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- PDB-4n0o: Complex structure of Arterivirus nonstructural protein 10 (helica... -

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Basic information

Entry
Database: PDB / ID: 4n0o
TitleComplex structure of Arterivirus nonstructural protein 10 (helicase) with DNA
Components
  • DNA
  • Replicase polyprotein 1ab
KeywordsHYDROLASE/DNA / arterivirus / helicase / zbd / nsp10 / complex / HYDROLASE-DNA complex
Function / homology
Function and homology information


serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease activity / Lyases; Phosphorus-oxygen lyases / endonuclease activity / symbiont-mediated suppression of host ISG15-protein conjugation / DNA helicase / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 ...serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease activity / Lyases; Phosphorus-oxygen lyases / endonuclease activity / symbiont-mediated suppression of host ISG15-protein conjugation / DNA helicase / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / RNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lyase activity / viral protein processing / host cell perinuclear region of cytoplasm / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / serine-type endopeptidase activity / viral translational frameshifting / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Protein of unknown function DUF3756 / Equine arteritis virus, non-structural protein 1 / Nsp2, transmembrane domain / Replicase polyprotein 1ab / Nidovirus helicase, RING/Ubox like zinc-binding domain / Protein of unknown function (DUF3756) / Papain-like auto-proteinase / Nsp2, transmembrane domain / Replicase polyprotein 1ab regulatory domain / RING/Ubox like zinc-binding domain ...Protein of unknown function DUF3756 / Equine arteritis virus, non-structural protein 1 / Nsp2, transmembrane domain / Replicase polyprotein 1ab / Nidovirus helicase, RING/Ubox like zinc-binding domain / Protein of unknown function (DUF3756) / Papain-like auto-proteinase / Nsp2, transmembrane domain / Replicase polyprotein 1ab regulatory domain / RING/Ubox like zinc-binding domain / Nonstructural protein 10, zinc-binding domain, arterivirus / NSP11, NendoU domain, arterivirus / NSP11, N-terminal, arterivirus / PRRSV nonstructural protein 11 N-terminal domain / Arteriviridae zinc-binding (AV ZBD) domain profile. / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain / Arterivirus Nsp2, peptidase C33 / Equine arteritis virus peptidase S32 / Serine protease, chymotrypsin-like serine protease, C-terminal / Arterivirus NSP4 peptidase domain / Arterivirus papain-like cysteine protease beta (PCPbeta) domain / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp7 alpha superfamily / Equine arterivirus Nsp2-type cysteine proteinase / Equine arteritis virus serine endopeptidase S32 / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp4 proteinase domain profile. / Arterivirus nsp2 cysteine protease (AV CP) domain profile. / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain profile. / Arterivirus papain-like cysteine protease beta (PCPbeta) domain profile. / Viral superfamily 1 RNA helicase core domain / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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
DNA / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesEquine arteritis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsDeng, Z. / Chen, Z.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase.
Authors: Deng, Z. / Lehmann, K.C. / Li, X. / Feng, C. / Wang, G. / Zhang, Q. / Qi, X. / Yu, L. / Zhang, X. / Feng, W. / Wu, W. / Gong, P. / Tao, Y. / Posthuma, C.C. / Snijder, E.J. / Gorbalenya, A.E. / Chen, Z.
History
DepositionOct 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Sep 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicase polyprotein 1ab
C: Replicase polyprotein 1ab
E: Replicase polyprotein 1ab
G: Replicase polyprotein 1ab
B: DNA
D: DNA
F: DNA
H: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,02527
Polymers190,9598
Non-polymers1,06519
Water15,006833
1
A: Replicase polyprotein 1ab
B: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0167
Polymers47,7402
Non-polymers2765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-21 kcal/mol
Surface area20040 Å2
MethodPISA
2
C: Replicase polyprotein 1ab
D: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0167
Polymers47,7402
Non-polymers2765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-33 kcal/mol
Surface area19860 Å2
MethodPISA
3
E: Replicase polyprotein 1ab
F: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0167
Polymers47,7402
Non-polymers2765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-32 kcal/mol
Surface area20270 Å2
MethodPISA
4
G: Replicase polyprotein 1ab
H: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9766
Polymers47,7402
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-22 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.628, 88.838, 128.781
Angle α, β, γ (deg.)81.74, 90.01, 71.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Replicase polyprotein 1ab / ORF1ab polyprotein / Nsp1 papain-like cysteine proteinase / PCP / Nsp2 cysteine proteinase / CP2 / ...ORF1ab polyprotein / Nsp1 papain-like cysteine proteinase / PCP / Nsp2 cysteine proteinase / CP2 / CP / Non-structural protein 3 / Nsp3 / 3C-like serine proteinase / 3CLSP / Nsp4 / Non-structural protein 5-6-7 / Nsp5-6-7 / Non-structural protein 5 / Nsp5 / Non-structural protein 6 / Nsp6 / Non-structural protein 7-alpha / Nsp7-alpha / Non-structural protein 7-beta / Nsp7-beta / Non-structural protein 8 / Nsp8 / RNA-directed RNA polymerase / Pol / RdRp / Nsp9 / Helicase / Hel / Nsp10 / Non-structural protein 11 / Nsp11 / Non-structural protein 12 / Nsp12


Mass: 45655.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine arteritis virus / Strain: equine arteritis virus / Gene: 1a-1b, nsp10, rep / Plasmid: pet-28a / Production host: Escherichia coli (E. coli) / Strain (production host): plasmid
References: UniProt: P19811, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Serine ...References: UniProt: P19811, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases, RNA-directed RNA polymerase, DNA helicase, RNA helicase
#2: DNA chain
DNA


Mass: 2084.392 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 833 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2M NH4SO4, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 4, 2012
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.532
11H, H-K, -L20.468
ReflectionResolution: 2.65→50 Å / Num. all: 69690 / Num. obs: 66954 / % possible obs: 96.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.65→2.7 Å / % possible all: 95.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N0N

4n0n


Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.358 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.16 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26353 3204 4.9 %RANDOM
Rwork0.24586 ---
obs0.24672 62321 95.74 %-
all-69690 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.364 Å2
Baniso -1Baniso -2Baniso -3
1--5.01 Å2-1.6 Å2-5.2 Å2
2--23.65 Å2-7.39 Å2
3----18.64 Å2
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11598 548 19 833 12998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01912496
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.93617172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17551563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95922.775418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.695151672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8421561
X-RAY DIFFRACTIONr_chiral_restr0.0820.21961
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0229336
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.648→2.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 220 -
Rwork0.186 4455 -
obs--92.03 %

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