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- PDB-5tx1: Cryo-Electron microscopy structure of species-D human adenovirus 26 -

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Basic information

Entry
Database: PDB / ID: 5tx1
TitleCryo-Electron microscopy structure of species-D human adenovirus 26
Components
  • Fiber
  • Hexon protein
  • PIIIa
  • PIX
  • PVI
  • PVIII
  • Penton
  • Unknown
KeywordsVIRUS / human adenovirus 26 / hexon / penton base / minor proteins
Function / homology
Function and homology information


hexon binding / 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 / adhesion receptor-mediated virion attachment to host cell / viral release from host cell / endocytosis involved in viral entry into host cell / viral capsid ...hexon binding / 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 / adhesion receptor-mediated virion attachment to host cell / viral release from host cell / endocytosis involved in viral entry into host cell / viral capsid / host cell cytoplasm / cell adhesion / symbiont entry into host cell / host cell nucleus / structural molecule activity / virion attachment to host cell
Similarity search - Function
Adenovirus Pll, hexon, subdomain 3 / 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 ...Adenovirus Pll, hexon, subdomain 3 / 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 / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
Hexon-interlacing protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-protein VI / Pre-hexon-linking protein VIII / Fiber / Hexon protein
Similarity search - Component
Biological speciesHuman adenovirus 26
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsReddy, V. / Yu, X. / Veesler, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI070771 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103692 United States
CitationJournal: Sci Adv / Year: 2017
Title: Cryo-EM structure of human adenovirus D26 reveals the conservation of structural organization among human adenoviruses.
Authors: Xiaodi Yu / David Veesler / Melody G Campbell / Mary E Barry / Francisco J Asturias / Michael A Barry / Vijay S Reddy /
Abstract: Human adenoviruses (HAdVs) cause acute respiratory, ocular, and gastroenteric diseases and are also frequently used as gene and vaccine delivery vectors. Unlike the archetype human adenovirus C5 ...Human adenoviruses (HAdVs) cause acute respiratory, ocular, and gastroenteric diseases and are also frequently used as gene and vaccine delivery vectors. Unlike the archetype human adenovirus C5 (HAdV-C5), human adenovirus D26 (HAdV-D26) belongs to species-D HAdVs, which target different cellular receptors, and is differentially recognized by immune surveillance mechanisms. HAdV-D26 is being championed as a lower seroprevalent vaccine and oncolytic vector in preclinical and human clinical studies. To understand the molecular basis for their distinct biological properties and independently validate the structures of minor proteins, we determined the first structure of species-D HAdV at 3.7 Å resolution by cryo-electron microscopy. All the hexon hypervariable regions (HVRs), including HVR1, have been identified and exhibit a distinct organization compared to those of HAdV-C5. Despite the differences in the arrangement of helices in the coiled-coil structures, protein IX molecules form a continuous hexagonal network on the capsid exterior. In addition to the structurally conserved region (3 to 300) of IIIa, we identified an extra helical domain comprising residues 314 to 390 that further stabilizes the vertex region. Multiple (two to three) copies of the cleaved amino-terminal fragment of protein VI (pVIn) are observed in each hexon cavity, suggesting that there could be ≥480 copies of VI present in HAdV-D26. In addition, a localized asymmetric reconstruction of the vertex region provides new details of the three-pronged "claw hold" of the trimeric fiber and its interactions with the penton base. These observations resolve the previous conflicting assignments of the minor proteins and suggest the likely conservation of their organization across different HAdVs.
History
DepositionNov 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.2Jul 18, 2018Group: Data collection / Experimental preparation / Category: em_sample_support / Item: _em_sample_support.grid_type
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
  • EMDB-8471
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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
O: Fiber
M: PIIIa
P: PIX
Q: PIX
R: PIX
S: PIX
U: PVIII
V: PVIII
1: PVI
2: PVI
3: PVI
4: PVI
5: PVI
6: PVI
7: PVI
8: PVI
9: PVI
X: Unknown
Y: Unknown
Z: Unknown


Theoretical massNumber of molelcules
Total (without water)1,525,57633
Polymers1,525,57633
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
O: Fiber
M: PIIIa
P: PIX
Q: PIX
R: PIX
S: PIX
U: PVIII
V: PVIII
1: PVI
2: PVI
3: PVI
4: PVI
5: PVI
6: PVI
7: PVI
8: PVI
9: PVI
X: Unknown
Y: Unknown
Z: Unknown
x 60


Theoretical massNumber of molelcules
Total (without water)91,534,5341980
Polymers91,534,5341980
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
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
N: Penton
O: Fiber
M: PIIIa
P: PIX
Q: PIX
R: PIX
S: PIX
U: PVIII
V: PVIII
1: PVI
2: PVI
3: PVI
4: PVI
5: PVI
6: PVI
7: PVI
8: PVI
9: PVI
X: Unknown
Y: Unknown
Z: Unknown
x 5


  • icosahedral pentamer
  • 7.63 MDa, 165 polymers
Theoretical massNumber of molelcules
Total (without water)7,627,878165
Polymers7,627,878165
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
N: Penton
O: Fiber
M: PIIIa
P: PIX
Q: PIX
R: PIX
S: PIX
U: PVIII
V: PVIII
1: PVI
2: PVI
3: PVI
4: PVI
5: PVI
6: PVI
7: PVI
8: PVI
9: PVI
X: Unknown
Y: Unknown
Z: Unknown
x 6


  • icosahedral 23 hexamer
  • 9.15 MDa, 198 polymers
Theoretical massNumber of molelcules
Total (without water)9,153,453198
Polymers9,153,453198
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 5 types, 20 molecules ABCDEFGHIJKLNMPQRSUV

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


Mass: 107218.703 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: Q3S8B3
#2: Protein Penton / / Penton base


Mass: 56312.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKL2
#4: Protein PIIIa / Protein IIIa


Mass: 43148.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKL1
#5: Protein
PIX / Protein IX


Mass: 13800.377 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKK7
#6: Protein PVIII / Protein VIII


Mass: 24633.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKM0

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Protein/peptide , 3 types, 13 molecules O123456789XYZ

#3: Protein/peptide Fiber /


Mass: 2276.526 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKM1
#7: Protein/peptide
PVI / Protein VI


Mass: 3348.683 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26 / References: UniProt: A4ZKL5
#8: Protein/peptide Unknown


Mass: 869.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 26

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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 26Adenoviridae / Type: VIRUS / Entity ID: #1-#10 / Source: NATURAL
Molecular weightValue: 150 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus 26
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Virus shellName: AdenovirusAdenoviridae / Diameter: 950 nm / Triangulation number (T number): 25
Buffer solutionpH: 8.1 / Details: 40 mM Tris, pH 8.1, 300 mM NaCl, 10 mM CaCl2
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Virus particles
Specimen supportDetails: 20mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 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: OTHER
Electron lensMode: OTHER / Nominal magnification: 22500 X / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K
Image recordingAverage exposure time: 7.6 sec. / Electron dose: 1.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2000
Image scansMovie frames/image: 38

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Processing

EM software
IDNameVersionCategory
4CTFFIND33CTF correction
7Omodel fitting
12FREALIGN9.113D reconstruction
13CNSmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 20000
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19000 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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