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- PDB-2w2g: Human SARS coronavirus unique domain -

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Basic information

Entry
Database: PDB / ID: 2w2g
TitleHuman SARS coronavirus unique domain
ComponentsNON-STRUCTURAL PROTEIN 3
KeywordsRNA BINDING PROTEIN / THIOL PROTEASE / RNA REPLICATION / VIRAL REPLICASE / RNA-BINDING / ZINC-FINGER / RIBOSOMAL FRAMESHIFTING / HYDROLASE / RNA-BINDING PROTEIN
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 / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / endonuclease activity / host cell Golgi apparatus / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase activity / proteolysis / zinc ion binding / identical protein binding / membrane
Similarity search - Function
Nsp3, SUD-N subdomain / Nsp3, SUD-M subdomain / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Leucine Aminopeptidase, subunit E; domain 1 / 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 ...Nsp3, SUD-N subdomain / Nsp3, SUD-M subdomain / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Leucine Aminopeptidase, subunit E; domain 1 / 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 / 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 / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) 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, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto 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. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, 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 / Papain-like protease, thumb domain 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 replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Replicase polyprotein 1a
Similarity search - Component
Biological speciesSARS CORONAVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsTan, J. / Vonrhein, C. / Smart, O.S. / Bricogne, G. / Bollati, M. / Kusov, Y. / Hansen, G. / Mesters, J.R. / Schmidt, C.L. / Hilgenfeld, R.
CitationJournal: Plos Pathog. / Year: 2009
Title: The Sars-Unique Domain (Sud) of Sars Coronavirus Contains Two Macrodomains that Bind G-Quadruplexes.
Authors: Tan, J. / Vonrhein, C. / Smart, O.S. / Bricogne, G. / Bollati, M. / Kusov, Y. / Hansen, G. / Mesters, J.R. / Schmidt, C.L. / Hilgenfeld, R.
History
DepositionOct 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NON-STRUCTURAL PROTEIN 3
B: NON-STRUCTURAL PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6544
Polymers58,4622
Non-polymers1922
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-39.7 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.360, 68.550, 94.210
Angle α, β, γ (deg.)90.00, 99.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.82507, 0.26201, -0.50061), (0.25107, -0.96372, -0.0906), (-0.50618, -0.05094, -0.86092)
Vector: 4.14445, 67.89175, 49.67422)

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Components

#1: Protein NON-STRUCTURAL PROTEIN 3 / PAPAIN-LIKE PROTEINASE / REPLICASE POLYPROTEIN 1A / ORF1A POLYPROTEIN


Mass: 29230.818 Da / Num. of mol.: 2 / Fragment: SARS UNIQUE DOMAIN, RESIDUES 1207-1470 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS CORONAVIRUS / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P0C6U8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 1446 TO ARG ENGINEERED RESIDUE IN CHAIN B, LYS 1446 TO ARG
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 6.5
Details: 20% PEGMME 5000,0.2M AMMONIUM SULFATE, 0.1M MES PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.25485
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 2, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25485 Å / Relative weight: 1
ReflectionResolution: 2.22→28.25 Å / Num. obs: 26598 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 48.34 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.9
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2 / % possible all: 61

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Processing

Software
NameVersionClassification
BUSTER-TNT2.7.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JZE

2jze


Resolution: 2.22→27.81 Å / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1364 5.13 %RANDOM
Rwork0.211 ---
obs0.214 26581 91.2 %-
Displacement parametersBiso mean: 60.39 Å2
Baniso -1Baniso -2Baniso -3
1--25.48014 Å20 Å22.61904 Å2
2--11.30787 Å20 Å2
3---14.17227 Å2
Refinement stepCycle: LAST / Resolution: 2.22→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3963 0 10 178 4151
LS refinement shellResolution: 2.22→2.31 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2625 88 5.17 %
Rwork0.2397 1613 -
all0.2409 1701 -
obs--91.25 %

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