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- PDB-6ln0: Crystal structure of three main domains of nonstructural protein ... -

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Basic information

Entry
Database: PDB / ID: 6ln0
TitleCrystal structure of three main domains of nonstructural protein 3 from Coronavirus
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / nonstructural protein 3
Function / homology
Function and homology information


RNA exonuclease activity / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / DNA helicase activity / methyltransferase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / methylation / endonuclease activity / DNA helicase ...RNA exonuclease activity / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / DNA helicase activity / methyltransferase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / methylation / endonuclease activity / DNA helicase / membrane => GO:0016020 / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Non-structural protein 5, deltacoronavirus / Nonstructural protein 14, deltacoronavirus / Nonstructural protein 15, middle domain, deltacoronavirus / Nonstructural protein 15, N-terminal, deltacoronavirus / RNA-dependent RNA polymerase, deltacoronavirus / Non-structural protein 6, deltacoronavirus / Non-structural protein 2, IBV-like / Viral (Superfamily 1) RNA helicase / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus ...Non-structural protein 5, deltacoronavirus / Nonstructural protein 14, deltacoronavirus / Nonstructural protein 15, middle domain, deltacoronavirus / Nonstructural protein 15, N-terminal, deltacoronavirus / RNA-dependent RNA polymerase, deltacoronavirus / Non-structural protein 6, deltacoronavirus / Non-structural protein 2, IBV-like / Viral (Superfamily 1) RNA helicase / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) 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. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 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 speciesPorcine deltacoronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.455 Å
AuthorsLi, M.X. / Peng, G.Q.
CitationJournal: Emerg Microbes Infect / Year: 2021
Title: Structure of the multiple functional domains from coronavirus nonstructural protein 3.
Authors: Li, M. / Ye, G. / Si, Y. / Shen, Z. / Liu, Z. / Shi, Y. / Xiao, S. / Fu, Z.F. / Peng, G.
History
DepositionDec 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 2.0Sep 29, 2021Group: Advisory / Database references ...Advisory / Database references / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / refine / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _refine.ls_R_factor_R_free / _refine.ls_number_reflns_R_free / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7672
Polymers49,7011
Non-polymers651
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.922, 71.348, 64.433
Angle α, β, γ (deg.)90.000, 92.260, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Non-structural protein 3


Mass: 49701.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine deltacoronavirus / Gene: ORF1ab / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A222YV61
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.44 Å3/Da / Density % sol: 64.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 20000, imidazole, Bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 22938 / % possible obs: 98.8 % / Redundancy: 16.2 % / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.035 / Rrim(I) all: 0.145 / Χ2: 2.416 / Net I/σ(I): 8 / Num. measured all: 372635
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.45-2.5412.50.98522680.9480.2740.60499.2
2.54-2.6414.40.79522710.960.2090.49899.10.823
2.64-2.7615.90.70422710.970.1780.59498.90.727
2.76-2.90.49122790.980.1290.65697.60.509
2.9-3.090.33823050.9890.0820.81899.60.348
3.09-3.320.2223090.9940.0531.24199.60.226
3.32-3.660.14923040.9940.0362.35899.20.153
3.66-4.190.11822640.9950.034.08297.60.121
4.19-5.280.09923220.9970.0245.568990.102
5.28-500.08123450.9950.026.62980.083

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ewo

3ewo


Resolution: 2.455→39.018 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.4
RfactorNum. reflection% reflection
Rfree0.228 933 8.72 %
Rwork0.2081 --
obs0.2125 22928 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.57 Å2 / Biso mean: 60.0475 Å2 / Biso min: 29.2 Å2
Refinement stepCycle: final / Resolution: 2.455→39.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 1 26 3307
Biso mean--48.75 55.98 -
Num. residues----425
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.455-2.51640.36991260.3112139493
2.5164-2.58440.36171440.2924150399
2.5844-2.66050.31311430.2647148499
2.6605-2.74630.31381530.2593148399
2.7463-2.84440.30671370.2669149898
2.8444-2.95830.33191440.269147798
2.9583-3.09290.3061470.27211509100
3.0929-3.25590.32891400.26211511100
3.2559-3.45970.26481500.2412150399
3.4597-3.72670.31151400.2181152199
3.7267-4.10130.26731420.2054148398
4.1013-4.69390.22321440.1736149097
4.6939-5.91060.22791460.1703153799
5.9106-39.0180.16581440.1443153598

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