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- PDB-3rnv: Structure of the autocatalytic cysteine protease domain of potyvi... -

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Basic information

Entry
Database: PDB / ID: 3rnv
TitleStructure of the autocatalytic cysteine protease domain of potyvirus helper-component proteinase
ComponentsHelper component proteinase
KeywordsHYDROLASE / cysteine protease / proteolysis
Function / homology
Function and homology information


nuclear-inclusion-a endopeptidase / helper-component proteinase / positive stranded viral RNA replication / RNA-protein covalent cross-linking / Hydrolases; Acting on peptide bonds (peptidases) / helical viral capsid / : / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement ...nuclear-inclusion-a endopeptidase / helper-component proteinase / positive stranded viral RNA replication / RNA-protein covalent cross-linking / Hydrolases; Acting on peptide bonds (peptidases) / helical viral capsid / : / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / RNA binding / ATP binding
Similarity search - Function
Helper component proteinase / Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Potyvirus P1 protease / Potyviridae polyprotein ...Helper component proteinase / Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile. / Potyviridae P1 protease domain profile. / Potyvirus NIa protease (NIa-pro) domain / Peptidase family C4 / Potyvirus NIa protease (NIa-pro) domain profile. / Potyvirus coat protein / Potyvirus coat protein / Cathepsin B; Chain A / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / 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 / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Biological speciesTurnip mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsYe, K.
CitationJournal: to be published
Title: Structure of the autocatalytic cysteine protease domain of potyvirus helper-component proteinase
Authors: Guo, B. / Lin, J. / Ye, K.
History
DepositionApr 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Helper component proteinase


Theoretical massNumber of molelcules
Total (without water)18,0451
Polymers18,0451
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Helper component proteinase

A: Helper component proteinase

A: Helper component proteinase

A: Helper component proteinase


Theoretical massNumber of molelcules
Total (without water)72,1804
Polymers72,1804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area6330 Å2
ΔGint-45 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.806, 98.806, 65.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Helper component proteinase / HC-Pro


Mass: 18045.018 Da / Num. of mol.: 1 / Fragment: cysteine protease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Turnip mosaic virus / Strain: Japanese / Gene: HC-Pro / Plasmid: pET28a-SMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P89509, helper-component proteinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 1M (NH4)2SO4, 4%(w/v) PEG3350, 0.1M Bis-Tris, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 11250 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 48.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 4.1 / Num. unique all: 552 / % possible all: 98.7

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→19 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.655 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27411 526 4.7 %RANDOM
Rwork0.24629 ---
obs0.24751 10612 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 0 17 1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.9681369
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.015122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34923.65941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67815186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.057154
X-RAY DIFFRACTIONr_chiral_restr0.0740.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02733
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5491.5612
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0432995
X-RAY DIFFRACTIONr_scbond_it1.4553400
X-RAY DIFFRACTIONr_scangle_it2.5214.5374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 41 -
Rwork0.379 777 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 31.577 Å / Origin y: 38.018 Å / Origin z: 13.347 Å
111213212223313233
T0.2783 Å2-0.1188 Å2-0.0319 Å2-0.4086 Å20.1894 Å2--0.2865 Å2
L1.3487 °2-1.5366 °2-0.0048 °2-3.2857 °2-0.6697 °2--0.9455 °2
S0.0124 Å °-0.3754 Å °-0.1674 Å °0.3855 Å °0.3964 Å °0.1202 Å °0.2153 Å °-0.4336 Å °-0.4089 Å °

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