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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 / homologyHexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Adenoviral core protein VII / Minor capsid protein VI / Hexon-associated protein (IIIa) / Adenovirus penton base protein / Adenovirus hexon associated protein, protein VIII / Hexon, adenovirus major coat protein, N-terminal domain / Adenovirus hexon protein / Group II dsDNA virus coat/capsid protein ...Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Adenoviral core protein VII / Minor capsid protein VI / Hexon-associated protein (IIIa) / Adenovirus penton base protein / Adenovirus hexon associated protein, protein VIII / Hexon, adenovirus major coat protein, N-terminal domain / Adenovirus hexon protein / Group II dsDNA virus coat/capsid protein / Hexon coat protein, subdomain 4 / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, N-terminal / Adenoviral core protein VII / Minor capsid protein VI / Pre-hexon-linking protein IIIa / Adenovirus penton base protein / Pre-hexon-linking protein VIII / Hexon, adenovirus major coat protein, C-terminal domain / hexon binding / viral capsid, decoration / viral procapsid / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / virion / viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / viral entry into host cell / host cell cytoplasm / virion attachment to host cell / host cell nucleus / DNA binding / Hexon-interlacing protein / Hexon protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-hexon-linking protein VIII / Pre-protein VI / Pre-histone-like nucleoprotein
Function and homology information
Specimen sourceHuman adenovirus C serotype 5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsDai, X.H. / Wu, L. / Sun, R. / Zhou, Z.H.
CitationJournal: J. Virol. / Year: 2017
Title: Atomic Structures of Minor Proteins VI and VII in the Human Adenovirus.
Authors: Xinghong Dai / Lily Wu / Ren Sun / Z Hong Zhou
Abstract: Human adenoviruses (Ad) are dsDNA viruses associated with infectious diseases, yet better known as tools for gene delivery and oncolytic anti-cancer therapy. Atomic structures of Ad provide the basis ...Human adenoviruses (Ad) are dsDNA viruses associated with infectious diseases, yet better known as tools for gene delivery and oncolytic anti-cancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts towards more effective applications. Since 2010, atomic models of human Ad5 have been independently derived from photographic film cryoEM and X-ray crystallography, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII and IX. To clarify these discrepancies, here we have employed the technology of direct electron-counting to obtain a cryoEM structure of human Ad5 at 3.2 Å resolution. Our improved structure unambiguously confirmed our previous cryoEM models of proteins IIIa, VIII and IX and explained the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavities of hexons - 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--by extension that of genome-condensing pVII--to hexons is consistent with the previously proposed dsDNA genome-capsid co-assembly for adenoviruses, which resembles that of ssRNA viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid, as exemplified by tailed bacteriophages and herpesviruses. Adenovirus is a double-edged sword to humans - as a widespread pathogen and a bioengineering tool for anti-cancer and gene therapy. Atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models from conventional/film cryoEM and X-ray crystallography for important cement proteins IIIa, VIII, and IX have caused confusion. Using the cutting-edge cryoEM 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 co-assembly mechanism for adenoviruses.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 18, 2017 / Release: Sep 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 27, 2017Structure modelrepositoryInitial release
1.1Oct 4, 2017Structure modelAdvisorypdbx_database_PDB_obs_spr_pdbx_database_PDB_obs_spr.replace_pdb_id
1.2Oct 18, 2017Structure modelAuthor supporting evidence / Database referencescitation / citation_author / pdbx_audit_support_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
1.3Jul 18, 2018Structure modelData collectionem_software_em_software.name

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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
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-7034
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  • Superimposition on EM map
  • EMDB-7034
  • Imaged by UCSF Chimera
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Movie viewer
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
Polyers1,568,67825
Non-polymers00
Water0
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
Polyers94,120,7031500
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
  • Evidence: microscopy
TypeNameSymmetry operationNumber
point symmetry operation1
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
Polyers7,843,392125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
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
Polyers9,412,070150
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

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Protein/peptide , 6 types, 22 molecules ABCDEFGHIJKLMQRSTUVYWX

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


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


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


Mass: 14468.134 Da / Num. of mol.: 4 / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P03281
#6: Protein/peptide Pre-protein VI / pVI / pVIn


Mass: 3584.953 Da / Num. of mol.: 3 / 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: (natural) Human adenovirus C serotype 5 / References: UniProt: P68951
#8: Protein/peptide Pre-protein VI / pVI


Mass: 23460.559 Da / Num. of mol.: 1 / 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/peptide Pre-hexon-linking protein IIIa / Capsid vertex-specific component IIIa / CVSC / Protein IIIa / pIIIa


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


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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Human adenovirus 5Adenoviridae / Type: VIRUS / Details: Cultured in HEK293T cells and purified from media
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22
Source: NATURAL
Molecular weightValue: 150 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus C serotype 5
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus 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
SpecimenDetails: Purified virion / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 / Nominal defocus max: 2000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80 kelvins
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) / Number of grids imaged: 1 / Number of real images: 5608
EM imaging opticsEnergyfilter name: Gatan Image Filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansSampling size: 2.5 microns / 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 selectionNumber of particles selected: 96375
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 53000 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref 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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