the archetype human adenovirus C5 ...Human adenoviruses (HAdVs) cause acute respiratory, ocular, and gastroenteric diseases and are also frequently used as gene and vaccine delivery vectors. Unlike the archetype human adenovirus C5 (HAdV-C5), human adenovirus D26 (HAdV-D26) belongs to species-D HAdVs, which target different cellular receptors, and is differentially recognized by immune surveillance mechanisms. HAdV-D26 is being championed as a lower seroprevalent vaccine and oncolytic vector in preclinical and human clinical studies. To understand the molecular basis for their distinct biological properties and independently validate the structures of minor proteins, we determined the first structure of species-D HAdV at 3.7 Å resolution by cryo-electron microscopy. All the hexon hypervariable regions (HVRs), including HVR1, have been identified and exhibit a distinct organization compared to those of HAdV-C5. Despite the differences in the arrangement of helices in the coiled-coil structures, protein IX molecules form a continuous hexagonal network on the capsid exterior. In addition to the structurally conserved region (3 to 300) of IIIa, we identified an extra helical domain comprising residues 314 to 390 that further stabilizes the vertex region. Multiple (two to three) copies of the cleaved amino-terminal fragment of protein VI (pVIn) are observed in each hexon cavity, suggesting that there could be ≥480 copies of VI present in HAdV-D26. In addition, a localized asymmetric reconstruction of the vertex region provides new details of the three-pronged "claw hold" of the trimeric fiber and its interactions with the penton base. These observations resolve the previous conflicting assignments of the minor proteins and suggest the likely conservation of their organization across different HAdVs. | |||||||||
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_8471.map.gz | 4.9 GB | EMDB map data format | |
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Header (meta data) | emd-8471-v30.xml emd-8471.xml | 20.7 KB 20.7 KB | Display Display | EMDB header |
Images | emd_8471.png | 250.2 KB | ||
Filedesc metadata | emd-8471.cif.gz | 7.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8471 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8471 | HTTPS FTP |
-Validation report
Summary document | emd_8471_validation.pdf.gz | 531.3 KB | Display | EMDB validaton report |
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Full document | emd_8471_full_validation.pdf.gz | 530.9 KB | Display | |
Data in XML | emd_8471_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_8471_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8471 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8471 | HTTPS FTP |
-Related structure data
Related structure data | 5tx1MC 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_8471.map.gz / Format: CCP4 / Size: 6.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | species-D human adenovirus 26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 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 26
Entire | Name: Human adenovirus 26 |
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Components |
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-Supramolecule #1: Human adenovirus 26
Supramolecule | Name: Human adenovirus 26 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#10 / NCBI-ID: 46928 / Sci species name: Human adenovirus 26 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Molecular weight | Theoretical: 150 MDa |
Virus shell | Shell ID: 1 / Name: Adenovirus / Diameter: 950.0 Å / T number (triangulation number): 25 |
-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 26 |
Molecular weight | Theoretical: 107.218703 KDa |
Sequence | String: MATPSMMPQW AYMHIAGQDA SEYLSPGLVQ FARATDTYFS LGNKFRNPTV APTHDVTTDR SQRLTLRFVP VDREATTYLY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPSFKPYSGT AYNSLAPKGA PNPSQWETKE KQGTTGGVQQ EKDVTKTFGV A ATGGINIT ...String: MATPSMMPQW AYMHIAGQDA SEYLSPGLVQ FARATDTYFS LGNKFRNPTV APTHDVTTDR SQRLTLRFVP VDREATTYLY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPSFKPYSGT AYNSLAPKGA PNPSQWETKE KQGTTGGVQQ EKDVTKTFGV A ATGGINIT NQGLLLGTDE TAENGKKDIY ADKTFQPEPQ VGEENWQENE AFYGGRALKK DTKMKPCYGS FARPTNEKGG QA KFKPVNE GEQPKDLDID FAYFDVPGGS PPAGGSGEEY KADIILYTEN VNLETPDTHV VYKPGTSDNS SEINLVQQSM PNR PNYIGF RDNFVGLMYY NSTGNMGVLA GQASQLNAVV DLQDRNTELS YQLLLDSLGD RTRYFSMWNS AVDSYDPDVR IIEN HGVED ELPNYCFPLN GTGTNSTYQG VKITNGNDGA EESEWEKDDA ISRQNQICKG NVYAMEINLQ ANLWKSFLYS NVALY LPDS YKYTPANVKL PANTNTYEYM NGRVVAPSLV DAYINIGARW SLDPMDNVNP FNHPRNAGLR YRSMLLGNGR YVPFHI QVP QKFFAIKNLL LLPGSYTYEW NFRKDVNMIL QSSLGNDLRV DGASVRFDSV NLYATFFPMA HNTASTLEAM LRNDTHD QS FNDYLSAANM LYPIPAKATN VPISIPSRNW AAFRGWSFTR LKTKETPSLG SGFDPYFVYS GSIPYLDGTF YLNHTFKK V SIMFDSSVSW PGNDRLLTPN EFEIKRSVDG EGYNVAQCNM TKDWFLVQML SHYNIGYQGF HVPEGYKDRM YSFFRNFQP MSRQVVDEIN YKDYKAVTLP FQHNNSGFTG YLAPTMRQGQ PYPANFPYPL IGQTAVPSVT QKKFLCDRVM WRIPFSSNFM SMGALTDLG QNMLYANSAH ALDMTFEVDP MDEPTLLYLL FEVFDVVRVH QPHRGVIEAV YLRTPFSAGN ATT UniProtKB: Hexon protein |
-Macromolecule #2: Penton
Macromolecule | Name: Penton / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus 26 |
Molecular weight | Theoretical: 56.312039 KDa |
Sequence | String: LEVPFVPPRY MAPTEGRNSI RYSELAPQYD TTRVYLVDNK SADIASLNYQ NDHSNFLTTV VQNNDFTPAE ASTQTINFDE RSRWGGDLK TILHTNMPNV NEYMFTSKFK ARVMVSRKHP EGVVETDLSQ DKLEYEWFEF TLPEGNFSET MTIDLMNNAI L ENYLQVGR ...String: LEVPFVPPRY MAPTEGRNSI RYSELAPQYD TTRVYLVDNK SADIASLNYQ NDHSNFLTTV VQNNDFTPAE ASTQTINFDE RSRWGGDLK TILHTNMPNV NEYMFTSKFK ARVMVSRKHP EGVVETDLSQ DKLEYEWFEF TLPEGNFSET MTIDLMNNAI L ENYLQVGR QNGVLESDIG VKFDSRNFKL GWDPVTKLVM PGVYTYEAFH PDVVLLPGCG VDFTESRLSN LLGIRKKQPF QE GFRIMYE DLEGGNIPAL LDVPKYLESK KKVEDETKNA AAATADTTTR GDTFATPAQE TAADKKVEVL PIEKDESGRS YNL IQGTHD TLYRSWYLSY TYGDPEKGVQ SWTLLTTPDV TCGAEQVYWS LPDLMQDPVT FRSTQQVSNY PVVGAELMPF RAKS FYNDL AVYSQLIRSY TSLTHVFNRF PDNQILCRPP APTITTVSEN VPALTDHGTL PLRSSIRGVQ RVTVTDARRR TCPYV YKAL GIVAPRVLSS RTF UniProtKB: Penton protein |
-Macromolecule #3: Fiber
Macromolecule | Name: Fiber / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus 26 |
Molecular weight | Theoretical: 2.276526 KDa |
Sequence | String: AKRLRVEDDF NPVYPYGYA UniProtKB: Fiber |
-Macromolecule #4: PIIIa
Macromolecule | Name: PIIIa / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus 26 |
Molecular weight | Theoretical: 43.148438 KDa |
Sequence | String: QQAPDPAIRA ALQSQPSGLA SDDWEAAMQR IMALTTRNPE SFRQQPQANR LSAILEAVVP SRTNPTHEKV LAIVNALAEN KAIRPDEAG LVYNALLERV GRYNSTNVQS NLDRLVTDVR EAVAQRERFK NEGLGSLVAL NAFLATQPAN VPRGQDDYTN F ISALRLMV ...String: QQAPDPAIRA ALQSQPSGLA SDDWEAAMQR IMALTTRNPE SFRQQPQANR LSAILEAVVP SRTNPTHEKV LAIVNALAEN KAIRPDEAG LVYNALLERV GRYNSTNVQS NLDRLVTDVR EAVAQRERFK NEGLGSLVAL NAFLATQPAN VPRGQDDYTN F ISALRLMV TEVPQSEVYQ SGPDYFFQTS RQGLQTVNLS QAFKNLRGLW GVQAPVGDRS TVSSLLTPNS RLLLLLIAPF TD SGSVNRN SYLGHLLTLY REAIGQAQVD EQTFQEITSV SRALGQNDTD SLRATLNFLL TNRQQKIPAQ YALSAEEERI LRY VQQSVG LFLMQEGATP SAALDMTARN MEPSMYAANR PFINKLMDYL HRAAAMNTDY FTNAILNPHW LP UniProtKB: Pre-hexon-linking protein IIIa |
-Macromolecule #5: PIX
Macromolecule | Name: PIX / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus 26 |
Molecular weight | Theoretical: 13.800377 KDa |
Sequence | String: MNGTGGAFEG GLFSPYLTTR LPGWAGVRQN VMGSTVDGRP VLPANSSTMT YATVGNSSLD STAAAAAAAA AMTATRLASS YMPSSGSSP SVPSSIIAEE KLLALLAELE ALSRQLAALT QQVSELREQQ QQQNK UniProtKB: Hexon-interlacing protein |
-Macromolecule #6: PVIII
Macromolecule | Name: PVIII / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus 26 |
Molecular weight | Theoretical: 24.633643 KDa |
Sequence | String: MSKEIPTPYM WSYQPQMGLA AGASQDYSTR MNWLSAGPSM ISRVNGVRSH RNQILLEQAA VTSTPRAKLN PRNWPSTLVY QEIPGPTTV LLPRDALAEV RMTNSGVQLA GGASRCPLRP QSGIKTLVIR GRGTQLNDEL VSSSIGLRPD GVFQLAGAGR S SFTPNQAY ...String: MSKEIPTPYM WSYQPQMGLA AGASQDYSTR MNWLSAGPSM ISRVNGVRSH RNQILLEQAA VTSTPRAKLN PRNWPSTLVY QEIPGPTTV LLPRDALAEV RMTNSGVQLA GGASRCPLRP QSGIKTLVIR GRGTQLNDEL VSSSIGLRPD GVFQLAGAGR S SFTPNQAY LTLQSSSSEP RSGGIGTLQF VEEFVPSVYF NPFSGSPGLY PDEFIPNFDA VREAVDGYD UniProtKB: Pre-hexon-linking protein VIII |
-Macromolecule #7: PVI
Macromolecule | Name: PVI / type: protein_or_peptide / ID: 7 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus 26 |
Molecular weight | Theoretical: 3.348683 KDa |
Sequence | String: DINFASLAPR HGTRPFMGTW NEIGTSQLNG G UniProtKB: Pre-protein VI |
-Macromolecule #8: Unknown
Macromolecule | Name: Unknown / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus 26 |
Molecular weight | Theoretical: 869.063 Da |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6.0 mg/mL |
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Buffer | pH: 8.1 / Details: 40 mM Tris, pH 8.1, 300 mM NaCl, 10 mM CaCl2 |
Grid | Model: C-flat / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 6 sec. / Details: 20mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 |
Details | Virus particles |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 2000 / Average exposure time: 7.6 sec. / Average electron dose: 1.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-5tx1: |