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- PDB-5wtf: Cryo-EM structure for Hepatitis A virus empty particle -

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Basic information

Entry
Database: PDB / ID: 5wtf
TitleCryo-EM structure for Hepatitis A virus empty particle
Components
  • VP0
  • VP1
  • VP3
KeywordsVIRUS / HAV / Neutralizing mechanism / Receptor recognition / Viral entry
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host multivesicular body / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host multivesicular body / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. ...Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesHepatitis A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWang, X. / Zhu, L. / Dang, M. / Hu, Z. / Gao, Q. / Yuan, S. / Sun, Y. / Zhang, B. / Ren, J. / Walter, T.S. ...Wang, X. / Zhu, L. / Dang, M. / Hu, Z. / Gao, Q. / Yuan, S. / Sun, Y. / Zhang, B. / Ren, J. / Walter, T.S. / Wang, J. / Fry, E.E. / Stuart, D.I. / Rao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation31570717 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Potent neutralization of hepatitis A virus reveals a receptor mimic mechanism and the receptor recognition site.
Authors: Xiangxi Wang / Ling Zhu / Minghao Dang / Zhongyu Hu / Qiang Gao / Shuai Yuan / Yao Sun / Bo Zhang / Jingshan Ren / Abhay Kotecha / Thomas S Walter / Junzhi Wang / Elizabeth E Fry / David I Stuart / Zihe Rao /
Abstract: Hepatitis A virus (HAV) infects ∼1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and ...Hepatitis A virus (HAV) infects ∼1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and little is known of how it enters cells and releases its RNA. Here we report a potent HAV-specific monoclonal antibody, R10, which neutralizes HAV infection by blocking attachment to the host cell. High-resolution cryo-EM structures of HAV full and empty particles and of the complex of HAV with R10 Fab reveal the atomic details of antibody binding and point to a receptor recognition site at the pentamer interface. These results, together with our observation that the R10 Fab destabilizes the capsid, suggest the use of a receptor mimic mechanism to neutralize virus infection, providing new opportunities for therapeutic intervention.
History
DepositionDec 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Nov 6, 2019Group: Data collection / Experimental preparation / Other
Category: atom_sites / cell ...atom_sites / cell / em_sample_support / em_software
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _em_sample_support.grid_type / _em_software.name
Revision 1.3Mar 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

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  • 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: VP1
B: VP0
C: VP3


Theoretical massNumber of molelcules
Total (without water)75,7633
Polymers75,7633
Non-polymers00
Water00
1
A: VP1
B: VP0
C: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)4,545,775180
Polymers4,545,775180
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: VP1
B: VP0
C: VP3
x 5


  • icosahedral pentamer
  • 379 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)378,81515
Polymers378,81515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP0
C: VP3
x 6


  • icosahedral 23 hexamer
  • 455 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)454,57718
Polymers454,57718
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: VP1
B: VP0
C: VP3
x 60


  • crystal asymmetric unit, crystal frame
  • 4.55 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)4,545,775180
Polymers4,545,775180
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(0.30901699, -0.95105651, 4.0E-8), (0.95105653, 0.309017, -6.0E-8), (4.0E-8, 5.0E-8, 1)
3generate(-0.809017, -0.58778525, 1.1E-7), (0.58778526, -0.80901699, -4.0E-8), (1.1E-7, 3.0E-8, 1)
4generate(-0.80901699, 0.58778525, 1.1E-7), (-0.58778526, -0.809017, 3.0E-8), (1.0E-7, -4.0E-8, 1)
5generate(0.309017, 0.95105651, 5.0E-8), (-0.95105653, 0.30901699, 6.0E-8), (4.0E-8, -6.0E-8, 1)
6generate(-0.94721363, 0.16245979, -0.27639311), (0.1624598, -0.5, -0.85065083), (-0.27639312, -0.85065081, 0.44721362)
7generate(-0.13819667, 0.95105651, -0.27639316), (-0.42532546, -0.309017, -0.85065079), (-0.89442716, -6.0E-8, 0.44721367)
8generate(0.86180337, 0.42532546, -0.27639322), (-0.42532546, 0.30901699, -0.85065079), (-0.27639323, 0.85065078, 0.44721363)
9generate(0.67082042, -0.68819092, -0.27639322), (0.1624598, 0.5, -0.85065082), (0.72360679, 0.52573115, 0.44721357)
10generate(-0.44721357, -0.85065083, -0.27639315), (0.52573107, -0.85065085), (0.72360685, -0.52573106, 0.44721356)
11generate(-0.86180337, 0.42532545, 0.27639323), (0.42532546, 0.30901699, 0.85065079), (0.27639323, 0.85065078, -0.44721362)
12generate(0.13819667, 0.95105651, 0.27639317), (0.42532545, -0.309017, 0.85065079), (0.89442716, -5.0E-8, -0.44721367)
13generate(0.94721363, 0.1624598, 0.27639311), (-0.1624598, -0.5, 0.85065082), (0.27639312, -0.85065081, -0.44721363)
14generate(0.44721357, -0.85065083, 0.27639314), (-0.52573107, 0.85065085), (-0.72360685, -0.52573106, -0.44721357)
15generate(-0.67082042, -0.68819093, 0.27639321), (-0.16245979, 0.5, 0.85065083), (-0.72360678, 0.52573115, -0.44721356)
16generate(0.80901699, -0.58778524, -1.1E-7), (-0.58778526, -0.80901699, 4.0E-8), (-1.1E-7, 3.0E-8, -1)
17generate(-0.30901699, -0.95105651, -5.0E-8), (-0.95105652, 0.30901699, 6.0E-8), (-4.0E-8, 6.0E-8, -1)
18generate(-1), (1), (-1)
19generate(-0.309017, 0.95105651, -4.0E-8), (0.95105653, 0.309017, -6.0E-8), (-4.0E-8, -5.0E-8, -1)
20generate(0.80901699, 0.58778525, -1.1E-7), (0.58778525, -0.80901699, -4.0E-8), (-1.0E-7, -3.0E-8, -1)
21generate(0.05278649, -0.68819092, 0.72360682), (0.68819093, -0.5, -0.52573116), (0.72360682, 0.52573115, 0.44721351)
22generate(-0.63819651, -0.26286559, 0.72360687), (-0.26286559, -0.80901699, -0.52573111), (0.72360686, -0.52573109, 0.44721351)
23generate(-0.44721357, 0.52573105, 0.72360686), (-0.85065085, -0.52573107), (-0.27639315, -0.85065083, 0.44721357)
24generate(0.36180339, 0.58778524, 0.72360681), (-0.26286559, 0.80901699, -0.5257311), (-0.89442719, -4.0E-8, 0.44721361)
25generate(0.67082042, -0.16245979, 0.72360678), (0.68819094, 0.5, -0.52573116), (-0.27639321, 0.85065081, 0.44721357)
26generate(-0.36180339, -0.26286559, 0.89442718), (-0.58778525, 0.80901699, 4.0E-8), (-0.72360681, -0.52573109, -0.4472136)
27generate(-0.36180339, 0.26286558, 0.89442719), (0.58778526, 0.80901699, -3.0E-8), (-0.7236068, 0.52573109, -0.4472136)
28generate(0.13819667, 0.42532545, 0.89442715), (0.95105652, -0.30901699, -6.0E-8), (0.27639317, 0.85065078, -0.44721366)
29generate(0.4472137, 0.89442713), (-1), (0.89442714, -0.4472137)
30generate(0.13819667, -0.42532545, 0.89442715), (-0.95105653, -0.30901699, 6.0E-8), (0.27639316, -0.85065078, -0.44721367)
31generate(-0.13819667, 0.42532546, -0.89442715), (-0.95105652, -0.309017, 6.0E-8), (-0.27639317, 0.85065077, 0.44721367)
32generate(0.36180339, 0.26286559, -0.89442718), (-0.58778526, 0.80901699, 4.0E-8), (0.7236068, 0.5257311, 0.4472136)
33generate(0.36180339, -0.26286559, -0.89442719), (0.58778526, 0.809017, -3.0E-8), (0.7236068, -0.52573109, 0.4472136)
34generate(-0.13819667, -0.42532545, -0.89442715), (0.95105653, -0.30901699, -6.0E-8), (-0.27639317, -0.85065078, 0.44721366)
35generate(-0.4472137, -0.89442713), (-1), (-0.89442714, 0.4472137)
36generate(0.44721357, 0.52573106, -0.72360685), (0.85065085, 0.52573107), (0.27639315, -0.85065083, -0.44721357)
37generate(0.63819651, -0.26286558, -0.72360687), (0.26286559, -0.80901699, 0.5257311), (-0.72360686, -0.5257311, -0.44721351)
38generate(-0.05278649, -0.68819092, -0.72360683), (-0.68819093, -0.5, 0.52573116), (-0.72360682, 0.52573115, -0.44721351)
39generate(-0.67082042, -0.1624598, -0.72360679), (-0.68819093, 0.49999999, 0.52573116), (0.27639322, 0.85065081, -0.44721357)
40generate(-0.36180339, 0.58778524, -0.7236068), (0.26286559, 0.80901699, 0.52573111), (0.89442719, -3.0E-8, -0.44721361)
41generate(0.0527865, 0.68819092, 0.72360682), (-0.68819094, -0.5, 0.52573115), (0.72360682, -0.52573115, 0.44721351)
42generate(0.67082042, 0.16245979, 0.72360678), (-0.68819094, 0.5, 0.52573116), (-0.27639322, -0.85065081, 0.44721357)
43generate(0.36180338, -0.58778525, 0.7236068), (0.26286559, 0.809017, 0.5257311), (-0.89442719, 3.0E-8, 0.44721361)
44generate(-0.44721357, -0.52573106, 0.72360685), (0.85065085, 0.52573106), (-0.27639315, 0.85065083, 0.44721357)
45generate(-0.63819651, 0.26286559, 0.72360686), (0.26286559, -0.809017, 0.52573109), (0.72360686, 0.52573109, 0.44721351)
46generate(-0.13819668, -0.95105651, -0.27639317), (0.42532546, -0.30901699, 0.85065079), (-0.89442716, 5.0E-8, 0.44721367)
47generate(-0.94721363, -0.16245979, -0.27639312), (-0.1624598, -0.5, 0.85065082), (-0.27639312, 0.85065081, 0.44721363)
48generate(-0.44721356, 0.85065083, -0.27639315), (-0.52573107, 0.85065085), (0.72360685, 0.52573106, 0.44721357)
49generate(0.67082042, 0.68819092, -0.27639322), (-0.1624598, 0.5, 0.85065083), (0.72360678, -0.52573115, 0.44721357)
50generate(0.86180336, -0.42532545, -0.27639323), (0.42532546, 0.309017, 0.85065079), (-0.27639323, -0.85065078, 0.44721363)
51generate(0.44721357, 0.85065083, 0.27639315), (0.52573107, -0.85065085), (-0.72360685, 0.52573106, -0.44721357)
52generate(0.94721363, -0.16245979, 0.27639312), (0.1624598, -0.5, -0.85065083), (0.27639312, 0.85065081, -0.44721363)
53generate(0.13819667, -0.95105651, 0.27639317), (-0.42532546, -0.30901699, -0.85065079), (0.89442716, 6.0E-8, -0.44721367)
54generate(-0.86180337, -0.42532546, 0.27639323), (-0.42532546, 0.309017, -0.85065079), (0.27639322, -0.85065077, -0.44721363)
55generate(-0.67082042, 0.68819092, 0.27639322), (0.1624598, 0.5, -0.85065082), (-0.72360679, -0.52573115, -0.44721357)
56generate(-0.36180339, -0.58778525, -0.7236068), (-0.26286559, 0.809017, -0.52573109), (0.89442719, 4.0E-8, -0.44721361)
57generate(-0.67082042, 0.16245979, -0.72360678), (0.68819094, 0.50000001, -0.52573115), (0.27639322, -0.85065081, -0.44721357)
58generate(-0.05278649, 0.68819092, -0.72360682), (0.68819094, -0.5, -0.52573116), (-0.72360682, -0.52573115, -0.44721351)
59generate(0.63819652, 0.26286559, -0.72360686), (-0.26286559, -0.809017, -0.5257311), (-0.72360686, 0.52573109, -0.44721351)
60generate(0.44721357, -0.52573105, -0.72360685), (-0.85065085, -0.52573106), (0.27639315, 0.85065083, -0.44721357)

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Components

#1: Protein VP1


Mass: 25161.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis A virus / Organ: Homo sapiens / Cell line (production host): vero / Production host: Chlorocebus aethiops (grivet) / References: UniProt: P08617*PLUS
#2: Protein VP0


Mass: 22765.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis A virus / Organ: Homo sapiens / Cell line (production host): vero / Production host: Chlorocebus aethiops (grivet) / References: UniProt: P08617*PLUS
#3: Protein VP3


Mass: 27835.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis A virus / Cell line (production host): vero / Production host: Chlorocebus aethiops (grivet) / References: UniProt: P08617*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: Hepatitis A virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 6 MDa / Experimental value: NO
Source (natural)Organism: Hepatitis A virus
Source (recombinant)Organism: Chlorocebus aethiops (grivet) / Cell: vero / Plasmid: no plasmids
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: capsid / Diameter: 300 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4 / Details: PBS Buffer
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
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: 298 K / Details: blot for 3s 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 FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3000 nm / Cs: 2 mm
Specimen holderSpecimen holder model: OTHER
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 1.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 500
Image scansWidth: 3710 / Height: 3710 / Movie frames/image: 25 / Used frames/image: 1-25

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Processing

SoftwareName: PHENIX / Version: 1.10_2155: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN2particle selectionEMAN2 e2boxer.py was used to automatically select particle images
4Gctf3CTF correction
7CHIMERAmodel fitting
9PHENIXmodel refinement
11RELION1.3final Euler assignment
13RELION1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5000
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4000 / Num. of class averages: 45 / Symmetry type: POINT
Atomic model buildingB value: 150 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0085490
ELECTRON MICROSCOPYf_angle_d0.7667485
ELECTRON MICROSCOPYf_dihedral_angle_d10.8684369
ELECTRON MICROSCOPYf_chiral_restr0.049840
ELECTRON MICROSCOPYf_plane_restr0.005955

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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