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- PDB-9rcz: Structure of the N-terminal domain of non-structural protein 1 (N... -

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Basic information

Entry
Database: PDB / ID: 9rcz
TitleStructure of the N-terminal domain of non-structural protein 1 (Nsp1) from SARS-CoV-2
ComponentsORF1a polyprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nsp1
Function / homology
Function and homology information


host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / endonuclease activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification ...host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / endonuclease activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / single-stranded RNA binding / host cell perinuclear region of cytoplasm / regulation of autophagy / viral protein processing / 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 / 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 / Betacoronavirus Nsp3c-M 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 / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLennartz, F. / Weiss, M.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz AssociationFISCOV Innovationspool Germany
CitationJournal: To Be Published
Title: Crystallographic fragment screening against SARS-CoV-2 Nsp1 using the F2X-Entry Screen and a newly developed fragment library.
Authors: Lennartz, F. / Wollenhaupt, J. / Oelker, M. / Froeling, P. / Mueller, U. / Deckers, A. / Grathwol, C. / Braese, S. / Jung, N. / Weiss, M.S.
History
DepositionMay 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ORF1a polyprotein


Theoretical massNumber of molelcules
Total (without water)12,7351
Polymers12,7351
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6440 Å2
Unit cell
Length a, b, c (Å)36.750, 36.750, 142.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-229-

HOH

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Components

#1: Protein ORF1a polyprotein


Mass: 12734.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: ORF1ab / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8B1K137
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 and 25% (w/v) PEG 3350. Reproducibility was improved by seeding.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.45→47.48 Å / Num. obs: 33017 / % possible obs: 99.8 % / Redundancy: 6.78 % / Biso Wilson estimate: 19.64 Å2 / CC1/2: 1 / Net I/σ(I): 20.3
Reflection shellResolution: 1.45→1.54 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5385 / CC1/2: 0.35

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→29.06 Å / SU ML: 0.1772 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.37
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2077 1668 5.05 %
Rwork0.1829 31348 -
obs0.1842 33016 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.4 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 0 88 961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059911
X-RAY DIFFRACTIONf_angle_d0.89211238
X-RAY DIFFRACTIONf_chiral_restr0.0719145
X-RAY DIFFRACTIONf_plane_restr0.0072162
X-RAY DIFFRACTIONf_dihedral_angle_d12.2715344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.30971430.31062634X-RAY DIFFRACTION100
1.49-1.540.27991410.28392629X-RAY DIFFRACTION99.96
1.54-1.60.29811440.27122597X-RAY DIFFRACTION99.67
1.6-1.660.28391360.24832619X-RAY DIFFRACTION100
1.66-1.740.28841380.22242624X-RAY DIFFRACTION99.96
1.74-1.830.26121400.21432614X-RAY DIFFRACTION100
1.83-1.940.18661390.19412577X-RAY DIFFRACTION99.27
1.94-2.090.19071320.18662621X-RAY DIFFRACTION100
2.09-2.30.24371310.17362630X-RAY DIFFRACTION100
2.3-2.630.19221400.18572594X-RAY DIFFRACTION99.45
2.63-3.320.20251400.17212602X-RAY DIFFRACTION99.96
3.32-29.060.17721440.15162607X-RAY DIFFRACTION99.64
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)
11.076896490392.2059534359-0.3166858241964.35107636661-0.9966454502880.588552489797-0.1760667511580.09198899861460.0227854456711-0.509704283874-0.008326360506-0.341194830258-0.381444145987-0.05037697571570.1932838248550.377838931966-0.02004757192330.0153603406580.2252069278720.04395640656790.26601134379.6655214026-14.9830539048-0.557180654336
21.37426803053-0.03323864412540.02641862505732.180127685610.3012547884211.875870030770.0620568230812-0.103425392665-0.1690264222790.2534988206970.1293566493580.00722110465123-0.0595684167197-0.14665740108-0.1178191491210.1964293939920.001091823164240.02225206376220.1328994132590.01015061854880.1695134854573.76582873868-26.48924812714.2939223834
34.14387193306-0.02650029797092.042145716163.119639850512.600935085265.50999766835-0.3759686469110.2094206531490.6738447340690.1736833882840.428739353089-0.353921518155-0.5348075522830.65272712563-0.1179148170570.342709301218-0.0665774911694-0.04596952224710.1532700715340.007681951403050.24727274334813.6751556867-15.19925111512.9776584185
410.00226176870.0175939013591-0.6110042669012.96089033778-0.02717158822442.97154778822-0.3523143302390.05055095049020.3328108156950.08641895344530.173264091368-0.0711448290255-0.2225001123590.2227140392950.09807673185790.188818320242-0.02342690074240.001164643088110.1540782467670.007581021026790.154635939487.21283757011-22.14878505797.04875988073
54.120947617762.16933571202-3.416989188272.29765968645-2.350289571683.09377980773-0.03626340648920.129999873827-0.450481241957-0.1282207674710.5960880680731.1789300290.735164863259-1.25551311149-0.006975480291630.2857289357030.05570690206770.08468993419570.4168684781660.1360492686080.440164025742-7.29144922593-22.081531778111.2627808841
61.583088982540.991470042862-1.206195259843.88344736639-0.8753421951992.520988826370.0557157668023-0.02954005590160.08970153388360.5475971355150.2007550280120.523422516631-0.535565030212-0.291305736697-0.1975173265460.2668779713240.02555297464970.07099436594710.166483314882-0.01314107220320.2572388906990.408060674739-17.428563054414.9624092271
71.697116418470.3802447144693.433833524884.518482484770.146870743447.10345336571-0.8886312250560.7888890710931.17843363813-1.942937774820.430223123092-0.0238203487212-0.2093730597330.2622279528280.3064384393330.808330644286-0.181287773744-0.08363925956980.4999646871350.1339697423730.5146857793972.88475239273-8.91594775686-5.05009583469
82.40007270369-0.589168012816-1.448899970791.397337983350.2656935769162.78217422682-0.128639952044-0.21506101850.4119317443220.0698539455747-0.007305437098040.28642159685-0.519786987217-0.009491844587680.01633011352690.4078089394620.01554305363280.03793580346630.1550003034880.001574139784650.3323880358371.25463047038-8.5660914036813.0304728668
91.492875071930.353193396764-0.2263721731451.511244758580.8847565726281.90806401589-0.07112587734660.09870059395230.1179426087440.08789738868730.08421846557540.0271882859465-0.147074740818-0.0104441947379-0.04260268731590.183132112337-0.0255696813030.01427033210940.1412745313620.007758908651520.1542740598094.54212917255-24.62695430797.44821447751
103.347052200091.1930014193-0.153634951758.24864819834-0.3797191284741.94576665687-0.3264888584420.4392161073840.644869086499-0.7393102650310.404965247679-0.0304710626086-0.513070623419-0.339902185063-0.01856785121040.350855465587-0.01305390411180.02338812170040.2723044146470.06824408499430.2533292514465.57522081856-15.12674891960.0353753894234
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 11 through 20 )11 - 201 - 10
22chain 'B' and (resid 21 through 34 )21 - 3411 - 24
33chain 'B' and (resid 35 through 48 )35 - 4825 - 38
44chain 'B' and (resid 49 through 54 )49 - 5439 - 44
55chain 'B' and (resid 55 through 60 )55 - 6045 - 50
66chain 'B' and (resid 61 through 73 )61 - 7351 - 63
77chain 'B' and (resid 74 through 83 )74 - 8364 - 71
88chain 'B' and (resid 84 through 102 )84 - 10272 - 90
99chain 'B' and (resid 103 through 116 )103 - 11691 - 104
1010chain 'B' and (resid 117 through 125 )117 - 125105 - 113

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