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- PDB-9p0f: Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 fr... -

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Entry
Database: PDB / ID: 9p0f
TitleCrystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2
ComponentsNon-structural protein 4
KeywordsVIRAL PROTEIN / Center for Structural Biology of Infectious Diseases / CSBID / nsp4 / Structural Genomics
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 / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...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 / 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 / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation / 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 / 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 / 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. / 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
Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Satchell, K.J.F. / 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)75N93022C00035 United States
CitationJournal: To Be Published
Title: Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionJun 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: 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 4
B: Non-structural protein 4
C: Non-structural protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2557
Polymers31,1633
Non-polymers924
Water41423
1
A: Non-structural protein 4
B: Non-structural protein 4
C: Non-structural protein 4
hetero molecules

A: Non-structural protein 4
B: Non-structural protein 4
C: Non-structural protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,51114
Polymers62,3276
Non-polymers1848
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11450 Å2
ΔGint-156 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.691, 125.541, 89.862
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 409 - 500 / Label seq-ID: 1 - 92

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Non-structural protein 4 / nsp4


Mass: 10387.767 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: P0DTC1
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.3 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Protein: 2.8 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3; Screen: ComPAS (H8), 0.2M Sodium acetate, 0.1M MES (pH 6.5), 2.0M Sodium chloride; Cryo: 4.0M Sodium formate.
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 17527 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.9 % / Biso Wilson estimate: 65.2 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.035 / Rrim(I) all: 0.132 / Rsym value: 0.128 / Χ2: 1.017 / Net I/σ(I): 27.1
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 832 / CC1/2: 0.926 / CC star: 0.981 / Rpim(I) all: 0.562 / Χ2: 1.007 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→29.69 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 30.394 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 876 5 %RANDOM
Rwork0.2162 ---
obs0.2184 16598 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 237.55 Å2 / Biso mean: 93.37 Å2 / Biso min: 58.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.87 Å20 Å2-0 Å2
2--0.56 Å2-0 Å2
3----4.44 Å2
Refinement stepCycle: final / Resolution: 2.35→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 4 23 2214
Biso mean--103.3 91.3 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132286
X-RAY DIFFRACTIONr_bond_other_d0.0350.0152085
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.653081
X-RAY DIFFRACTIONr_angle_other_deg2.2911.5744806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.1795279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.36922.973111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.25315378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.486159
X-RAY DIFFRACTIONr_chiral_restr0.0640.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022601
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02537
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A3026
12B3026
21A3048
22C3048
31B3046
32C3046
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.503 75 -
Rwork0.461 1201 -
all-1276 -
obs--100 %
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)
12.17081.93010.53297.5917-7.254411.5975-0.09540.01050.03870.089-0.02890.0675-0.07540.01240.12430.19370.03770.02580.35510.01810.02160.724.97337.653
23.89282.5236-7.21264.9753-5.201625.262-0.45460.2819-0.4735-0.3365-0.1385-0.9531.55942.04220.59310.19410.16290.0750.69350.02150.249213.042-0.18132.128
330.1338-26.6972-8.385434.009310.035316.72130.7884-0.0253-0.9812-0.94480.8103-3.3487-0.88911.3679-1.59861.348-0.16410.29671.7761-0.12211.87318.1594.13322.679
40.83040.30550.83483.32-0.398513.6392-0.06890.2895-0.0109-0.1459-0.1663-0.436-0.46281.29020.23510.1778-0.08630.02560.49530.04550.06147.6279.00827.996
55.71082.19645.49172.18493.198511.04050.0033-0.0001-0.09540.0691-0.1583-0.02070.12350.05350.1550.25950.0054-0.03050.31530.01450.017913.6629.90337.627
613.5817-7.558610.99676.3501-8.620221.6775-0.28910.49050.8904-0.0771-0.1646-0.198-2.3849-0.48640.45380.80940.1498-0.06780.3325-0.01870.11459.46742.54631.082
714.57729.065912.363341.516-11.449320.7247-1.33610.27390.4383-1.44420.97810.0537-0.7529-0.21940.3581.06940.0061-0.20140.66440.19470.59537.88446.32220.692
82.28541.2147-1.251.562-0.572213.1823-0.05890.12430.3139-0.2868-0.09830.1514-0.797-1.09590.15720.25440.117-0.0390.46290.01590.05536.49833.528.008
92.7035-1.956-3.82584.20953.56310.4035-0.1318-0.10060.03530.0056-0.0572-0.09460.0036-0.04410.1890.1985-0.02290.00830.4097-0.0260.0183-14.64728.21837.636
104.82290.71631.357311.658112.313226.5983-0.18540.2753-0.437-0.1324-0.59550.9911.5253-2.03560.78090.3403-0.24710.0290.4542-0.0390.1673-23.79519.19131.339
1132.883812.6540.47498.19649.945328.69720.8092-0.2711-0.76661.1613-0.3014-0.41922.5535-0.4365-0.50780.8649-0.1881-0.07320.6454-0.48870.449-25.10912.29322.676
122.5194-0.8945-0.38540.9729-0.690613.1678-0.2070.2493-0.3734-0.19340.01140.21621.4035-0.32090.19550.4425-0.03380.01060.3023-0.0450.0722-14.65720.26227.605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A409 - 438
2X-RAY DIFFRACTION2A439 - 451
3X-RAY DIFFRACTION3A452 - 461
4X-RAY DIFFRACTION4A462 - 500
5X-RAY DIFFRACTION5B409 - 439
6X-RAY DIFFRACTION6B440 - 453
7X-RAY DIFFRACTION7B454 - 461
8X-RAY DIFFRACTION8B462 - 500
9X-RAY DIFFRACTION9C409 - 439
10X-RAY DIFFRACTION10C440 - 452
11X-RAY DIFFRACTION11C453 - 459
12X-RAY DIFFRACTION12C460 - 500

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