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- PDB-5hbz: Structure of EAV NSP11 K170A mutant at 3.10A -

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Basic information

Entry
Database: PDB / ID: 5hbz
TitleStructure of EAV NSP11 K170A mutant at 3.10A
ComponentsNon-structural protein 11
KeywordsHYDROLASE / nsp11 / Equine arteritis virus / Endoribonuclease / Nonstructural Protein 11 / Nidovirus / NF-kappaB
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 / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / 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 / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 / 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 / RING/Ubox like zinc-binding domain / Nonstructural protein 10, zinc-binding domain, arterivirus / NSP11, NendoU domain, arterivirus / NSP11, N-terminal, arterivirus / 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 / 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. / 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
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesEquine arteritis virus Bucyrus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsZhang, M.F. / Chen, Z.Z.
CitationJournal: J. Virol. / Year: 2017
Title: Structural Biology of the Arterivirus nsp11 Endoribonucleases.
Authors: Zhang, M. / Li, X. / Deng, Z. / Chen, Z. / Liu, Y. / Gao, Y. / Wu, W. / Chen, Z.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Nov 8, 2023Group: 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: Non-structural protein 11
B: Non-structural protein 11
C: Non-structural protein 11
D: Non-structural protein 11
E: Non-structural protein 11
F: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)146,1706
Polymers146,1706
Non-polymers00
Water00
1
A: Non-structural protein 11
D: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)48,7232
Polymers48,7232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-10 kcal/mol
Surface area20000 Å2
MethodPISA
2
B: Non-structural protein 11
F: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)48,7232
Polymers48,7232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-10 kcal/mol
Surface area20000 Å2
MethodPISA
3
C: Non-structural protein 11
E: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)48,7232
Polymers48,7232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-10 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.268, 248.268, 226.298
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Non-structural protein 11


Mass: 24361.734 Da / Num. of mol.: 6 / Mutation: K170A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine arteritis virus Bucyrus / Strain: Bucyrus / Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) / References: UniProt: P19811

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.63 Å3/Da / Density % sol: 73.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 48540 / Num. obs: 44766 / % possible obs: 99.2 % / Redundancy: 5.5 % / Net I/σ(I): 16
Reflection shellResolution: 3.1→3.15 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EYI

5eyi


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.927 / SU B: 12.79 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.877 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19893 2341 5 %RANDOM
Rwork0.19487 ---
obs0.19508 44766 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å20 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9946 0 0 0 9946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910254
X-RAY DIFFRACTIONr_bond_other_d0.0060.029344
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.95614021
X-RAY DIFFRACTIONr_angle_other_deg0.972321567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24651277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56823.793435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.941151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0021542
X-RAY DIFFRACTIONr_chiral_restr0.0810.21528
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022369
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_it3.3347.2165135
X-RAY DIFFRACTIONr_mcbond_other3.3297.2165134
X-RAY DIFFRACTIONr_mcangle_it5.41510.826403
X-RAY DIFFRACTIONr_mcangle_other5.41510.8216404
X-RAY DIFFRACTIONr_scbond_it3.1977.5025118
X-RAY DIFFRACTIONr_scbond_other3.197.5025115
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.32611.1357617
X-RAY DIFFRACTIONr_long_range_B_refined7.99257.62810719
X-RAY DIFFRACTIONr_long_range_B_other7.99457.63210720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.096→3.176 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 117 -
Rwork0.329 2699 -
obs--78.97 %

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