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- PDB-12hg: Crystal Structure of the N-terminal Domain of the Nsp8 from SARS-CoV2 -

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Basic information

Entry
Database: PDB / ID: 12hg
TitleCrystal Structure of the N-terminal Domain of the Nsp8 from SARS-CoV2
ComponentsNon-structural protein 8
KeywordsVIRAL PROTEIN / Nsp8 / Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / Biopreparedness Research Virtual Environment (BRaVE)
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / endonuclease activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / methylation / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome ...viral genome replication / methyltransferase activity / endonuclease activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / methylation / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / G-quadruplex RNA binding / symbiont-mediated suppression of host ISG15-protein conjugation / mRNA guanylyltransferase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell Golgi apparatus / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type deubiquitinase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / 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 / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding
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 / Coronavirus Nsp6 transmembrane protein 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 / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / Betacoronavirus single-stranded poly(A) binding domain / 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 / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus replicase NSP2, N-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 Nsp3 ectodomain (3Ecto) 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 replicase NSP7 / 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
Similarity search - Domain/homology
FORMIC ACID / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKim, Y. / Tesar, C. / Endres, M. / Joachimiak, A. / 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) United States
CitationJournal: To Be Published
Title: Crystal Structure of the N-terminal Domain of the Nsp8 from SARS-CoV2
Authors: Kim, Y. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionApr 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 8
B: Non-structural protein 8
C: Non-structural protein 8
D: Non-structural protein 8
E: Non-structural protein 8
F: Non-structural protein 8
G: Non-structural protein 8
H: Non-structural protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,83616
Polymers69,4228
Non-polymers4148
Water59433
1
A: Non-structural protein 8
B: Non-structural protein 8
hetero molecules

H: Non-structural protein 8
hetero molecules

C: Non-structural protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9418
Polymers34,7114
Non-polymers2304
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area5120 Å2
ΔGint-43 kcal/mol
Surface area17390 Å2
MethodPISA
2
E: Non-structural protein 8
F: Non-structural protein 8
hetero molecules

D: Non-structural protein 8
hetero molecules

G: Non-structural protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8958
Polymers34,7114
Non-polymers1844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area5240 Å2
ΔGint-44 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.879, 56.272, 81.043
Angle α, β, γ (deg.)90.000, 92.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Non-structural protein 8 / nsp8


Mass: 8677.761 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: P0DTC1
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid, pH 4.0, 2.5 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 30760 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 59.63 Å2 / CC1/2: 0.955 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.075 / Rrim(I) all: 0.192 / Net I/σ(I): 14.98
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2 / Num. unique obs: 1501 / CC1/2: 0.744 / Rpim(I) all: 0.303 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→40.59 Å / SU ML: 0.3511 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 29.7943
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2553 1423 4.66 %
Rwork0.223 29081 -
obs0.2244 30504 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.44 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4356 0 27 33 4416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274419
X-RAY DIFFRACTIONf_angle_d0.45965893
X-RAY DIFFRACTIONf_chiral_restr0.028649
X-RAY DIFFRACTIONf_plane_restr0.003768
X-RAY DIFFRACTIONf_dihedral_angle_d14.3481677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.34931800.30952806X-RAY DIFFRACTION99.4
2.43-2.530.2971380.27212922X-RAY DIFFRACTION99.87
2.53-2.650.29721420.26352852X-RAY DIFFRACTION99.83
2.65-2.790.30551550.26032897X-RAY DIFFRACTION99.61
2.79-2.960.31221370.26382903X-RAY DIFFRACTION99.48
2.96-3.190.27661450.2772893X-RAY DIFFRACTION99.9
3.19-3.510.29461190.2492949X-RAY DIFFRACTION99.71
3.51-4.020.28071350.20832895X-RAY DIFFRACTION99.28
4.02-5.060.23471240.19932972X-RAY DIFFRACTION99.84
5.06-40.590.21431480.19872992X-RAY DIFFRACTION99.18
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)
13.07125254648-1.6764877048-1.5197167322.95668763320.19229491724-0.699828286617-0.010712213030.4586160779141.572567078360.4142908823350.00543077055378-1.51522226249-0.368724782276-0.35405144750.0676342981480.847649375090.256602097151-0.05588248251420.818480671058-0.002750212290131.07014893637-19.567784747-2.3610229292916.0308650154
29.593426853314.275387239970.2140574113622.587481373120.1056377734995.025183497641.956931775750.8097700819-1.19349876969-0.840486487022-0.6127724430810.6744321691232.63761750920.385298001576-0.3452455332861.606492354780.670738554222-0.3121183461691.05702980017-0.1894417689440.98558768634122.64227100391.514510609822.5433737931
35.137938982640.3543105739450.9141097113084.82798913754-0.4497180795524.66767559290.624940842807-0.304637481665-1.440414960590.626026240613-0.1602452568840.6100432700711.729864269450.395075213369-0.6462340972671.048549204190.142134172881-0.1104382293160.6092468158670.124572709361.105252511527.070058607396.3949868791420.8464383728
49.29036011003-3.258319145171.338544843941.96785399948-1.37149908536-0.6740922411041.328647374992.16156838791-0.523393163015-0.800308049562-1.094296377140.3147907743590.4718017283920.466459751176-0.2580639449520.9426633682440.374519599428-0.1378634352391.04993443417-0.1714406204880.68095006204325.32295566542.0902489453914.6198272558
53.22831484928-0.05397530959630.6146381841193.02385929294-0.2219608178835.338134586640.161179004116-0.990093377512-0.3276308543690.8462021674240.06998672552130.356083776953-0.8024790967660.425349164658-0.227622930890.823582456663-0.0280980974850.03323338604840.5111476972050.07931652078330.43332173324324.858542989719.374345433340.0399608305
64.97550225097-4.19115439982-2.127209181416.008240789350.9165772404820.8720775606050.9920912927260.695140323057-0.471289009216-1.07555125958-0.8521709305220.281552960115-0.0137136985928-0.0637646721167-0.1128009366970.7387928794370.247048652709-0.07493050409710.54187871992-0.06721827784860.49342953850126.854399622810.272300899829.645772407
74.03121606597-0.2067776353220.24328615783.682160800252.42675534385.596834701550.6730920069110.866839683853-0.0436233564893-0.8552012261140.18926257535-0.1336257279171.855954947820.925659716677-0.5955725075091.41588794645-0.0174945124459-0.1316205225190.5397555114170.09258683072510.58666140180725.8662123518.9725542922239.4430570287
82.020874233371.179584205911.403750948926.246205248291.722603742132.771887984930.02089569756730.003627425053110.206717543245-0.156740963164-0.2464633083280.5536675387550.274453955675-0.3358467669550.148540468480.646433366415-0.0804213079721-0.03091769864890.4843942855730.01159977078840.38271180727324.883658051417.471883324449.2792938311
92.670281234080.9718385237820.5332342021723.02226281942-0.9613035384730.8662472107151.14779587345-2.84969110907-3.05040650163-1.04377782241-0.383542046766-0.5221923851452.690942468980.03744763172770.364903370411.3510163213-0.230662915812-0.03160637690771.177311400260.6767808972011.2391218636515.6841087607-13.422235529461.6975153596
10-1.06592940951-0.32506642159-2.233153802180.7664658299090.1069216625521.77252904332-0.0846447254564-0.443490006322-0.15777684569-1.757830754940.1287744803970.3352141263861.89860891546-0.09980357507130.1207168046331.28703860881-0.0523632268182-0.03859314544210.7843311083030.2575291660420.67931108489821.5792626925-11.502111664759.2377058007
117.81936164278-0.01041505050070.1255158800024.11862581853.663701532933.29479775342-0.969365015540.4079537063081.843626701711.03508347969-0.938175699469-1.08687300855-1.75723354031.10623262183-0.2733301828821.18637613075-0.0731004443567-0.1997501492771.177252583640.5489266492261.1182387384317.1530266301-15.116691148916.7675646147
12-1.06131749853-1.056365885820.09388862082162.69542560939-2.457176927275.56870697478-0.3437697990060.2701636691390.3360241490070.89215524796-0.459132063284-0.376572513729-0.9921681492020.6712241228151.012489612720.692458750532-0.175290773074-0.1460916021640.9089229327710.3267595895250.74193253108823.0745460788-17.073958122819.3715476101
134.33091340212-0.05104372260531.074465404352.123293233030.2816300866173.95011330167-0.2986780726460.137176914362-0.649520138377-0.1929967213860.2021197114590.7860776888340.379444138387-0.702419509279-0.1317137691530.4763546353340.1104899572070.007554700000810.6007927341190.02504174797630.890181866012-0.344895999631-33.122702273313.7033803159
141.095997692632.21757016397-2.655758882176.74076303368-3.73750958444.321289837730.0040243672143-0.206682830095-0.4183547135850.368515723242-0.83756670557-1.09500650606-0.1760594632330.724033333760.7616515986990.433401354987-0.0302549608689-0.08591743605150.5407367697630.222493693740.60388437299710.2763452561-23.986029266212.109939498
154.74124128887-0.234649826105-4.759504173662.169693672221.085934716075.14894998413-0.4988898751550.1567307679920.265597830192-0.9291256520021.75721573345-0.9518494975761.30007292098-0.008909771402390.2519677522281.28179111683-0.1248630873550.2281858265811.15049667015-0.06085980985851.23725065181-5.03983803865-32.82813766513.24363429166
164.927981747230.8489920281932.797738068146.795451571012.383234345373.675754944110.06211725190650.03405216516080.7396966300280.956585011004-0.118745746154-0.7025544195190.07955736059140.287346107246-0.2553331451580.4632286052970.0222618807225-0.1321499630470.470234942827-0.03275897850290.704660951807-5.47288046604-27.22976361213.9735095091
176.47025240547-4.99973676919-0.6066954140683.848997377110.5034131101740.240010378129-0.36840417435-0.9482997423133.070393810281.020379420220.931950336445-1.73689647825-1.79889413658-1.61304647712-0.1247204161471.639898991640.6414984985020.03191135195091.20511479609-0.1440467090071.3178998304-22.6896187273-0.49161959905522.2979147697
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 10 through 76 )HO10 - 769 - 75
22chain 'A' and (resid 0 through 9 )AA0 - 91 - 10
33chain 'A' and (resid 10 through 31 )AA10 - 3111 - 32
44chain 'A' and (resid 32 through 75 )AA32 - 7533 - 76
55chain 'B' and (resid 4 through 31 )BB4 - 311 - 28
66chain 'B' and (resid 32 through 69 )BB32 - 6929 - 66
77chain 'C' and (resid 4 through 31 )CE4 - 311 - 28
88chain 'C' and (resid 32 through 68 )CE32 - 6829 - 65
99chain 'D' and (resid 2 through 9 )DF2 - 91 - 8
1010chain 'D' and (resid 10 through 76 )DF10 - 769 - 75
1111chain 'E' and (resid -1 through 9 )EI-1 - 91 - 11
1212chain 'E' and (resid 10 through 76 )EI10 - 7612 - 78
1313chain 'F' and (resid 4 through 31 )FJ4 - 311 - 28
1414chain 'F' and (resid 32 through 69 )FJ32 - 6929 - 66
1515chain 'G' and (resid 4 through 9 )GM4 - 91 - 6
1616chain 'G' and (resid 10 through 68 )GM10 - 687 - 65
1717chain 'H' and (resid 2 through 9 )HO2 - 91 - 8

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