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- PDB-7ara: Rhinovirus A2 2A protease in complex with zVAM.fmk -

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Basic information

Entry
Database: PDB / ID: 7ara
TitleRhinovirus A2 2A protease in complex with zVAM.fmk
Components2A protease
KeywordsVIRAL PROTEIN / Chymotrypsin-like cysteine protease / rhinoviral 2A protease / zVAM.fmk
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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / 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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / 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 / virion attachment to host cell / structural molecule activity / 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
Chem-S7N / Chem-S7Q / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.243 Å
AuthorsDeutschmann-Olek, K.M. / Skern, T. / Bezerra, G.A. / Yue, W.W.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP28183 Austria
Austrian Science FundW1258 Austria
CitationJournal: Virology / Year: 2021
Title: Defining substrate selection by rhinoviral 2A proteinase through its crystal structure with the inhibitor zVAM.fmk.
Authors: Deutschmann-Olek, K.M. / Yue, W.W. / Bezerra, G.A. / Skern, T.
History
DepositionOct 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2A protease
B: 2A protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4866
Polymers32,4522
Non-polymers1,0344
Water61334
1
A: 2A protease
hetero molecules

B: 2A protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4866
Polymers32,4522
Non-polymers1,0344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x+y-1,-x,z+1/31
Buried area1290 Å2
ΔGint-13 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.647, 74.647, 160.831
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 2A protease


Mass: 16226.165 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 2 / Production host: Escherichia coli (E. coli)
References: UniProt: P04936, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Chemical ChemComp-S7N / (phenylmethyl) ~{N}-[(2~{R})-3-methyl-1-[[(2~{S})-1-[[(3~{S})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate / Z-VAM-FMK;zVAM.fmk


Mass: 451.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H33N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-S7Q / (phenylmethyl) ~{N}-[(2~{S})-3-methyl-1-[[(2~{R})-1-[[(3~{R})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate / zVAM.fmk


Mass: 451.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H33N3O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.99 Å3/Da / Density % sol: 69.14 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 7.5 % PEG8000, 0.3 M KCNS, 5 % 2-methyl-2-butanol, 10 % glycerol, 10 mM b-mercaptoethanol and 50 mM sodium-potassium phosphate buffer pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.243→64.646 Å / Num. obs: 12111 / % possible obs: 93.3 % / Redundancy: 19.2 % / Biso Wilson estimate: 45.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.044 / Rrim(I) all: 0.194 / Net I/σ(I): 12.9 / Num. measured all: 232197
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.243-2.546192.074115456080.5830.4842.1311.880.3
8.188-64.64617.40.05105176040.9980.0130.05238.399.8

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXv1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HRV

2hrv


Resolution: 2.243→60 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2572 566 4.67 %
Rwork0.2142 11541 -
obs0.2162 12107 47.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.44 Å2 / Biso mean: 47.225 Å2 / Biso min: 12.03 Å2
Refinement stepCycle: final / Resolution: 2.243→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2179 0 64 34 2277
Biso mean--74.61 34.69 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052316
X-RAY DIFFRACTIONf_angle_d0.9733139
X-RAY DIFFRACTIONf_chiral_restr0.038333
X-RAY DIFFRACTIONf_plane_restr0.004405
X-RAY DIFFRACTIONf_dihedral_angle_d15.112805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.243-2.46870.4107120.39133826
2.4687-2.8260.367560.3508112419
2.826-3.56040.29231990.2654371861
3.5604-600.23772990.18986317100

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