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- EMDB-8471: Cryo-Electron microscopy structure of species-D human adenovirus 26 -

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Entry
Database: EMDB / ID: EMD-8471
TitleCryo-Electron microscopy structure of species-D human adenovirus 26
Map dataspecies-D human adenovirus 26
Sample
  • Virus: Human adenovirus 26
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton
    • Protein or peptide: Fiber
    • Protein or peptide: PIIIa
    • Protein or peptide: PIX
    • Protein or peptide: PVIII
    • Protein or peptide: PVI
    • Protein or peptide: Unknown
Keywordshuman adenovirus 26 / hexon / penton base / minor proteins / 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 / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / viral release from host cell / endocytosis involved in viral entry into host cell / viral capsid ...hexon binding / 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 / viral release from host cell / endocytosis involved in viral entry into 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
Adenovirus Pll, hexon, subdomain 3 / 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 / Adenovirus Pll, hexon, subdomain 2 / Minor capsid protein VI ...Adenovirus Pll, hexon, subdomain 3 / 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 / Adenovirus Pll, hexon, subdomain 2 / 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 / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
Hexon-interlacing protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-protein VI / Pre-hexon-linking protein VIII / Fiber / Hexon protein
Similarity search - Component
Biological speciesHuman adenovirus 26
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsReddy V / Yu X
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI070771 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103692 United States
CitationJournal: 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
DepositionNov 15, 2016-
Header (metadata) releaseJan 25, 2017-
Map releaseMay 31, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
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  • Surface view colored by radius
  • Surface level: 0.012
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  • Surface view with fitted model
  • Atomic models: PDB-5tx1
  • Surface level: 0.012
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5tx1
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8471.png

Downloads & links

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Map

FileDownload / File: emd_8471.map.gz / Format: CCP4 / Size: 6.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationspecies-D human adenovirus 26
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy EMDB: 0.02 / Movie #1: 0.012
Minimum - Maximum-0.06903934 - 0.115228586
Average (Standard dev.)-0.001875943 (±0.005534527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-600-600-600
Dimensions120012001200
Spacing120012001200
CellA=B=C: 1571.9999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z120012001200
origin x/y/z0.0000.0000.000
length x/y/z1572.0001572.0001572.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-600-600-600
NC/NR/NS120012001200
D min/max/mean-0.0690.115-0.002

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Supplemental data

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Sample components

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Entire : Human adenovirus 26

EntireName: Human adenovirus 26
Components
  • Virus: Human adenovirus 26
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton
    • Protein or peptide: Fiber
    • Protein or peptide: PIIIa
    • Protein or peptide: PIX
    • Protein or peptide: PVIII
    • Protein or peptide: PVI
    • Protein or peptide: Unknown

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Supramolecule #1: Human adenovirus 26

SupramoleculeName: 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
Molecular weightTheoretical: 150 MDa
Virus shellShell ID: 1 / Name: Adenovirus / Diameter: 950.0 Å / T number (triangulation number): 25

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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 26
Molecular weightTheoretical: 107.218703 KDa
SequenceString: 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

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Macromolecule #2: Penton

MacromoleculeName: Penton / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 26
Molecular weightTheoretical: 56.312039 KDa
SequenceString: 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

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Macromolecule #3: Fiber

MacromoleculeName: Fiber / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 26
Molecular weightTheoretical: 2.276526 KDa
SequenceString:
AKRLRVEDDF NPVYPYGYA

UniProtKB: Fiber

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Macromolecule #4: PIIIa

MacromoleculeName: PIIIa / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 26
Molecular weightTheoretical: 43.148438 KDa
SequenceString: 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

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Macromolecule #5: PIX

MacromoleculeName: PIX / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 26
Molecular weightTheoretical: 13.800377 KDa
SequenceString:
MNGTGGAFEG GLFSPYLTTR LPGWAGVRQN VMGSTVDGRP VLPANSSTMT YATVGNSSLD STAAAAAAAA AMTATRLASS YMPSSGSSP SVPSSIIAEE KLLALLAELE ALSRQLAALT QQVSELREQQ QQQNK

UniProtKB: Hexon-interlacing protein

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Macromolecule #6: PVIII

MacromoleculeName: PVIII / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 26
Molecular weightTheoretical: 24.633643 KDa
SequenceString: 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

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Macromolecule #7: PVI

MacromoleculeName: PVI / type: protein_or_peptide / ID: 7 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 26
Molecular weightTheoretical: 3.348683 KDa
SequenceString:
DINFASLAPR HGTRPFMGTW NEIGTSQLNG G

UniProtKB: Pre-protein VI

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Macromolecule #8: Unknown

MacromoleculeName: Unknown / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 26
Molecular weightTheoretical: 869.063 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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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

Concentration6.0 mg/mL
BufferpH: 8.1 / Details: 40 mM Tris, pH 8.1, 300 mM NaCl, 10 mM CaCl2
GridModel: C-flat / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 6 sec. / Details: 20mA
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3
DetailsVirus particles

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 20000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4cwu
PDB Unreleased entry

Initial angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 6
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 19000

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5tx1:
Cryo-Electron microscopy structure of species-D human adenovirus 26

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