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- PDB-3zif: Cryo-EM structures of two intermediates provide insight into aden... -

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Basic information

Entry
Database: PDB / ID: 3zif
TitleCryo-EM structures of two intermediates provide insight into adenovirus assembly and disassembly
Components
  • HEXON PROTEIN
  • PENTON PROTEIN
  • PIX
  • PVIII
KeywordsVIRUS / ASSEMBLY INTERMEDIATE
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral process / endocytosis involved in viral entry into host cell / viral capsid / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
: / Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / 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 ...: / Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / 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
Similarity search - Domain/homology
Penton protein / Pre-hexon-linking protein VIII / Hexon protein / PIX
Similarity search - Component
Biological speciesBOVINE ADENOVIRUS 3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsCheng, L. / Huang, X. / Li, X. / Xiong, W. / Sun, W. / Yang, C. / Zhang, K. / Wang, Y. / Liu, H. / Ji, G. ...Cheng, L. / Huang, X. / Li, X. / Xiong, W. / Sun, W. / Yang, C. / Zhang, K. / Wang, Y. / Liu, H. / Ji, G. / Sun, F. / Zheng, C. / Zhu, P.
CitationJournal: Virology / Year: 2014
Title: Cryo-EM structures of two bovine adenovirus type 3 intermediates.
Authors: Lingpeng Cheng / Xiaoxing Huang / Xiaomin Li / Wei Xiong / Wei Sun / Chongwen Yang / Kai Zhang / Ying Wang / Hongrong Liu / Xiaojun Huang / Gang Ji / Fei Sun / Congyi Zheng / Ping Zhu /
Abstract: Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained ...Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure represents a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level.
History
DepositionJan 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AK" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AK" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DK" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GK" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JK" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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-2273
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  • Superimposition on EM map
  • EMDB-2273
  • Imaged by UCSF Chimera
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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: PIX
O: PIX
P: PIX
Q: PIX
R: PVIII


Theoretical massNumber of molelcules
Total (without water)1,371,53618
Polymers1,371,53618
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: PIX
O: PIX
P: PIX
Q: PIX
R: PVIII
x 60


Theoretical massNumber of molelcules
Total (without water)82,292,1441080
Polymers82,292,1441080
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
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: PIX
O: PIX
P: PIX
Q: PIX
R: PVIII
x 5


  • icosahedral pentamer
  • 6.86 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)6,857,67990
Polymers6,857,67990
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: PIX
O: PIX
P: PIX
Q: PIX
R: PVIII
x 6


  • icosahedral 23 hexamer
  • 8.23 MDa, 108 polymers
Theoretical massNumber of molelcules
Total (without water)8,229,214108
Polymers8,229,214108
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein
HEXON PROTEIN / / LATE PROTEIN 2 / BOVINE ADENOVIRUS 3


Mass: 103148.008 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) BOVINE ADENOVIRUS 3 / References: UniProt: P03278
#2: Protein PENTON PROTEIN / / BOVINE ADENOVIRUS 3


Mass: 55135.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOVINE ADENOVIRUS 3 / References: UniProt: O71096
#3: Protein
PIX / BOVINE ADENOVIRUS 3


Mass: 13719.456 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) BOVINE ADENOVIRUS 3 / References: UniProt: Q64845
#4: Protein PVIII / BOVINE ADENOVIRUS 3


Mass: 23746.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOVINE ADENOVIRUS 3 / References: UniProt: O92788

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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: BOVINE ADENOVIRUS TYPE 3 / Type: VIRUS
Buffer solutionName: PBS / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Details: LIQUID ETHAN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Feb 2, 2011
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 125390 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GENERIC GATAN
Image scansNum. digital images: 1275
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1IMIRS3D reconstruction
2ISAF3D reconstruction
CTF correctionDetails: INDIVIDUAL IMAGES
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 4.5 Å / Num. of particles: 11910 / Actual pixel size: 1.16 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2273. (DEPOSITION ID: 11337).
Symmetry type: POINT
RefinementHighest resolution: 4.5 Å
Refinement stepCycle: LAST / Highest resolution: 4.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms94377 0 0 0 94377

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