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- PDB-7s78: Structure of a cell-entry defective human adenovirus provides ins... -

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Basic information

Entry
Database: PDB / ID: 7s78
TitleStructure of a cell-entry defective human adenovirus provides insights into precursor proteins and capsid maturation
Components
  • (Pre-hexon-linking protein ...) x 2
  • Hexon protein
  • Hexon-interlacing protein
  • Penton protein
  • Pre-protein VI
  • Unknown-1
  • Unknown-2
KeywordsVIRUS / Adenovirus / ts1 mutant / minor protein precursors / virus maturation
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 / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral life cycle / viral capsid ...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 / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral life cycle / viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / structural molecule activity / virion attachment to host cell
Similarity search - Function
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 / Adenovirus Pll, hexon, subdomain 2 / Minor capsid protein VI / Minor capsid protein VI ...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 / Adenovirus Pll, hexon, subdomain 2 / Minor capsid protein VI / Minor capsid protein VI / 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
Hexon-interlacing protein / Hexon protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-hexon-linking protein VIII / Pre-protein VI
Similarity search - Component
Biological speciesHuman adenovirus C serotype 5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsReddy, V.S. / Yu, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI146644 United States
CitationJournal: J Mol Biol / Year: 2022
Title: Structure of a Cell Entry Defective Human Adenovirus Provides Insights into Precursor Proteins and Capsid Maturation.
Authors: Xiaodi Yu / Tina-Marie Mullen / Vahid Abrishami / Juha T Huiskonen / Glen R Nemerow / Vijay S Reddy /
Abstract: Maturation of adenoviruses is distinguished by proteolytic processing of several interior minor capsid proteins and core proteins by the adenoviral protease and subsequent reorganization of ...Maturation of adenoviruses is distinguished by proteolytic processing of several interior minor capsid proteins and core proteins by the adenoviral protease and subsequent reorganization of adenovirus core. We report the results derived from the icosahedrally averaged cryo-EM structure of a cell entry defective form of adenovirus, designated ts1, at a resolution of 3.7 Å as well as of the localized reconstructions of unique hexons and penton base. The virion structure revealed the structures and organization of precursors of minor capsid proteins, pIIIa, pVI and pVIII, which are closely associated with the hexons on the capsid interior. In addition to a well-ordered helical domain (a.a. 310-397) of pIIIa, highlights of the structure include the precursors of VIII display significantly different structures near the cleavage sites. Moreover, we traced residues 4-96 of the membrane lytic protein (pVI) that includes an amphipathic helix occluded deep in the hexon cavity suggesting the possibility of co-assembly of hexons with the precursors of VI. In addition, we observe a second copy of pVI ordered up to residue L40 in the peripentonal hexons and a few fragments of density corresponding to 2nd and 3rd copies of pVI in other hexons. However, we see no evidence of precursors of VII binding in the hexon cavity. These findings suggest the possibility that differently bound pVI molecules undergo processing at the N-terminal cleavage sites at varying efficiencies, subsequently creating competition between the cleaved and uncleaved forms of VI, followed by reorganization, processing, and release of VI molecules from the hexon cavities.
History
DepositionSep 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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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
  • EMDB-24881
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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
N: Penton protein
M: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
U: Pre-hexon-linking protein VIII
V: Pre-hexon-linking protein VIII
W: Pre-protein VI
X: Pre-protein VI
Y: Pre-protein VI
Z: Pre-protein VI
0: Pre-protein VI
1: Pre-protein VI
2: Pre-protein VI
3: Pre-protein VI
4: Pre-protein VI
5: Unknown-1
6: Unknown-2


Theoretical massNumber of molelcules
Total (without water)1,778,76131
Polymers1,778,76131
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
N: Penton protein
M: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
U: Pre-hexon-linking protein VIII
V: Pre-hexon-linking protein VIII
W: Pre-protein VI
X: Pre-protein VI
Y: Pre-protein VI
Z: Pre-protein VI
0: Pre-protein VI
1: Pre-protein VI
2: Pre-protein VI
3: Pre-protein VI
4: Pre-protein VI
5: Unknown-1
6: Unknown-2
x 60


Theoretical massNumber of molelcules
Total (without water)106,725,6521860
Polymers106,725,6521860
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
N: Penton protein
M: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
U: Pre-hexon-linking protein VIII
V: Pre-hexon-linking protein VIII
W: Pre-protein VI
X: Pre-protein VI
Y: Pre-protein VI
Z: Pre-protein VI
0: Pre-protein VI
1: Pre-protein VI
2: Pre-protein VI
3: Pre-protein VI
4: Pre-protein VI
5: Unknown-1
6: Unknown-2
x 5


  • icosahedral pentamer
  • 8.89 MDa, 155 polymers
Theoretical massNumber of molelcules
Total (without water)8,893,804155
Polymers8,893,804155
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
N: Penton protein
M: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
U: Pre-hexon-linking protein VIII
V: Pre-hexon-linking protein VIII
W: Pre-protein VI
X: Pre-protein VI
Y: Pre-protein VI
Z: Pre-protein VI
0: Pre-protein VI
1: Pre-protein VI
2: Pre-protein VI
3: Pre-protein VI
4: Pre-protein VI
5: Unknown-1
6: Unknown-2
x 6


  • icosahedral 23 hexamer
  • 10.7 MDa, 186 polymers
Theoretical massNumber of molelcules
Total (without water)10,672,565186
Polymers10,672,565186
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))

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Components

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Protein , 4 types, 26 molecules ABCDEFGHIJKLNPQRSWXYZ01234

#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 / Strain: Ad2-ts1 / 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 / Strain: Ad2-ts1 / References: UniProt: P12538
#4: 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 / Strain: Ad2-ts1 / References: UniProt: P03281
#6: Protein
Pre-protein VI / pVI


Mass: 27027.510 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Human adenovirus C serotype 5 / Strain: Ad2-ts1 / References: UniProt: P24937

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

#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 / Strain: Ad2-ts1 / References: UniProt: P12537
#5: 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 / Strain: Ad2-ts1 / References: UniProt: P24936

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Protein/peptide , 2 types, 2 molecules 56

#7: Protein/peptide Unknown-1


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus C serotype 5 / Strain: Ad2-ts1
#8: Protein/peptide Unknown-2


Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus C serotype 5 / Strain: Ad2-ts1

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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 C serotype 5 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 150 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus C serotype 5 / Strain: Ad2-ts1
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Homo sapiens / Strain: Ad2-ts1
Virus shellName: Capsid / Diameter: 1000 nm / Triangulation number (T number): 25
Buffer solutionpH: 8.1 / Details: 40 mM Tris, pH 8.1
Buffer componentConc.: 40 mM / Name: Tris
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20mA / Grid material: COPPER / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 12 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 1510
Image scansMovie frames/image: 38

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND4.1CTF correction
7Cootmodel fitting
11cisTEMclassification
12cisTEM3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 21320
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11277 / Algorithm: FOURIER SPACE / Num. of class averages: 18 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3IYN

3iyn
PDB Unreleased entry

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