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- PDB-8ufl: Crystal Structure of SARS-Unique Domain (SUD) of Nsp3 from SARS c... -

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Entry
Database: PDB / ID: 8ufl
TitleCrystal Structure of SARS-Unique Domain (SUD) of Nsp3 from SARS coronavirus
ComponentsPapain-like protease nsp3
KeywordsVIRAL PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSBID / Nsp3 / SUD / Center for Structural Biology of Infectious Diseases
Function / homology
Function and homology information


Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / methylation / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / proteolysis / zinc ion binding / membrane / identical protein binding
Similarity search - Function
Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like ...Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Coronavirus 3Ecto domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / 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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsMinasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Kiryukhina, O. / Brunzelle, J.S. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal Structure of SARS-Unique Domain (SUD) of Nsp3 from SARS coronavirus
Authors: Minasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Kiryukhina, O. / Brunzelle, J.S. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Papain-like protease nsp3
B: Papain-like protease nsp3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,47828
Polymers58,9502
Non-polymers1,52826
Water2,252125
1
A: Papain-like protease nsp3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,27415
Polymers29,4751
Non-polymers79914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Papain-like protease nsp3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,20413
Polymers29,4751
Non-polymers72812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.700, 84.862, 93.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 390 - 649 / Label seq-ID: 5 - 264

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Papain-like protease nsp3


Mass: 29475.059 Da / Num. of mol.: 2 / Fragment: SARS-Unique Domain (SUD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Gene: 1a / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: P0C6U8
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 6.4 mg/ml, 0.3M Sodium chloride, 0.01M Tris pH 8.3; Screen: Classics II (F6), 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2020 / Details: Be
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 19083 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 41.1 Å2 / CC1/2: 0.966 / CC star: 0.991 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.052 / Rrim(I) all: 0.123 / Rsym value: 0.112 / Χ2: 1.006 / Net I/σ(I): 15.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 908 / CC1/2: 0.738 / CC star: 0.922 / Rpim(I) all: 0.37 / Rrim(I) all: 0.883 / Rsym value: 0.8 / Χ2: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→29.8 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 25.841 / SU ML: 0.286 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.105 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 928 4.9 %RANDOM
Rwork0.2135 ---
obs0.2162 18109 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.95 Å2 / Biso mean: 48.197 Å2 / Biso min: 7.46 Å2
Baniso -1Baniso -2Baniso -3
1--3.14 Å2-0 Å20 Å2
2--2.93 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 2.51→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 66 126 4236
Biso mean--77.39 35.56 -
Num. residues----523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134191
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174051
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.655677
X-RAY DIFFRACTIONr_angle_other_deg0.3331.5779388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.5815526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.21823.023172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.20215767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.8921518
X-RAY DIFFRACTIONr_chiral_restr0.0590.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0550.024560
X-RAY DIFFRACTIONr_gen_planes_other0.050.02844
Refine LS restraints NCS

Ens-ID: 1 / Number: 7416 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.51→2.57 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.314 70 -
Rwork0.307 1262 -
obs--95.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3584-0.15941.22350.65380.443.81650.0164-0.2994-0.02110.1360.0906-0.02580.0396-0.0469-0.10690.04-0.00470.00790.0848-0.00670.064731.061120.48663.6417
24.35822.7534-0.21263.0536-2.5998.4386-0.2768-0.45850.01160.2504-0.112-0.2847-0.7936-0.00850.38880.16860.0974-0.0690.1064-0.03190.119526.722426.752111.055
31.9451-0.15591.43177.4691-1.83752.5041-0.0432-0.01780.2231-0.27260.27410.43470.2153-0.1679-0.23080.0551-0.0027-0.05720.11530.03650.16655.51125.008725.1348
42.26950.57390.45924.0529-1.11931.37920.01290.00540.00140.3474-0.0959-0.15110.12730.15640.0830.09220.0245-0.01170.06950.00190.063116.5926-0.929834.8285
52.6229-1.3171.95155.4177-1.12935.2383-0.10430.40520.33140.0248-0.1118-0.3009-0.30280.40340.21610.0179-0.0256-0.01150.13890.07680.168513.716111.155623.9214
64.6862.52793.01899.7049-2.28434.29780.16880.1212-0.05420.20310.17540.7710.06160.2968-0.34410.04490.00620.00380.14470.04240.086234.354719.598547.0572
71.62111.38293.01029.45640.760411.7484-0.44210.39510.2182-0.44780.96051.1529-1.18070.2009-0.51840.1784-0.0732-0.07350.19170.15050.313730.217724.491438.9603
810.4545-7.0572-3.998810.6086-0.47576.2053-0.12461.0660.0323-0.2719-0.19040.7426-0.70730.03150.31490.3333-0.2841-0.2760.3850.20440.3437.057627.172937.0358
92.1972-1.9913-0.51723.64961.40372.9090.07450.049-0.58540.2318-0.04610.10960.3763-0.1759-0.02840.24-0.0484-0.04050.19090.05210.297656.69345.486316.7575
102.7605-0.91461.62653.103-0.4332.53780.0415-0.3165-0.32330.3461-0.08290.00130.1395-0.40420.04140.0594-0.05390.00320.1395-0.00180.084152.551916.265223.1296
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 490
2X-RAY DIFFRACTION2A491 - 517
3X-RAY DIFFRACTION3A518 - 546
4X-RAY DIFFRACTION4A547 - 594
5X-RAY DIFFRACTION5A595 - 651
6X-RAY DIFFRACTION6B390 - 463
7X-RAY DIFFRACTION7B464 - 490
8X-RAY DIFFRACTION8B491 - 518
9X-RAY DIFFRACTION9B519 - 587
10X-RAY DIFFRACTION10B588 - 650

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