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- PDB-6wji: 2.05 Angstrom Resolution Crystal Structure of C-terminal Dimeriza... -

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Basic information

Entry
Database: PDB / ID: 6wji
Title2.05 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / nucleocapsid phosphoprotein / SARS-CoV-2
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / CD28 dependent PI3K/Akt signaling / MHC class I protein binding ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / CD28 dependent PI3K/Akt signaling / MHC class I protein binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / molecular condensate scaffold activity / protein sequestering activity / VEGFR2 mediated vascular permeability / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / NOD1/2 Signaling Pathway / MHC class I protein complex / Interleukin-1 signaling / viral capsid / Interferon alpha/beta signaling / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / Induction of Cell-Cell Fusion / Attachment and Entry / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / RNA binding / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid / Nucleocapsid protein, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.052 Å
AuthorsMinasov, G. / Shuvalova, L. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Spectr / Year: 2023
Title: Serodominant SARS-CoV-2 Nucleocapsid Peptides Map to Unstructured Protein Regions.
Authors: Vandervaart, J.P. / Inniss, N.L. / Ling-Hu, T. / Minasov, G. / Wiersum, G. / Rosas-Lemus, M. / Shuvalova, L. / Achenbach, C.J. / Hultquist, J.F. / Satchell, K.J.F. / Bachta, K.E.R.
History
DepositionApr 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name ..._entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name
Revision 1.3Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,51215
Polymers81,1936
Non-polymers3199
Water11,205622
1
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1354
Polymers27,0642
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-48 kcal/mol
Surface area11220 Å2
MethodPISA
2
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1715
Polymers27,0642
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-55 kcal/mol
Surface area11350 Å2
MethodPISA
3
E: Nucleoprotein
F: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2066
Polymers27,0642
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-67 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.612, 122.317, 130.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleoprotein / / Nucleocapsid protein / Protein N / N / NC / SARS-CoV-2 nucleocapsid protein


Mass: 13532.190 Da / Num. of mol.: 6
Fragment: C-terminal dimerization domain (UNP residues 257-364)
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) / Variant (production host): magic / References: UniProt: P0DTC9
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20.0 mg/mL protein in 0.1 M sodium chloride, 0.01 M Tris, pH 8.3 against Classics II screen D8 (0.1 M HEPES, pH 7.5, 25% w/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 9, 2020 / Details: Be
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 43336 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 17.1 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.073 / Rrim(I) all: 0.187 / Rsym value: 0.171 / Χ2: 1.019 / Net I/σ(I): 9.7
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1770 / CC1/2: 0.698 / CC star: 0.907 / Rpim(I) all: 0.288 / Rrim(I) all: 0.697 / Rsym value: 0.63 / Χ2: 0.998 / % possible all: 80.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CJR

2cjr


Resolution: 2.052→29.881 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.062 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.181
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2275 2192 5.062 %
Rwork0.1869 --
all0.189 --
obs-43303 96.857 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.645 Å2
Baniso -1Baniso -2Baniso -3
1-1.169 Å20 Å20 Å2
2---0.386 Å20 Å2
3----0.784 Å2
Refinement stepCycle: LAST / Resolution: 2.052→29.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 9 622 5827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135354
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174844
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.6687240
X-RAY DIFFRACTIONr_angle_other_deg0.3941.58711284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4395646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.42922.2300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.60815902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1261536
X-RAY DIFFRACTIONr_chiral_restr0.0720.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.026058
X-RAY DIFFRACTIONr_gen_planes_other0.0480.021186
X-RAY DIFFRACTIONr_nbd_refined0.2080.21148
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.24630
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22642
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.22016
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2559
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.229
X-RAY DIFFRACTIONr_nbd_other0.1910.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.229
X-RAY DIFFRACTIONr_mcbond_it0.7691.1612596
X-RAY DIFFRACTIONr_mcbond_other0.7691.1612595
X-RAY DIFFRACTIONr_mcangle_it1.3221.7333238
X-RAY DIFFRACTIONr_mcangle_other1.3221.7333239
X-RAY DIFFRACTIONr_scbond_it0.961.2972758
X-RAY DIFFRACTIONr_scbond_other0.961.2972758
X-RAY DIFFRACTIONr_scangle_it1.6211.8964002
X-RAY DIFFRACTIONr_scangle_other1.6211.8964002
X-RAY DIFFRACTIONr_lrange_it4.64114.6786521
X-RAY DIFFRACTIONr_lrange_other4.39814.1496380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.052-2.1050.2851290.22925450.23132260.8740.88682.8890.197
2.105-2.1630.2431640.22329500.22431620.8910.89998.4820.188
2.163-2.2250.2311560.20928360.2130450.9140.90898.25940.179
2.225-2.2930.2921460.23728250.23930440.8850.90497.60180.21
2.293-2.3680.2551440.19227100.19528610.9150.9399.75530.162
2.368-2.450.2581590.19126150.19528370.9110.93397.77930.161
2.45-2.5420.2461360.18825680.19127090.9290.93699.81540.16
2.542-2.6450.2541290.1824280.18425990.9140.94498.3840.156
2.645-2.7620.2321290.17623760.17925450.9380.94598.42830.159
2.762-2.8950.2021230.19122630.19224040.9470.94299.25120.175
2.895-3.050.2351060.18621510.18822840.9210.94498.81790.172
3.05-3.2330.225890.19820590.19921880.9280.93998.17180.187
3.233-3.4540.2421080.19819110.220590.9320.94498.05730.191
3.454-3.7260.247850.18518120.18819360.9250.9597.98550.183
3.726-4.0760.176740.15216690.15317860.9670.97197.59240.152
4.076-4.5460.167930.14714900.14816310.9720.97497.0570.152
4.546-5.2290.182970.15712990.15814560.9680.97695.87910.161
5.229-6.3560.228540.17711440.1812550.9590.96695.45820.174
6.356-8.7920.236420.1819110.18410140.940.95493.98420.179
8.792-29.8810.202290.1845490.1856350.9610.96891.02360.202
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)
111.72642.45356.19276.84160.13793.4834-0.1953-0.07510.0807-0.16260.1163-0.1403-0.092-0.06650.07910.08480.0109-0.03650.0393-0.0130.0614-0.29038.2626-21.6174
22.51770.1785-2.31573.1346-2.68867.6420.0102-0.06990.20920.0834-0.1134-0.1054-0.40640.09830.10320.03580.0068-0.02940.0171-0.02250.06346.35619.8427-11.8059
32.26380.61590.32780.90060.34820.6971-0.07650.01620.0576-0.04870.0898-0.08580.01270.1163-0.01330.02580.0089-0.00260.0342-0.00430.02318.09010.0499-17.026
40.90710.18180.09150.2249-0.18220.2251-0.0114-0.0897-0.024-0.0333-0.0249-0.0460.03660.00710.03630.02320.01540.01040.0425-0.01940.04279.3449-4.6863-11.5757
59.26823.12063.57991.63171.82085.8233-0.13280.433-0.1981-0.09010.1062-0.3002-0.14210.38920.02660.05580.0030.00740.10240.00180.14517.737-11.6169-27.0979
62.858-0.6843-0.66983.40890.15095.00090.04090.1566-0.152-0.1079-0.02760.13940.2837-0.17-0.01330.0498-0.0177-0.00020.0202-0.01960.0429-5.2559-14.7106-28.9637
71.95630.07192.12250.01820.18923.23110.0934-0.00220.0289-0.0103-0.0025-0.00980.0934-0.0599-0.09090.08930.0025-0.01190.0707-0.00840.10361.1545-1.6159-19.6155
81.4468-0.41710.73431.3317-0.57261.2903-0.02350.0365-0.00650.09460.00530.0743-0.0485-0.09580.01820.0376-0.01090.02130.0356-0.0110.0156-8.5867-6.0713-19.8922
97.2198-2.63584.86466.5865-2.24913.3441-0.3448-0.2570.28810.31920.1671-0.247-0.2684-0.16180.17770.0558-0.0132-0.01920.0348-0.01170.0712-0.477-6.2964-51.6339
102.6272-0.6056-1.57944.77244.44246.4912-0.02150.13530.3253-0.0655-0.0136-0.0594-0.2187-0.1370.03510.03980.0036-0.01690.03750.02310.0729-5.7685-5.0337-61.7862
112.1204-0.7980.04260.9567-0.00890.8413-0.023-0.0505-0.0152-0.00560.03120.0976-0.0644-0.0589-0.00830.0423-0.01510.00340.0302-0.00580.0163-8.401-14.5419-56.0822
121.0941-0.4564-0.20830.4013-0.16040.3567-0.0285-0.0212-0.0576-0.0294-0.03290.00030.07450.02480.06140.0622-0.01490.01870.0538-0.00890.0294-9.3686-19.2144-61.6937
135.1122-1.75374.02771.6039-0.81837.772-0.0753-0.3133-0.14610.15010.01860.05810.0775-0.22010.05670.0559-0.02540.02430.04630.01360.0401-3.72-28.7379-43.6549
141.1663-0.4822-1.01073.08153.34287.8787-0.0451-0.0793-0.16020.08410.006-0.04210.1850.14090.03910.02480.01180.00960.01080.01420.02776.992-29.7494-46.8418
151.36920.21890.62280.45290.51781.1516-0.02440.0350.00560.0511-0.0155-0.0260.00490.05520.03980.04780.01360.01120.02340.02240.0222-1.578-18.8407-55.985
161.45391.03240.038211.94591.8010.6627-0.032-0.09650.00640.04320.0787-0.26670.01780.1447-0.04670.01920.0021-0.0040.0501-0.00380.008115.4779-19.7232-49.1742
176.30265.9279-3.75766.1938-4.90285.3403-0.07730.039-0.1249-0.00790.0103-0.1265-0.03610.06690.0670.05770.0299-0.01860.06470.0190.0343-4.383311.167-38.1668
186.2062-1.70032.1115.524-1.67363.9466-0.0449-0.60930.20240.3928-0.1074-0.0429-0.5126-0.2090.15230.12360.0070.00350.0831-0.01740.0177-12.374920.246-34.9388
191.39330.4469-0.52171.0754-1.05142.05120.007-0.0173-0.0690.03260.04920.059-0.0398-0.127-0.05620.03210.0186-0.0010.02970.01410.027-12.321115.115-45.9375
203.24511.57530.50682.15550.5291.7998-0.04450.0157-0.0295-0.0490.05770.0849-0.0677-0.2559-0.01320.08140.05210.010.07520.03030.0633-17.974119.1099-47.8171
217.77491.6614-2.73181.8637-1.8683.8963-0.11740.1133-0.151-0.2770.07340.04590.18990.03820.04410.047-0.0097-0.01590.0352-0.01230.0198-4.694814.9737-64.1329
224.0727-2.25552.3396.67190.07121.967-0.1495-0.19390.1196-0.20870.04350.3818-0.2317-0.20820.1060.0778-0.0101-0.01250.07880.01480.0613-4.475428.8114-61.6919
231.9468-0.0638-0.25790.6036-0.04371.0239-0.04870.00960.0030.05820.0442-0.0802-0.01250.04680.00450.04930.0061-0.0090.02340.01470.0359-4.597120.4746-52.8708
243.0749-2.02113.86281.9041-4.21969.8101-0.1881-0.12940.1790.09830.034-0.1114-0.17770.01380.15410.0456-0.0065-0.00890.0268-0.03190.07198.024728.418-52.1573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA257 - 263
2X-RAY DIFFRACTION2ALLA264 - 281
3X-RAY DIFFRACTION3ALLA282 - 323
4X-RAY DIFFRACTION4ALLA324 - 364
5X-RAY DIFFRACTION5ALLB257 - 264
6X-RAY DIFFRACTION6ALLB265 - 300
7X-RAY DIFFRACTION7ALLB301 - 323
8X-RAY DIFFRACTION8ALLB324 - 364
9X-RAY DIFFRACTION9ALLC257 - 264
10X-RAY DIFFRACTION10ALLC265 - 282
11X-RAY DIFFRACTION11ALLC283 - 323
12X-RAY DIFFRACTION12ALLC324 - 364
13X-RAY DIFFRACTION13ALLD257 - 274
14X-RAY DIFFRACTION14ALLD275 - 299
15X-RAY DIFFRACTION15ALLD300 - 340
16X-RAY DIFFRACTION16ALLD341 - 364
17X-RAY DIFFRACTION17ALLE257 - 269
18X-RAY DIFFRACTION18ALLE270 - 281
19X-RAY DIFFRACTION19ALLE282 - 323
20X-RAY DIFFRACTION20ALLE324 - 364
21X-RAY DIFFRACTION21ALLF257 - 274
22X-RAY DIFFRACTION22ALLF275 - 288
23X-RAY DIFFRACTION23ALLF289 - 340
24X-RAY DIFFRACTION24ALLF341 - 364

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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