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Entry
Database: PDB / ID: 6b1t
TitleImproved cryoEM structure of human adenovirus type 5 with atomic details of minor proteins VI and VII
Components
  • (Pre-hexon-linking protein ...) x 2
  • (Pre-protein VI) x 2
  • Hexon protein
  • Hexon-interlacing protein
  • Penton protein
  • Pre-histone-like nucleoprotein
KeywordsVIRUS / human adenovirus / cement protein / dsDNA genome packaging / genome-capsid co-assembly
Function / homology
Function and homology information


hexon binding / protein transport along microtubule / 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 / viral life cycle ...hexon binding / protein transport along microtubule / 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 / viral life cycle / viral penetration into host nucleus / viral capsid / host cell / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / DNA binding
Similarity search - Function
Adenoviral core protein VII / Adenoviral core protein VII / 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 ...Adenoviral core protein VII / Adenoviral core protein VII / 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
Similarity search - Domain/homology
Hexon-interlacing protein / Hexon protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-hexon-linking protein VIII / Pre-protein VI / Pre-histone-like nucleoprotein
Similarity search - Component
Biological speciesHuman adenovirus C serotype 5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDai, X.H. / Wu, L. / Sun, R. / Zhou, Z.H.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR001881 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
CitationJournal: J Virol / Year: 2017
Title: Atomic Structures of Minor Proteins VI and VII in Human Adenovirus.
Authors: Xinghong Dai / Lily Wu / Ren Sun / Z Hong Zhou /
Abstract: Human adenoviruses (Ad) are double-stranded DNA (dsDNA) viruses associated with infectious diseases, but they are better known as tools for gene delivery and oncolytic anticancer therapy. Atomic ...Human adenoviruses (Ad) are double-stranded DNA (dsDNA) viruses associated with infectious diseases, but they are better known as tools for gene delivery and oncolytic anticancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts toward more effective applications. Since 2010, atomic models of human Ad5 have been derived independently from photographic film cryo-electron microscopy (cryo-EM) and X-ray crystallography studies, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII, and IX. To clarify these discrepancies, we employed the technology of direct electron counting to obtain a cryo-EM structure of human Ad5 at 3.2-Å resolution. Our improved structure unambiguously confirms our previous cryo-EM models of proteins IIIa, VIII, and IX and explains the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavity of hexon-the cleaved N terminus of precursor protein VI (pVIn), the cleaved N terminus of precursor protein VII (pVIIn2), and mature protein VI. The binding of pVIIn2-and, by extension, that of genome-condensing pVII-to hexons is consistent with the previously proposed dsDNA genome-capsid coassembly for adenoviruses, which resembles that of single-stranded RNA (ssRNA) viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid exemplified by tailed bacteriophages and herpesviruses. Adenovirus is a double-edged sword to humans: it is a widespread pathogen but can be used as a bioengineering tool for anticancer and gene therapies. The atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models for the important cement proteins IIIa, VIII, and IX from conventional/film cryo-EM and X-ray crystallography studies have caused confusion. Using cutting-edge cryo-EM technology with electron counting, we improved the structure of human adenovirus type 5 and confirmed our previous models of cement proteins IIIa, VIII, and IX, thus clarifying the inconsistent structures. The improved structure also reveals atomic details of membrane-lytic protein VI and genome-condensing protein VII and supports the previously proposed genome-capsid coassembly mechanism for adenoviruses.
History
DepositionSep 18, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionSep 27, 2017ID: 3IYN
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Advisory / Category: pdbx_database_PDB_obs_spr / Item: _pdbx_database_PDB_obs_spr.replace_pdb_id
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.4Apr 17, 2019Group: Data collection / Database references / Structure summary
Category: citation / em_entity_assembly
Item: _citation.journal_volume / _citation.title / _em_entity_assembly.entity_id_list
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Pre-hexon-linking protein IIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Hexon-interlacing protein
U: Pre-protein VI
V: Pre-protein VI
W: Pre-histone-like nucleoprotein
X: Pre-protein VI
Y: Pre-protein VI


Theoretical massNumber of molelcules
Total (without water)1,568,67825
Polymers1,568,67825
Non-polymers00
Water00
1
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Pre-hexon-linking protein IIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Hexon-interlacing protein
U: Pre-protein VI
V: Pre-protein VI
W: Pre-histone-like nucleoprotein
X: Pre-protein VI
Y: Pre-protein VI
x 60


Theoretical massNumber of molelcules
Total (without water)94,120,7031500
Polymers94,120,7031500
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Pre-hexon-linking protein IIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Hexon-interlacing protein
U: Pre-protein VI
V: Pre-protein VI
W: Pre-histone-like nucleoprotein
X: Pre-protein VI
Y: Pre-protein VI
x 5


  • icosahedral pentamer
  • 7.84 MDa, 125 polymers
Theoretical massNumber of molelcules
Total (without water)7,843,392125
Polymers7,843,392125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Pre-hexon-linking protein IIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Hexon-interlacing protein
U: Pre-protein VI
V: Pre-protein VI
W: Pre-histone-like nucleoprotein
X: Pre-protein VI
Y: Pre-protein VI
x 6


  • icosahedral 23 hexamer
  • 9.41 MDa, 150 polymers
Theoretical massNumber of molelcules
Total (without water)9,412,070150
Polymers9,412,070150
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 4 types, 18 molecules ABCDEFGHIJKLMQRSTX

#1: Protein
Hexon protein / CP-H / Protein II


Mass: 108107.617 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P04133
#2: Protein Penton protein / CP-P / Penton base protein / Protein III


Mass: 63356.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P12538
#5: Protein
Hexon-interlacing protein / Protein IX


Mass: 14468.134 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P03281
#8: Protein Pre-protein VI / pVI


Mass: 23460.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P24937

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Pre-hexon-linking protein ... , 2 types, 3 molecules NOP

#3: Protein Pre-hexon-linking protein IIIa / Capsid vertex-specific component IIIa / CVSC / Protein IIIa / pIIIa


Mass: 65322.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P12537
#4: Protein Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 24710.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P24936

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Protein/peptide , 2 types, 4 molecules UVYW

#6: Protein/peptide Pre-protein VI / pVI / pVIn


Mass: 3584.953 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P24937
#7: Protein/peptide Pre-histone-like nucleoprotein / Pre-core protein VII / pVII / pVIIn2


Mass: 1198.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P68951

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human adenovirus 5 / Type: VIRUS / Details: Cultured in HEK293T cells and purified from media / Entity ID: all / Source: NATURAL
Molecular weightValue: 150 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus C serotype 5
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: capsid / Diameter: 900 nm / Triangulation number (T number): 25
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HClC4H11NO31
2150 mMsodium chlorideNaCl1
31 mMmagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Purified virion
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80 K
Image recordingAverage exposure time: 9 sec. / Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5608
EM imaging opticsEnergyfilter name: Gatan Image Filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansSampling size: 2.5 µm / Width: 7676 / Height: 7420 / Movie frames/image: 32 / Used frames/image: 2-32

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Processing

SoftwareName: PHENIX / Version: dev_2875: / Classification: refinement
EM software
IDNameCategory
2Leginonimage acquisition
4CTFFIND3CTF correction
7UCSF Chimeramodel fitting
9IMIRSinitial Euler assignment
10IMIRSfinal Euler assignment
12eLite3D3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 96375
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53000 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008102532
ELECTRON MICROSCOPYf_angle_d0.846139427
ELECTRON MICROSCOPYf_dihedral_angle_d7.39861040
ELECTRON MICROSCOPYf_chiral_restr0.05714905
ELECTRON MICROSCOPYf_plane_restr0.00718313

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