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- EMDB-72774: Structure of the Adenovirus-7 VLP, Class 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-72774
TitleStructure of the Adenovirus-7 VLP, Class 2
Map data
Sample
  • Complex: Adenovirus 7 Virus-like particles
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Hexon protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Penton protein
    • Protein or peptide: Hexon-interlacing protein IX
    • Protein or peptide: Pre-hexon-linking protein VIII
KeywordsAdenovirus / vaccine / VLP / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / viral procapsid / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell / host cell cytoplasm ...hexon binding / viral capsid, decoration / viral procapsid / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell / host cell cytoplasm / endocytosis involved in viral entry into host cell / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI / Adenovirus penton base protein ...Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI / Adenovirus penton base protein / Adenovirus penton base protein / 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 / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Hexon protein / Hexon-interlacing protein IX / Pre-hexon-linking protein VIII / Pre-protein VI / Pre-hexon-linking protein IIIa / Penton protein
Similarity search - Component
Biological speciesHuman adenovirus 7
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKhayat R / Madoo K
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5SC1GM139701 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5G12MD007603-30 United States
Simons Foundation349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Department of Defense (DOD, United States)W81XH19C0169 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structure of Human adenovirus 7 virus-like particles, a platform for developing nanotherapeutics and studying capsid assembly.
Authors: Kiyano Madoo / Ryan Mazboudi / Zubaida Marufee Islam / Jonathan Luo / Robert A Kuschner / Paul Gottlieb / John J Dennehy / Rinat R Abzalimov / Jose M Galarza / Reza Khayat /
Abstract: Adenoviridae family members routinely infect humans, exhibit significant genetic diversity, and are associated with a variety of illnesses. Types 4 and 7 frequently circulate in the United States and ...Adenoviridae family members routinely infect humans, exhibit significant genetic diversity, and are associated with a variety of illnesses. Types 4 and 7 frequently circulate in the United States and are major causes of respiratory disease. Infections can result in hospitalization and, in severe cases, death. Although a live wild-type-virus vaccine targeting these two types exists, its use is restricted to military personnel due to concerns about viral-shedding and potential for genetic recombination. To overcome these limitations, we recently developed a virus-like particle (VLP) platform as an alternative vaccination strategy. These VLPs are stable, lack genomic material, and elicit a potent humoral immune response in mice, effectively neutralizing adenoviral infection. Here, we describe the cryo-EM structure of adenovirus 7 (AdV-7) VLPs. Structural insights are essential to ensure that neutralizing antigens displayed on the VLPs accurately mimic those of the virion, guide the design of particles with improved stability and efficacy, and enable engineering of VLPs with antigenic properties targeting multiple adenovirus types. The structure shows that hexon, penton, pIIIa, pVI, pVIII, and IX assemble comparable to AdV-5, hexon and penton neutralizing epitopes are appropriately displayed for antibody recognition, penton insertion into the hexon shell promotes cement protein pIIIa to increase its interaction with the peripentonal hexons, and presence of the core-genome is associated with increased interaction between cement protein pVIII and hexon. Finally, limited proteolysis and mass spectrometry demonstrate that VLP incorporated hexons digest more readily than virion incorporated hexons, indicating the greater dynamic nature of the VLP.
History
DepositionSep 18, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72774.png

Downloads & links

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Map

FileDownload / File: emd_72774.map.gz / Format: CCP4 / Size: 107.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 280 pix.
= 303.24 Å		1.08 Å/pix.
x 428 pix.
= 463.524 Å		1.08 Å/pix.
x 235 pix.
= 254.505 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-7.1269174 - 10.653544999999999
Average (Standard dev.)-0.000000000007169 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-18892
Dimensions428235280
Spacing280428235
CellA: 303.24 Å / B: 463.524 Å / C: 254.50499 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72774_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72774_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Adenovirus 7 Virus-like particles

EntireName: Adenovirus 7 Virus-like particles
Components
  • Complex: Adenovirus 7 Virus-like particles
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Hexon protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Penton protein
    • Protein or peptide: Hexon-interlacing protein IX
    • Protein or peptide: Pre-hexon-linking protein VIII

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Supramolecule #1: Adenovirus 7 Virus-like particles

SupramoleculeName: Adenovirus 7 Virus-like particles / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Adenovirus 7 Virus-like particles
Source (natural)Organism: Human adenovirus 7
Molecular weightTheoretical: 18.2 MDa

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Macromolecule #1: Pre-protein VI

MacromoleculeName: Pre-protein VI / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 7
Molecular weightTheoretical: 27.17884 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEDINFSSLA PRHGTRPYMG TWSDIGTSQL NGGAFNWSSI WSGLKNFGST VKTYGNKAWN SSTGQALRNK LKEQNFQQKV VDGIASGIN GVVDLANQAV QKQINSRLDP PPATPGEMEV EEELPPLEKR GDKRPRPELE QTLVTRADEP PSYEEAVKLG M PTTRPVAH ...String:
MEDINFSSLA PRHGTRPYMG TWSDIGTSQL NGGAFNWSSI WSGLKNFGST VKTYGNKAWN SSTGQALRNK LKEQNFQQKV VDGIASGIN GVVDLANQAV QKQINSRLDP PPATPGEMEV EEELPPLEKR GDKRPRPELE QTLVTRADEP PSYEEAVKLG M PTTRPVAH MATGVMKPSQ SHRPATLDLP PPPASAALVP KPVATRKPTA VQPVAVARPR PGGTPRPKAN WQSTLNSIVG LG VQSVKRR RCY

UniProtKB: Pre-protein VI

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Macromolecule #2: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 7
Molecular weightTheoretical: 105.807125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATPSMMPQW AYMHIAGQDA SEYLSPGLVQ FARATDTYFS MGNKFRNPTV APTHDVTTDR SQRLMLRFVP VDREDNTYSY KVRYTLAVG DNRVLDMAST FFDIRGVLDR GPSFKPYSGT AYNSLAPKGA PNTSQWIVTA GEERAVTTTT NTFGIASMKG D NITKEGLE ...String:
MATPSMMPQW AYMHIAGQDA SEYLSPGLVQ FARATDTYFS MGNKFRNPTV APTHDVTTDR SQRLMLRFVP VDREDNTYSY KVRYTLAVG DNRVLDMAST FFDIRGVLDR GPSFKPYSGT AYNSLAPKGA PNTSQWIVTA GEERAVTTTT NTFGIASMKG D NITKEGLE IGKDITADNK PIYADKTYQP EPQVGEESWT DTDGTNEKFG GRALKPATKM KPCYGSFARP TNIKGGQAKN RK VKPTEGD VETEEPDIDM EFFDGREAAD AFSPEIVLYT ENVNLETPDS HVVYKPGTSD DNSHANLGQQ AMPNRPNYIG FRD NFVGLM YYNSTGNMGV LAGQASQLNA VVDLQDRNTE LSYQLLLDSL GDRTRYFSMW NQAVDSYDPD VRIIENHGIE DELP NYCFP LDGIGPAKTY QGIKSKDNGW EKDDNVSKSN EIAIGNNQAM EINIQANLWR SFLYSNVALY LPDVYKYTPT NITLP ANTN TYEYMNGRVV SPSLVDSYIN IGARWSLDPM DNVNPFNHHR NAGLRYRSML LGNGRYVPFH IQVPQKFFAV KNLLLL PGS YTYEWNFRKD VNMVLQSSLG NDLRTDGATI SFTSINLYAT FFPMAHNTAS TLEAMLRNDT NDQSFNDYLS AANMLYP IP ANATNIPISI PSRNWAAFRG WSFTRLKTKE TPSLGSGFDP YFVYSGSIPY LDGTFYLNHT FKKVSIMFDS SVSWPGND R LLSPNEFEIK RTVDGEGYNV AQCNMTKDWF LVQMLANYNI GYQGFYIPEG YKDRMYSFFR NFQPMSRQVV DEVNYTDYK AVTLPYQHNN SGFVGYLAPT MRQGEPYPAN YPYPLIGTTA VKSVTQKKFL CDRTMWRIPF SSNFMSMGAL TDLGQNMLYA NSAHALDMT FEVDPMDEPT LLYLLFEVFD VVRVHQPHRG VIEAVYLRTP FSAGNATT

UniProtKB: Hexon 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 7
Molecular weightTheoretical: 65.798375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEQQQAPDPA MRAALQSQPS GINSSDDWTQ AMQRIMALTT RNPEAFRQQP QANRLSAILE AVVPSRSNPT HEKVLAIVNA LVENKAIRP DEAGLVYNAL LERVARYNSS NVQTNLDRMV TDVREAVSQR ERFQRDANLG SLVALNAFLS TQPANVPRGQ Q DYTNFLSA ...String:
MEQQQAPDPA MRAALQSQPS GINSSDDWTQ AMQRIMALTT RNPEAFRQQP QANRLSAILE AVVPSRSNPT HEKVLAIVNA LVENKAIRP DEAGLVYNAL LERVARYNSS NVQTNLDRMV TDVREAVSQR ERFQRDANLG SLVALNAFLS TQPANVPRGQ Q DYTNFLSA LRLMVAEVPQ SEVYQSGPDY FFQTSRQGLQ TVNLTQAFKN LKGLWGVHAP VGDRATVSSL LTPNSRLLLL LV SPFTDSG SIDRNSYLGY LLNLYREAIG QSQVDEQTYQ EITQVSRALG QEDTGSLEAT LNFLLTNRSQ KIPPQYALTA EEE RILRYV QQSVGLFLMQ EGATPTAALD MTARNMEPSM YASNRPFINK LLDYLHRAAA MNSDYFTNAI LNPHWLPPPG FYTG EYDMP DPNDGFLWDD VDSSIFSPPP GYTVWKKEGG DTRHSSVSLS RTAGAAATVP EAASPFPSLP FSLNSVRSSE LGRIT RPRL MGEDEYLNDS LLRPEREKNF PNNGIESLVD KMSRWKTYAQ DHRDEPKILG ATSRPTRRRQ RHDRQMGLVW DDEDSA DDS SVLDLGGRGG GNPFAHLRPR FGRML

UniProtKB: Pre-hexon-linking protein IIIa

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Macromolecule #4: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 7
Molecular weightTheoretical: 61.941543 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRRRAVLGGA MVYPEGPPPS YESVMQQQAA MIQPPLEAPF VPPRYLAPTE GRNSIRYSEL SPLYDTTKLY LVDNKSADIA SLNYQNDHS NFLTTVVQNN DFTPTEASTQ TINFDERSRW GGQLKTIMHT NMPNVNEYMF SNKFKARVMV SRKAPEGVIV N DTYDHKED ...String:
MRRRAVLGGA MVYPEGPPPS YESVMQQQAA MIQPPLEAPF VPPRYLAPTE GRNSIRYSEL SPLYDTTKLY LVDNKSADIA SLNYQNDHS NFLTTVVQNN DFTPTEASTQ TINFDERSRW GGQLKTIMHT NMPNVNEYMF SNKFKARVMV SRKAPEGVIV N DTYDHKED ILKYEWFEFT LPEGNFSATM TIDLMNNAII DNYLEIGRQN GVLESDIGVK FDTRNFRLGW DPETKLIMPG VY TYEAFHP DIVLLPGCGV DFTESRLSNL LGIRKRHPFQ EGFKIMYEDL EGGNIPALLD VTAYEESKKD TTTETTTLAV AEE TSEDDN ITRGDTYITE KQKREAAAAE VKKELKIQPL EKDSKSRSYN VLEDKINTAY RSWYLSYNYG NPEKGIRSWT LLTT SDVTC GAEQVYWSLP DMMQDPVTFR STRQVNNYPV VGAELMPVFS KSFYNEQAVY SQQLRQATSL THVFNRFPEN QILIR PPAP TITTVSENVP ALTDHGTLPL RSSIRGVQRV TVTDARRRTC PYVYKALGIV APRVLSSRTF

UniProtKB: Penton protein

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Macromolecule #5: Hexon-interlacing protein IX

MacromoleculeName: Hexon-interlacing protein IX / type: protein_or_peptide / ID: 5
Details: Due to the low quality of map in certain regions, the identites of some of the amino acids in the model were left as unknown (UNK).
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 7
Molecular weightTheoretical: 13.125939 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGSASFEGG VFSPYLTGRL PPWAGVRQNV MGSTVDGRPV QPANSSTLTY ATLSSSPLDA AAAAAATAAA NTILGMGYYG SIVANSSSS NN(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...String:
MSGSASFEGG VFSPYLTGRL PPWAGVRQNV MGSTVDGRPV QPANSSTLTY ATLSSSPLDA AAAAAATAAA NTILGMGYYG SIVANSSSS NN(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)AKS K

UniProtKB: Hexon-interlacing protein IX

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Macromolecule #6: Pre-hexon-linking protein VIII

MacromoleculeName: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 7
Molecular weightTheoretical: 24.902814 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKEIPTPYM WSYQPQMGLA AGASQDYSTR MNWLSAGPSM ISRVNDIRAY RNQLLLEQSA LTTTPRQHLN PRNWPAALVY QETPAPTTV LLPRDAQAEV HMTNAGVQLA GGSALCRHRP QQSIKRLVIR GRGIQLNDES VSSSLGLRPD GVFQIAGCGR S SFTPRQAV ...String:
MSKEIPTPYM WSYQPQMGLA AGASQDYSTR MNWLSAGPSM ISRVNDIRAY RNQLLLEQSA LTTTPRQHLN PRNWPAALVY QETPAPTTV LLPRDAQAEV HMTNAGVQLA GGSALCRHRP QQSIKRLVIR GRGIQLNDES VSSSLGLRPD GVFQIAGCGR S SFTPRQAV LTLESSSSQP RSGGIGTLQF VEEFTPSVYF NPFSGSPGQY PDEFIPNFDA ISESVDGYD

UniProtKB: Pre-hexon-linking protein VIII

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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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil Active R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 13608 / Average exposure time: 50.0 sec. / Average electron dose: 53.35 e/Å2 / Details: Not all images had particles.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 2.5 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.13) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 92863
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.13)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9ycj:
Structure of the Adenovirus-7 VLP, Class 2

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