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- PDB-4l3b: X-ray structure of the HRV2 A particle uncoating intermediate -

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Basic information

Entry
Database: PDB / ID: 4l3b
TitleX-ray structure of the HRV2 A particle uncoating intermediate
Components
  • Protein VP1
  • Protein VP2
  • Protein VP3
KeywordsVIRUS / HRV2 capsid
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / 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 / host cell nucleus / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHuman rhinovirus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.5 Å
AuthorsVives-Adrian, L. / Querol-Audi, J. / Garriga, D. / Pous, J. / Verdaguer, N.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle.
Authors: Angela Pickl-Herk / Daniel Luque / Laia Vives-Adrián / Jordi Querol-Audí / Damià Garriga / Benes L Trus / Nuria Verdaguer / Dieter Blaas / José R Castón /
Abstract: During infection, viruses undergo conformational changes that lead to delivery of their genome into host cytosol. In human rhinovirus A2, this conversion is triggered by exposure to acid pH in the ...During infection, viruses undergo conformational changes that lead to delivery of their genome into host cytosol. In human rhinovirus A2, this conversion is triggered by exposure to acid pH in the endosome. The first subviral intermediate, the A-particle, is expanded and has lost the internal viral protein 4 (VP4), but retains its RNA genome. The nucleic acid is subsequently released, presumably through one of the large pores that open at the icosahedral twofold axes, and is transferred along a conduit in the endosomal membrane; the remaining empty capsids, termed B-particles, are shuttled to lysosomes for degradation. Previous structural analyses revealed important differences between the native protein shell and the empty capsid. Nonetheless, little is known of A-particle architecture or conformation of the RNA core. Using 3D cryo-electron microscopy and X-ray crystallography, we found notable changes in RNA-protein contacts during conversion of native virus into the A-particle uncoating intermediate. In the native virion, we confirmed interaction of nucleotide(s) with Trp(38) of VP2 and identified additional contacts with the VP1 N terminus. Study of A-particle structure showed that the VP2 contact is maintained, that VP1 interactions are lost after exit of the VP1 N-terminal extension, and that the RNA also interacts with residues of the VP3 N terminus at the fivefold axis. These associations lead to formation of a well-ordered RNA layer beneath the protein shell, suggesting that these interactions guide ordered RNA egress.
History
DepositionJun 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein VP1
B: Protein VP2
C: Protein VP3


Theoretical massNumber of molelcules
Total (without water)88,0423
Polymers88,0423
Non-polymers00
Water0
1
A: Protein VP1
B: Protein VP2
C: Protein VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,282,531180
Polymers5,282,531180
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: Protein VP1
B: Protein VP2
C: Protein VP3
x 5


  • icosahedral pentamer
  • 440 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)440,21115
Polymers440,21115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Protein VP1
B: Protein VP2
C: Protein VP3
x 6


  • icosahedral 23 hexamer
  • 528 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)528,25318
Polymers528,25318
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: Protein VP1
B: Protein VP2
C: Protein VP3
x 15


  • crystal asymmetric unit, crystal frame
  • 1.32 MDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)1,320,63345
Polymers1,320,63345
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)311.930, 357.830, 386.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017)
3generate(-0.809017, -0.5, -0.309017), (0.5, -0.309017, -0.809017), (0.309017, -0.809017, 0.5)
4generate(-0.809017, 0.5, 0.309017), (-0.5, -0.309017, -0.809017), (-0.309017, -0.809017, 0.5)
5generate(0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017)
6generate(-0.5, -0.309017, 0.809017), (-0.309017, -0.809017, -0.5), (0.809017, -0.5, 0.309017)
7generate(1), (-1), (-1)
8generate(0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017)
9generate(0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017)
10generate(-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017)
11generate(0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5)
12generate(0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017)
13generate(-1), (-1), (1)
14generate(-0.809017, -0.5, 0.309017), (-0.5, 0.309017, -0.809017), (0.309017, -0.809017, -0.5)
15generate(-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017)

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Components

#1: Protein Protein VP1 / P1D / Virion protein 1


Mass: 32924.797 Da / Num. of mol.: 1 / Fragment: UNP residues 568-856 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus A2 / References: UniProt: P04936
#2: Protein Protein VP2 / P1B / Virion protein 2


Mass: 29009.588 Da / Num. of mol.: 1 / Fragment: UNP residues 70-330 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus A2 / References: UniProt: P04936
#3: Protein Protein VP3 / P1C / Virion protein 3


Mass: 26107.793 Da / Num. of mol.: 1 / Fragment: UNP residues 331-567 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus A2 / References: UniProt: P04936

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5 M ammonium sulfate, 1 M sodium/potassium phosphate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 4, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→262.63 Å / Num. obs: 15750 / % possible obs: 12.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.163 / Rsym value: 0.163 / Net I/σ(I): 4.4
Reflection shellResolution: 4.5→4.74 Å / % possible all: 12.5

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Processing

Software
NameVersionClassification
DNAdata collection
DMmodel building
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TN9

3tn9


Resolution: 6.5→121.39 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.32 2204 RANDOM
Rwork0.309 --
obs0.309 14024 -
Refinement stepCycle: LAST / Resolution: 6.5→121.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5514 0 0 0 5514

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