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- PDB-7jlt: Crystal Structure of SARS-CoV-2 NSP7-NSP8 complex. -

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Basic information

Entry
Database: PDB / ID: 7jlt
TitleCrystal Structure of SARS-CoV-2 NSP7-NSP8 complex.
Components
  • Non-structural protein 7
  • Non-structural protein 8
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / 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 toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / SARS-CoV-2 modulates host translation machinery / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase 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 / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / 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 / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) 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 / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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. / 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.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBiswal, M. / Hai, R. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI147057 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Two conserved oligomer interfaces of NSP7 and NSP8 underpin the dynamic assembly of SARS-CoV-2 RdRP.
Authors: Biswal, M. / Diggs, S. / Xu, D. / Khudaverdyan, N. / Lu, J. / Fang, J. / Blaha, G. / Hai, R. / Song, J.
History
DepositionJul 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 23, 2021Group: 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
Revision 1.4Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 7
B: Non-structural protein 8
C: Non-structural protein 7
D: Non-structural protein 8


Theoretical massNumber of molelcules
Total (without water)62,4784
Polymers62,4784
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-83 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.828, 110.566, 42.904
Angle α, β, γ (deg.)90.000, 105.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Non-structural protein 7 / nsp7


Mass: 9335.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD1
#2: Protein Non-structural protein 8 / nsp8


Mass: 21903.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Magnesium Chloride Hexahydrate, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 10428 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.073 / Rrim(I) all: 0.149 / Χ2: 0.631 / Net I/σ(I): 4.8 / Num. measured all: 41299
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.83.90.82710370.6270.4690.9550.44799.8
2.8-2.913.80.64610230.6930.3730.7490.46798.8
2.91-3.043.70.51610490.7150.3070.6030.52698.6
3.04-3.23.90.37910240.8590.2160.4380.52899.6
3.2-3.43.80.25310440.9350.1450.2920.56398.8
3.4-3.6640.1710450.9690.0960.1960.65699.5
3.66-4.033.80.13110340.9760.0760.1520.7198.5
4.03-4.6240.08610320.9880.0480.0990.77299
4.62-5.814.30.07410590.9930.040.0840.79899.9
5.81-504.40.06210810.9950.0340.0710.773100

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Processing

Software
NameVersionClassification
PHENIXdev_3908refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AHM

2ahm


Resolution: 2.7→41.3 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 30.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 1041 10 %
Rwork0.2365 9364 -
obs0.2411 10405 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.05 Å2 / Biso mean: 57.8091 Å2 / Biso min: 27.98 Å2
Refinement stepCycle: final / Resolution: 2.7→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 0 50 2985
Biso mean---50.63 -
Num. residues----393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.850.35551440.29811289143395
2.85-3.020.33931480.28751337148599
3.02-3.260.32891500.28621351150199
3.26-3.580.31521480.23551330147899
3.58-4.10.32211460.23351313145999
4.1-5.170.23341510.20391364151599
5.17-41.30.23631540.223413801534100
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)
14.5779-0.5308-1.2317.98852.82353.103-1.1160.82420.3495-0.79480.11430.3239-0.0585-0.50420.70020.3931-0.25980.21960.51070.06760.372932.71154.595415.9052
22.67950.38982.0590.07480.34292.4421-0.5452-0.1410.8831.40670.59170.1545-0.2826-0.3322-0.02530.7229-0.0558-0.26071.00250.54771.159547.28732.672624.6763
32.0955-2.09812.82975.733-0.25245.8313-0.0894-1.22891.1717-0.06890.1134-0.39-0.3024-0.39-0.46390.4391-0.08780.08740.4531-0.02030.499536.01712.499721.3384
46.9227-4.5161.09275.1281.00843.64740.4423-0.2944-0.8297-0.49920.00840.54670.33-0.4806-0.53680.40740.0741-0.01330.52550.15360.376536.564712.184811.7891
51.6927-1.31130.07631.67770.76411.64770.8398-0.31550.23040.6049-0.67240.28480.3969-0.3987-0.82110.81850.09270.08270.60560.2250.540743.648-4.0974.3681
63.17251.0364-0.90445.4004-0.25344.1320.05711.2701-0.3645-0.61020.2272-0.65480.15480.2543-0.22360.386-0.10740.00180.45750.03560.551437.7838-4.806511.5689
77.48123.1308-1.7085.80930.69965.1820.2760.20830.6822-0.1152-0.46430.49640.1752-0.63370.62120.3073-0.09-0.02950.54710.06750.353142.217512.64865.3378
86.3266-0.1304-0.25256.61662.24530.7631-0.45050.52461.03741.4279-1.2977-1.23990.1336-0.32560.7380.73390.0465-0.19790.46010.13220.477951.270316.51136.1014
93.21711.7894-1.9685.4614-1.48663.05840.27750.27940.29490.334-0.1533-0.2879-0.2550.0094-0.33090.44160.0152-0.00910.39150.09550.482352.259119.6999-1.1451
102.3848-1.05242.27495.14980.87323.4049-0.04660.70570.0914-0.55390.0045-0.0267-0.580.26370.27940.4349-0.08870.07490.49750.04870.538956.94318.5248-3.3912
115.45721.2331-0.84866.05811.65871.33570.28470.2897-0.77060.9412-0.0769-0.06181.1570.45480.04140.51840.034-0.08080.51670.01560.485329.3478-4.053522.7532
124.5054-1.5214-0.67978.59853.43941.2915-0.3624-0.004-0.42760.3380.69850.42280.90770.8666-0.58890.4693-0.00210.07860.45660.12770.377332.8338-12.375223.8579
135.4098-1.41011.87674.4430.32070.7067-0.0510.559-0.30960.8279-0.34330.09140.371-0.9409-0.09470.5187-0.03480.07150.46560.0970.3922.4897-9.506724.8472
149.2831-5.33792.92855.09010.54683.3006-0.9014-0.63050.8148-0.84620.7499-1.7067-0.1075-0.8234-0.7020.7414-0.0646-0.08140.55950.11310.708312.436.928423.2881
153.94241.17610.95764.8481-0.96743.0460.08420.53340.47080.13810.12920.41350.10970.3593-0.35450.3953-0.0488-0.09410.59090.12090.357819.2958-0.348422.2971
164.20641.986-2.26266.0608-0.69522.90780.0888-0.136-0.46780.5095-0.06560.3330.0991-0.2799-0.09880.3736-0.0709-0.0740.50260.04630.36297.7991-18.171334.0363
174.46352.89142.35934.1044-0.58483.43630.55011.40090.50650.58380.8059-1.7912.04481.4474-0.39340.3715-0.03210.10880.45090.16220.61713.8658-21.994931.0084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )A1 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 25 )A21 - 25
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 44 )A26 - 44
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 60 )A45 - 60
5X-RAY DIFFRACTION5chain 'A' and (resid 61 through 79 )A61 - 79
6X-RAY DIFFRACTION6chain 'B' and (resid 77 through 98 )B77 - 98
7X-RAY DIFFRACTION7chain 'B' and (resid 99 through 126 )B99 - 126
8X-RAY DIFFRACTION8chain 'B' and (resid 127 through 132 )B127 - 132
9X-RAY DIFFRACTION9chain 'B' and (resid 133 through 170 )B133 - 170
10X-RAY DIFFRACTION10chain 'B' and (resid 171 through 191 )B171 - 191
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 25 )C1 - 25
12X-RAY DIFFRACTION12chain 'C' and (resid 26 through 44 )C26 - 44
13X-RAY DIFFRACTION13chain 'C' and (resid 45 through 67 )C45 - 67
14X-RAY DIFFRACTION14chain 'C' and (resid 68 through 79 )C68 - 79
15X-RAY DIFFRACTION15chain 'D' and (resid 77 through 111 )D77 - 111
16X-RAY DIFFRACTION16chain 'D' and (resid 112 through 183 )D112 - 183
17X-RAY DIFFRACTION17chain 'D' and (resid 184 through 193 )D184 - 193

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