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- EMDB-25786: Refined capsid structure of human adenovirus D26 at 3.4 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-25786
TitleRefined capsid structure of human adenovirus D26 at 3.4 A resolution
Map dataCropped version of the original cryo-EM map 928x928x928 pixels.
Sample
  • Tissue: Human adenovirus 26
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Fiber
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: PIX
    • Protein or peptide: PVIII
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Unknown fragment
KeywordsHuman Adenovirus D26 HAdV-D26 Ad26 Hexon Penton base IX / 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 / 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 / Minor capsid protein VI / 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 / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein / 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 / 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: 3.38 Å
AuthorsReddy VS / Yu X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI146644 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
DepositionDec 21, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
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  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7tau
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7tau
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25786.png

Downloads & links

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Map

FileDownload / File: emd_25786.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCropped version of the original cryo-EM map 928x928x928 pixels.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 832 pix.
= 1089.92 Å		1.31 Å/pix.
x 832 pix.
= 1089.92 Å		1.31 Å/pix.
x 832 pix.
= 1089.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8 / Movie #1: 4
Minimum - Maximum-32.776363000000003 - 54.450029999999998
Average (Standard dev.)-0.0555016 (±3.6922314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-415-415-415
Dimensions832832832
Spacing832832832
CellA=B=C: 1089.9199 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z832832832
origin x/y/z0.0000.0000.000
length x/y/z1089.9201089.9201089.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS-415-415-415
NC/NR/NS832832832
D min/max/mean-32.77654.450-0.056

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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
  • Tissue: Human adenovirus 26
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Fiber
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: PIX
    • Protein or peptide: PVIII
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Unknown fragment

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Supramolecule #1: Human adenovirus 26

SupramoleculeName: Human adenovirus 26 / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Adenovirus
Source (natural)Organism: Human adenovirus 26

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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 protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 26
Molecular weightTheoretical: 58.647703 KDa
SequenceString: MRRAVVSSSP PPSYESVMAQ ATLEVPFVPP RYMAPTEGRN SIRYSELAPQ YDTTRVYLVD NKSADIASLN YQNDHSNFLT TVVQNNDFT PAEASTQTIN FDERSRWGGD LKTILHTNMP NVNEYMFTSK FKARVMVSRK HPEGVVETDL SQDKLEYEWF E FTLPEGNF ...String:
MRRAVVSSSP PPSYESVMAQ ATLEVPFVPP RYMAPTEGRN SIRYSELAPQ YDTTRVYLVD NKSADIASLN YQNDHSNFLT TVVQNNDFT PAEASTQTIN FDERSRWGGD LKTILHTNMP NVNEYMFTSK FKARVMVSRK HPEGVVETDL SQDKLEYEWF E FTLPEGNF SETMTIDLMN NAILENYLQV GRQNGVLESD IGVKFDSRNF KLGWDPVTKL VMPGVYTYEA FHPDVVLLPG CG VDFTESR LSNLLGIRKK QPFQEGFRIM YEDLEGGNIP ALLDVPKYLE SKKKVEDETK NAAAATADTT TRGDTFATPA QET AADKKV EVLPIEKDES GRSYNLIQGT HDTLYRSWYL SYTYGDPEKG VQSWTLLTTP DVTCGAEQVY WSLPDLMQDP VTFR STQQV SNYPVVGAEL MPFRAKSFYN DLAVYSQLIR SYTSLTHVFN RFPDNQILCR PPAPTITTVS ENVPALTDHG TLPLR SSIR GVQRVTVTDA RRRTCPYVYK ALGIVAPRVL SSRTF

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: 41.039184 KDa
SequenceString: MAKRLRVEDD FNPVYPYGYA RNQNIPFLTP PFVSSDGFKN FPPGVLSLKL ADPITINNGD VSLKVGGGLA VEQQTGNLSV NPDAPLQVA SDKLQLALAP PFEVRDGKLA LKAGNGLKVL DNSITGLTGL LNTLVVLTGR GIGTEELKND DGVTNKGVGL R VRLGDDGG ...String:
MAKRLRVEDD FNPVYPYGYA RNQNIPFLTP PFVSSDGFKN FPPGVLSLKL ADPITINNGD VSLKVGGGLA VEQQTGNLSV NPDAPLQVA SDKLQLALAP PFEVRDGKLA LKAGNGLKVL DNSITGLTGL LNTLVVLTGR GIGTEELKND DGVTNKGVGL R VRLGDDGG LTFDKKGDLV AWNKKDDRRT LWTTPDTSPN CKMSTEKDSK LTLTLTKCGS QVLGNVSLLA VTGEYHQMTA TT KKDVKIS LLFDENGILL PSSSLSKDYW NYRSDDSIVS QKYNNAVPFM PNLTAYPKPS AQNAKNYSRT KIISNVYLGA LTY QPVIIT IAFNQETENG CAYSITFTFT WQKDYSAQQF DVTSFTFSYL TQENKDKD

UniProtKB: Fiber

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Macromolecule #4: Pre-hexon-linking protein IIIa

MacromoleculeName: Pre-hexon-linking protein IIIa / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 26
Molecular weightTheoretical: 62.201371 KDa
SequenceString: MSQQAPDPAI RAALQSQPSG LASDDWEAAM QRIMALTTRN PESFRQQPQA NRLSAILEAV VPSRTNPTHE KVLAIVNALA ENKAIRPDE AGLVYNALLE RVGRYNSTNV QSNLDRLVTD VREAVAQRER FKNEGLGSLV ALNAFLATQP ANVPRGQDDY T NFISALRL ...String:
MSQQAPDPAI RAALQSQPSG LASDDWEAAM QRIMALTTRN PESFRQQPQA NRLSAILEAV VPSRTNPTHE KVLAIVNALA ENKAIRPDE AGLVYNALLE RVGRYNSTNV QSNLDRLVTD VREAVAQRER FKNEGLGSLV ALNAFLATQP ANVPRGQDDY T NFISALRL MVTEVPQSEV YQSGPDYFFQ TSRQGLQTVN LSQAFKNLRG LWGVQAPVGD RSTVSSLLTP NSRLLLLLIA PF TDSGSVN RNSYLGHLLT LYREAIGQAQ VDEQTFQEIT SVSRALGQND TDSLRATLNF LLTNRQQKIP AQYALSAEEE RIL RYVQQS VGLFLMQEGA TPSAALDMTA RNMEPSMYAA NRPFINKLMD YLHRAAAMNT DYFTNAILNP HWLPPPGFYT GEYD MPDPN DGFLWDDVDS AVFSPTFQKR QEAPPSEGAV GRSPFPSLGS LHSLPGSVNS GRVSRPRLLG EDEYLNDSLL QPPRA KNAM ANNGIESLVD KLNRWKTYAQ DHRDAPAPRR QRHDRQRGLV WDDEDSADDS SVLDLGGSGG VNPFAHLQPK LGRRMF

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: Pre-protein VI

MacromoleculeName: Pre-protein VI / type: protein_or_peptide / ID: 7 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 26
Molecular weightTheoretical: 25.546086 KDa
SequenceString: MEDINFASLA PRHGTRPFMG TWNEIGTSQL NGGAFNWSSV WSGLKNFGST LRTYGNKAWN SSTGQLLREK LKDQNFQQKV VDGLASGIN GVVDIANQAV QREINSRLDP RPPTVVEMED ATLPPPKGEK RPRPDAEETI LQVDEPPSYE EAVKAGMPTT R IIAPLATG ...String:
MEDINFASLA PRHGTRPFMG TWNEIGTSQL NGGAFNWSSV WSGLKNFGST LRTYGNKAWN SSTGQLLREK LKDQNFQQKV VDGLASGIN GVVDIANQAV QREINSRLDP RPPTVVEMED ATLPPPKGEK RPRPDAEETI LQVDEPPSYE EAVKAGMPTT R IIAPLATG VMKPATLDLP PPPAPAPPKA TPVVQAPPVA TAVRRVPARR QAQNWQSTLH SIVGLGVKSL KRRRCY

UniProtKB: Pre-protein VI

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Macromolecule #8: Unknown fragment

MacromoleculeName: Unknown fragment / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 26
Molecular weightTheoretical: 1.294587 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(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

Concentration5 mg/mL
BufferpH: 8.1 / Component - Concentration: 40.0 mM / Component - Formula: Tris / Component - Name: Tris / Details: 40 mM Tris pH 8.1 300 mM NaCl 10 mM CaCl2
GridModel: C-flat-1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 / Details: Blot for 3 seconds before plunging.
DetailsGradient purified virus

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 2000 / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 37026
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5tx1

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 30834
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 2 / Software - Name: cisTEM
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5tx1


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 150 / Target criteria: Correlation coefficient
Output model

PDB-7tau:
Refined capsid structure of human adenovirus D26 at 3.4 A resolution

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