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- PDB-4s1t: Crystal structure of the mutant I26A/N52A of the endoribonuclease... -

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Basic information

Entry
Database: PDB / ID: 4s1t
TitleCrystal structure of the mutant I26A/N52A of the endoribonuclease from human coronavirus 229E
ComponentsUridylate-specific endoribonuclease
KeywordsHYDROLASE / HCoV-229e / endoribonuclease / trimeric nsp15 / double mutation
Function / homology
Function and homology information


host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methyltransferase cap1 ...host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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 / 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 / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Nsp15 N-terminal domain-like / nsp15 middle domain / : / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Double Stranded RNA Binding Domain ...Nsp15 N-terminal domain-like / nsp15 middle domain / : / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Double Stranded RNA Binding Domain / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / : / Coronavirus 3Ecto domain profile. / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, 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
Similarity search - Domain/homology
PHOSPHATE ION / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesHuman coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.504 Å
AuthorsHuo, T. / Liu, X.
CitationJournal: To be Published
Title: Crystal structure and mutational analysis of the endoribonuclease from human coronavirus 229E
Authors: Huo, T. / Liu, X. / Yang, C. / Rao, Z.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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 / _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: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
C: Uridylate-specific endoribonuclease
D: Uridylate-specific endoribonuclease
E: Uridylate-specific endoribonuclease
F: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,50312
Polymers232,9336
Non-polymers5706
Water9,350519
1
A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
F: Uridylate-specific endoribonuclease
hetero molecules

A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
F: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,50312
Polymers232,9336
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area20190 Å2
ΔGint-138 kcal/mol
Surface area81130 Å2
MethodPISA
2
C: Uridylate-specific endoribonuclease
D: Uridylate-specific endoribonuclease
E: Uridylate-specific endoribonuclease
hetero molecules

C: Uridylate-specific endoribonuclease
D: Uridylate-specific endoribonuclease
E: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,50312
Polymers232,9336
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area20250 Å2
ΔGint-132 kcal/mol
Surface area81090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.445, 140.285, 426.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-582-

HOH

21F-562-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 0:136 OR RESSEQ 151:165 OR RESSEQ 171:346 )
211CHAIN B AND (RESSEQ 0:136 OR RESSEQ 151:165 OR RESSEQ 171:346 )
311CHAIN C AND (RESSEQ 0:136 OR RESSEQ 151:165 OR RESSEQ 171:346 )
411CHAIN D AND (RESSEQ 0:136 OR RESSEQ 151:165 OR RESSEQ 171:346 )
511CHAIN E AND (RESSEQ 0:136 OR RESSEQ 151:165 OR RESSEQ 171:346 )
611CHAIN F AND (RESSEQ 0:136 OR RESSEQ 151:165 OR RESSEQ 171:346 )

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Components

#1: Protein
Uridylate-specific endoribonuclease / nsp15 / Nonstructural protein 15


Mass: 38822.234 Da / Num. of mol.: 6 / Mutation: I26A, N52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P0C6X1, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M sodium citrate tribasic dehydrate, pH 8.5, 15% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 89338 / % possible obs: 99.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 5.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.429 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RS4

4rs4


Resolution: 2.504→43.222 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2848 4354 5.03 %RANDOM
Rwork0.241 ---
all0.2431 ---
obs0.2431 86626 96.65 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.612 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-22.0555 Å2-0 Å2-0 Å2
2---8.8805 Å2-0 Å2
3----13.175 Å2
Refinement stepCycle: LAST / Resolution: 2.504→43.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16074 0 30 519 16623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01716432
X-RAY DIFFRACTIONf_angle_d1.51422313
X-RAY DIFFRACTIONf_dihedral_angle_d16.125820
X-RAY DIFFRACTIONf_chiral_restr0.1122566
X-RAY DIFFRACTIONf_plane_restr0.0062816
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2588X-RAY DIFFRACTIONPOSITIONAL
12B2588X-RAY DIFFRACTIONPOSITIONAL0.091
13C2588X-RAY DIFFRACTIONPOSITIONAL0.093
14D2588X-RAY DIFFRACTIONPOSITIONAL0.097
15E2588X-RAY DIFFRACTIONPOSITIONAL0.102
16F2588X-RAY DIFFRACTIONPOSITIONAL0.089
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5044-2.53280.40541400.3279239187
2.5328-2.56260.3191340.2926257892
2.5626-2.59390.34031430.2932252591
2.5939-2.62670.36411430.2861258392
2.6267-2.66120.31491460.294260093
2.6612-2.69770.33311400.2897260193
2.6977-2.73620.38921400.3127265694
2.7362-2.77710.35531260.2998265295
2.7771-2.82050.35681550.2975267496
2.8205-2.86670.3561460.2887269096
2.8667-2.91610.33671540.2923271597
2.9161-2.96910.37261440.278274897
2.9691-3.02620.33381360.2893272597
3.0262-3.0880.33221370.2887278898
3.088-3.15510.3711250.2623280098
3.1551-3.22850.30831410.2705274598
3.2285-3.30920.28731440.2692282499
3.3092-3.39860.28321660.2679275299
3.3986-3.49860.31071510.2636279999
3.4986-3.61140.29261450.2553285099
3.6114-3.74050.2981510.2387280299
3.7405-3.89010.2911430.2301282199
3.8901-4.0670.24581370.2204281899
4.067-4.28130.25131550.2023282599
4.2813-4.54930.21811480.1944287699
4.5493-4.90010.22541600.1965281399
4.9001-5.39230.26181480.19772880100
5.3923-6.17070.23981520.21262893100
6.1707-7.76710.22761610.20132905100
7.7671-43.22890.24011430.2069294396

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