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- PDB-5gka: cryo-EM structure of human Aichi virus -

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Basic information

Entry
Database: PDB / ID: 5gka
Titlecryo-EM structure of human Aichi virus
Components
  • Genome polyprotein
  • capsid protein VP0
  • capsid protein VP1
KeywordsVIRUS / Picornavirus / entry / receptor binding / gastroenteritis
Function / homology
Function and homology information


host cell Golgi membrane / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase ...host cell Golgi membrane / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase / symbiont entry into host cell / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
LRAT domain profile. / LRAT domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. ...LRAT domain profile. / LRAT domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesAichi virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhu, L. / Wang, X.X. / Ren, J.S. / Tuthill, T.J. / Fry, E.E. / Rao, Z.H. / Stuart, D.I.
Funding support China, United Kingdom, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology2014CB542800 China
Medical Research Council (United Kingdom)G100099 United Kingdom
CitationJournal: Nat Microbiol / Year: 2016
Title: Structure of human Aichi virus and implications for receptor binding.
Authors: Ling Zhu / Xiangxi Wang / Jingshan Ren / Abhay Kotecha / Thomas S Walter / Shuai Yuan / Teruo Yamashita / Tobias J Tuthill / Elizabeth E Fry / Zihe Rao / David I Stuart /
Abstract: Aichi virus (AiV), an unusual and poorly characterized picornavirus, classified in the genus Kobuvirus, can cause severe gastroenteritis and deaths in children below the age of five years, especially ...Aichi virus (AiV), an unusual and poorly characterized picornavirus, classified in the genus Kobuvirus, can cause severe gastroenteritis and deaths in children below the age of five years, especially in developing countries. The seroprevalence of AiV is approximately 60% in children under the age of ten years and reaches 90% later in life. There is no available vaccine or effective antiviral treatment. Here, we describe the structure of AiV at 3.7 Å. This first high-resolution structure for a kobuvirus is intermediate between those of the enteroviruses and cardioviruses, with a shallow, narrow depression bounded by the prominent VP0 CD loops (linking the C and D strands of the β-barrel), replacing the depression known as the canyon, frequently the site of receptor attachment in enteroviruses. VP0 is not cleaved to form VP2 and VP4, so the 'VP2' β-barrel structure is complemented with a unique extended structure on the inside of the capsid. On the outer surface, a polyproline helix structure, not seen previously in picornaviruses is present at the C terminus of VP1, a position where integrin binding motifs are found in some other picornaviruses. A peptide corresponding to this polyproline motif somewhat attenuates virus infectivity, presumably blocking host-cell attachment. This may guide cellular receptor identification.
History
DepositionJul 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Source and taxonomy
Revision 1.2Apr 26, 2017Group: Other / Source and taxonomy
Revision 1.3Oct 18, 2017Group: Author supporting evidence / Data processing / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.4Mar 27, 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
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Assembly

Deposited unit
A: capsid protein VP1
B: capsid protein VP0
C: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)90,1283
Polymers90,1283
Non-polymers00
Water0
1
A: capsid protein VP1
B: capsid protein VP0
C: Genome polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)5,407,669180
Polymers5,407,669180
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: capsid protein VP1
B: capsid protein VP0
C: Genome polyprotein
x 5


  • icosahedral pentamer
  • 451 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)450,63915
Polymers450,63915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: capsid protein VP1
B: capsid protein VP0
C: Genome polyprotein
x 6


  • icosahedral 23 hexamer
  • 541 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)540,76718
Polymers540,76718
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
6
A: capsid protein VP1
B: capsid protein VP0
C: Genome polyprotein
x 60


  • crystal asymmetric unit, crystal frame
  • 5.41 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)5,407,669180
Polymers5,407,669180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.67082038, -0.68819098, -0.2763932), (0.16245988, 0.5, -0.85065081), (0.7236068, 0.52573108, 0.44721361)
3generate(0.13819656, -0.95105651, 0.27639323), (-0.42532537, -0.309017, -0.85065083), (0.89442721, -4.0E-8, -0.44721355)
4generate(0.13819656, -0.42532537, 0.89442722), (-0.95105652, -0.309017, -3.0E-8), (0.27639323, -0.85065082, -0.44721355)
5generate(0.67082037, 0.16245988, 0.72360681), (-0.68819098, 0.5, 0.52573109), (-0.27639319, -0.85065079, 0.44721361)
6generate(-0.63819666, -0.26286553, 0.72360677), (-0.26286553, -0.809017, -0.52573112), (0.72360675, -0.52573111, 0.44721365)
7generate(0.05278635, 0.68819098, 0.72360679), (-0.68819098, -0.5, 0.5257311), (0.72360678, -0.52573108, 0.44721365)
8generate(0.67082038, 0.68819098, -0.2763932), (-0.16245988, 0.5, 0.85065081), (0.7236068, -0.52573108, 0.44721361)
9generate(0.36180341, -0.26286554, -0.8944272), (0.58778525, 0.80901699, 2.0E-8), (0.72360679, -0.52573112, 0.44721359)
10generate(-0.44721361, -0.85065079, -0.27639324), (0.52573115, -0.8506508), (0.72360675, -0.52573114, 0.44721361)
11generate(-0.05278635, -0.68819098, -0.72360679), (-0.68819098, -0.5, 0.52573109), (-0.72360677, 0.52573108, -0.44721365)
12generate(-0.67082038, -0.68819098, 0.2763932), (-0.16245988, 0.5, 0.85065081), (-0.7236068, 0.52573108, -0.44721361)
13generate(-0.36180341, 0.26286554, 0.8944272), (0.58778525, 0.809017, 2.0E-8), (-0.72360679, 0.52573111, -0.44721359)
14generate(0.44721361, 0.85065079, 0.27639324), (0.52573115, -0.8506508), (-0.72360676, 0.52573114, -0.44721361)
15generate(0.63819666, 0.26286553, -0.72360677), (-0.26286554, -0.809017, -0.52573113), (-0.72360675, 0.52573112, -0.44721365)
16generate(-0.30901699, 0.95105651, 2.0E-8), (0.95105652, 0.30901699, 3.0E-8), (2.0E-8, 3.0E-8, -1)
17generate(-0.05278635, 0.68819097, -0.72360679), (0.68819098, -0.5, -0.52573109), (-0.72360678, -0.52573108, -0.44721365)
18generate(-0.44721353, -0.89442723), (-1), (-0.89442722, 0.44721353)
19generate(-0.94721357, -0.16245988, -0.27639325), (-0.16245988, -0.5, 0.85065081), (-0.27639326, 0.8506508, 0.44721357)
20generate(-0.86180342, 0.42532537, 0.27639319), (0.42532537, 0.309017, 0.85065083), (0.27639318, 0.85065081, -0.44721358)
21generate(-0.3618034, -0.58778525, -0.7236068), (-0.26286554, 0.80901699, -0.52573113), (0.89442719, -3.0E-8, -0.44721359)
22generate(-0.86180342, -0.42532537, 0.27639319), (-0.42532537, 0.30901699, -0.85065083), (0.27639319, -0.85065082, -0.44721357)
23generate(-0.44721362, 0.52573114, 0.72360677), (-0.85065079, -0.52573115), (-0.27639323, -0.85065078, 0.44721362)
24generate(0.30901699, 0.95105651, -3.0E-8), (-0.95105652, 0.309017, -3.0E-8), (-2.0E-8, 4.0E-8, 1)
25generate(0.36180341, 0.26286553, -0.8944272), (-0.58778525, 0.809017, -2.0E-8), (0.72360679, 0.52573111, 0.44721359)
26generate(-0.13819656, 0.95105651, -0.27639323), (-0.42532537, -0.309017, -0.85065083), (-0.8944272, 4.0E-8, 0.44721356)
27generate(-0.13819656, 0.42532537, -0.89442722), (-0.95105652, -0.30901699, -3.0E-8), (-0.27639322, 0.85065082, 0.44721355)
28generate(-0.67082037, -0.16245988, -0.72360681), (-0.68819098, 0.5, 0.52573109), (0.27639319, 0.85065079, -0.44721362)
29generate(-1), (1), (-1)
30generate(-0.67082038, 0.68819098, 0.27639319), (0.16245988, 0.5, -0.85065081), (-0.7236068, -0.52573108, -0.44721361)
31generate(0.94721357, 0.16245988, 0.27639326), (-0.16245988, -0.5, 0.85065081), (0.27639326, -0.85065079, -0.44721358)
32generate(0.86180342, -0.42532537, -0.27639319), (0.42532537, 0.309017, 0.85065083), (-0.27639318, -0.85065081, 0.44721357)
33generate(0.309017, -0.95105651, -2.0E-8), (0.95105652, 0.30901699, 4.0E-8), (-3.0E-8, -3.0E-8, 1)
34generate(0.05278635, -0.68819098, 0.72360679), (0.68819098, -0.5, -0.52573109), (0.72360677, 0.52573108, 0.44721365)
35generate(0.44721353, 0.89442723), (-1), (0.89442722, -0.44721353)
36generate(-0.44721361, -0.52573114, 0.72360677), (0.85065079, 0.52573115), (-0.27639324, 0.85065078, 0.44721361)
37generate(0.13819656, 0.42532538, 0.89442722), (0.95105652, -0.30901699, 4.0E-8), (0.27639322, 0.85065081, -0.44721355)
38generate(0.80901699, 0.58778525, 6.0E-8), (0.58778526, -0.80901699, 2.0E-8), (7.0E-8, 2.0E-8, -1)
39generate(0.63819666, -0.26286554, -0.72360676), (0.26286554, -0.80901699, 0.52573113), (-0.72360675, -0.52573111, -0.44721365)
40generate(-0.13819656, -0.95105651, -0.27639322), (0.42532537, -0.30901699, 0.85065083), (-0.89442721, -3.0E-8, 0.44721355)
41generate(-0.36180341, -0.26286553, 0.8944272), (-0.58778526, 0.80901699, -2.0E-8), (-0.72360679, -0.52573112, -0.44721359)
42generate(0.3618034, 0.58778525, 0.7236068), (-0.26286554, 0.80901699, -0.52573113), (-0.89442719, 2.0E-8, 0.44721359)
43generate(0.86180342, 0.42532537, -0.27639319), (-0.42532537, 0.30901699, -0.85065083), (-0.27639318, 0.85065082, 0.44721358)
44generate(0.44721361, -0.52573114, -0.72360677), (-0.85065079, -0.52573115), (0.27639324, 0.85065078, -0.44721361)
45generate(-0.30901699, -0.95105651, 3.0E-8), (-0.95105652, 0.30901699, -4.0E-8), (3.0E-8, -4.0E-8, -1)
46generate(0.94721357, -0.16245988, 0.27639325), (0.16245988, -0.5, -0.85065081), (0.27639325, 0.85065079, -0.44721357)
47generate(0.80901699, -0.58778525, 7.0E-8), (-0.58778525, -0.80901699, -2.0E-8), (7.0E-8, -2.0E-8, -1)
48generate(0.44721361, -0.85065079, 0.27639324), (-0.52573115, 0.8506508), (-0.72360675, -0.52573114, -0.44721361)
49generate(0.3618034, -0.58778525, 0.7236068), (0.26286553, 0.809017, 0.52573113), (-0.89442719, -2.0E-8, 0.44721359)
50generate(0.67082038, -0.16245988, 0.72360681), (0.68819098, 0.5, -0.52573109), (-0.27639319, 0.85065079, 0.44721361)
51generate(-0.44721361, 0.85065079, -0.27639324), (-0.52573115, 0.8506508), (0.72360676, 0.52573114, 0.44721361)
52generate(-0.3618034, 0.58778525, -0.7236068), (0.26286554, 0.809017, 0.52573112), (0.89442719, 2.0E-8, -0.44721359)
53generate(-0.67082037, 0.16245988, -0.72360681), (0.68819098, 0.5, -0.5257311), (0.27639319, -0.8506508, -0.44721361)
54generate(-0.94721357, 0.16245988, -0.27639326), (0.16245988, -0.5, -0.85065081), (-0.27639325, -0.85065079, 0.44721358)
55generate(-0.809017, 0.58778525, -7.0E-8), (-0.58778525, -0.80901699, -2.0E-8), (-7.0E-8, 3.0E-8, 1)
56generate(-0.13819655, -0.42532538, -0.89442722), (0.95105652, -0.309017, 3.0E-8), (-0.27639323, -0.85065081, 0.44721355)
57generate(-0.80901699, -0.58778525, -6.0E-8), (0.58778525, -0.809017, 2.0E-8), (-7.0E-8, -2.0E-8, 1)
58generate(-0.63819666, 0.26286554, 0.72360676), (0.26286554, -0.80901699, 0.52573113), (0.72360675, 0.52573112, 0.44721365)
59generate(0.13819656, 0.95105651, 0.27639323), (0.42532537, -0.30901699, 0.85065083), (0.8944272, 4.0E-8, -0.44721356)
60generate(0.44721361, 0.52573114, -0.72360677), (0.85065079, 0.52573115), (0.27639323, -0.85065078, -0.44721361)

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Components

#1: Protein capsid protein VP1 /


Mass: 27195.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aichi virus (strain Human/A846/88/1989)
Production host: Chlorocebus aethiops (grivet) / References: UniProt: O91464*PLUS
#2: Protein capsid protein VP0 /


Mass: 38978.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aichi virus (strain Human/A846/88/1989)
Production host: Chlorocebus aethiops (grivet) / References: UniProt: O91464*PLUS
#3: Protein Genome polyprotein


Mass: 23954.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aichi virus (strain Human/A846/88/1989)
Cell (production host): green monkey kidney (Vero) cells / Production host: Chlorocebus aethiops (grivet) / References: UniProt: O91464*PLUS

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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: Aichi virus A846/88 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 6 MDa / Experimental value: NO
Source (natural)Organism: Aichi virus A846/88
Source (recombinant)Organism: Chlorocebus aethiops (grivet) / Cell: green monkey kidney (Vero) cells / Plasmid: No plasmids
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Aichi virus A846/88
Virus shellName: Capsid / Diameter: 300 nm / Triangulation number (T number): 1
Buffer solutionpH: 7 / Details: 1*PBS, pH 7.0
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 295 K / Details: Blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 37027 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderCryogen: HELIUM
Image recordingAverage exposure time: 2 sec. / Electron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 776
Image scansWidth: 3710 / Height: 3710 / Movie frames/image: 25 / Used frames/image: 3-22

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4GctfCTF correction
9RELION1.3initial Euler assignment
10RELION1.3final Euler assignment
11RELION1.3classification
12RELION1.33D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18566 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficent

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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