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- PDB-7exm: The N-terminal crystal structure of SARS-CoV-2 NSP2 -

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Entry
Database: PDB / ID: 7exm
TitleThe N-terminal crystal structure of SARS-CoV-2 NSP2
ComponentsNon-structural protein 2
KeywordsVIRAL PROTEIN / zinc finger / nucleic acid binding protein
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / methylation / double membrane vesicle viral factory outer membrane ...viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / 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 / SARS-CoV-2 modulates host translation machinery / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane
Similarity search - Function
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 / Carbamoyl-phosphate synthase subdomain signature 2. ...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 / Carbamoyl-phosphate synthase subdomain signature 2. / 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 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsMa, J. / Chen, Z.
CitationJournal: Virol Sin / Year: 2021
Title: Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2.
Authors: Ma, J. / Chen, Y. / Wu, W. / Chen, Z.
History
DepositionMay 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 2.0Aug 18, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / citation / database_2 / entity / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_auth_evidence / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_conf / struct_conn
Item: _atom_type.scat_Cromer_Mann_c / _citation.title ..._atom_type.scat_Cromer_Mann_c / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_d_res_high / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.d_resolution_high / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _struct_conn.pdbx_dist_value
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Sep 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 2
B: Non-structural protein 2
C: Non-structural protein 2
D: Non-structural protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,97017
Polymers124,0934
Non-polymers87713
Water16,664925
1
A: Non-structural protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2194
Polymers31,0231
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2194
Polymers31,0231
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-structural protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3125
Polymers31,0231
Non-polymers2884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-structural protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2194
Polymers31,0231
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.926, 159.603, 63.552
Angle α, β, γ (deg.)90.000, 91.194, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Non-structural protein 2 / nsp2 / p65 homolog


Mass: 31023.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 925 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 89477 / % possible obs: 93 % / Redundancy: 6 % / CC1/2: 0.999 / Net I/σ(I): 17.9
Reflection shellResolution: 1.96→2.06 Å / Num. unique obs: 4474 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.96→42.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.192 / SU B: 4.43 / SU ML: 0.122 / Average fsc free: 0.9075 / Average fsc work: 0.9167 / Cross valid method: FREE R-VALUE / ESU R: 0.201 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2256 4021 5.08 %
Rwork0.1997 75133 -
all0.201 --
obs-79154 95.909 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.823 Å2
Baniso -1Baniso -2Baniso -3
1-0.057 Å2-0 Å20.053 Å2
2---0.317 Å20 Å2
3---0.258 Å2
Refinement stepCycle: LAST / Resolution: 1.96→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8394 0 0 925 9319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0138657
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177693
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.65811739
X-RAY DIFFRACTIONr_angle_other_deg1.151.57617778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40351106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17623.099426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.805151356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5581539
X-RAY DIFFRACTIONr_chiral_restr0.0450.21135
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021986
X-RAY DIFFRACTIONr_nbd_refined0.1640.21583
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.27364
X-RAY DIFFRACTIONr_nbtor_refined0.1540.24131
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.23842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2657
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0270.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1290.231
X-RAY DIFFRACTIONr_nbd_other0.170.2133
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.241
X-RAY DIFFRACTIONr_mcbond_it1.2623.3664402
X-RAY DIFFRACTIONr_mcbond_other1.2623.3664401
X-RAY DIFFRACTIONr_mcangle_it2.1825.0375493
X-RAY DIFFRACTIONr_mcangle_other2.1825.0375494
X-RAY DIFFRACTIONr_scbond_it1.2833.4464255
X-RAY DIFFRACTIONr_scbond_other1.2833.4464256
X-RAY DIFFRACTIONr_scangle_it2.1525.1156239
X-RAY DIFFRACTIONr_scangle_other2.1525.1156239
X-RAY DIFFRACTIONr_lrange_it4.49539.3739601
X-RAY DIFFRACTIONr_lrange_other4.43439.2559549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.0110.2772030.2574501X-RAY DIFFRACTION76.4754
2.011-2.0660.2842360.2554739X-RAY DIFFRACTION83.5713
2.066-2.1260.3012830.2454851X-RAY DIFFRACTION89.3336
2.126-2.1910.2662990.2315044X-RAY DIFFRACTION95.4448
2.191-2.2630.2542870.2215111X-RAY DIFFRACTION99.889
2.263-2.3420.252680.2234974X-RAY DIFFRACTION99.9238
2.342-2.430.2542610.224833X-RAY DIFFRACTION99.9608
2.43-2.5290.2542830.2164556X-RAY DIFFRACTION100
2.529-2.6410.2332400.2124449X-RAY DIFFRACTION99.9787
2.641-2.770.2342040.2064269X-RAY DIFFRACTION99.933
2.77-2.9190.252480.2033992X-RAY DIFFRACTION99.9764
2.919-3.0950.2252070.1963815X-RAY DIFFRACTION99.9751
3.095-3.3080.2081720.1873612X-RAY DIFFRACTION99.9472
3.308-3.5720.2031640.1873368X-RAY DIFFRACTION99.9434
3.572-3.9110.1911510.1783110X-RAY DIFFRACTION100
3.911-4.3690.1951370.1642789X-RAY DIFFRACTION99.7613
4.369-5.0390.1731460.1672463X-RAY DIFFRACTION99.9617
5.039-6.1560.211270.1982075X-RAY DIFFRACTION99.8187
6.156-8.640.21640.1971667X-RAY DIFFRACTION99.9423
8.64-42.40.251400.209904X-RAY DIFFRACTION95.8376

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