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- PDB-6wkp: Crystal structure of RNA-binding domain of nucleocapsid phosphopr... -

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Basic information

Entry
Database: PDB / ID: 6wkp
TitleCrystal structure of RNA-binding domain of nucleocapsid phosphoprotein from SARS CoV-2, monoclinic crystal form
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / RNA BINDING PROTEIN / CSGID / COVID-19 / SARS COV-2 / RNA-binding domain / nucleocapsid protein / nucleoprotein / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling ...: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / RNA stem-loop binding / Interleukin-1 signaling / Interferon alpha/beta signaling / viral capsid / PIP3 activates AKT signaling / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / 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 protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile.
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsChang, C. / Michalska, K. / Jedrzejczak, R. / Maltseva, N. / Endres, M. / Godzik, A. / Kim, Y. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Iscience / Year: 2024
Title: Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies.
Authors: Kim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Ma, H. / Dugan, H.L. / Stamper, C.T. / Chang, C. / Li, L. / Changrob, S. / Zheng, N.Y. / Huang, M. / Ramanathan, A. / ...Authors: Kim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Ma, H. / Dugan, H.L. / Stamper, C.T. / Chang, C. / Li, L. / Changrob, S. / Zheng, N.Y. / Huang, M. / Ramanathan, A. / Wilson, P. / Michalska, K. / Joachimiak, A.
History
DepositionApr 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 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: Derived calculations / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / pdbx_struct_conn_angle / struct_conn
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Oct 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
Revision 1.4Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,06310
Polymers56,4114
Non-polymers6526
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-152 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.388, 71.848, 106.961
Angle α, β, γ (deg.)90.000, 92.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14102.780 Da / Num. of mol.: 4 / Fragment: RNA-binding domain (UNP residues 47-173)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, 30% PEG4000

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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: Apr 7, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 14108 / % possible obs: 97.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.046 / Rrim(I) all: 0.102 / Χ2: 0.989 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.80.5976650.8790.3260.6840.67690
2.75-2.83.80.5256510.8630.2870.6010.72491.3
2.8-2.8540.5556920.8560.3010.6340.8495.1
2.85-2.9140.4776730.8860.2610.5460.71196.8
2.91-2.974.10.4116990.90.220.4690.73897.9
2.97-3.044.10.3367200.9410.1790.3820.74698.4
3.04-3.123.90.3356730.9440.1780.3811.2795.2
3.12-3.24.40.2986960.9710.1540.3371.06598.3
3.2-3.34.80.247390.9670.120.2691.06199.7
3.3-3.44.80.1777200.9850.0880.1980.80499.3
3.4-3.524.90.1456990.9840.0720.1630.88299.7
3.52-3.664.90.1287160.9890.0630.1430.98599.2
3.66-3.834.90.0987280.9880.0480.111.06499.3
3.83-4.034.50.0796950.9920.040.0891.21498.2
4.03-4.294.70.0757220.9880.0360.0841.20997.4
4.29-4.625.20.0666970.9930.0320.0741.13999.3
4.62-5.0850.0557240.9930.0270.0611.05399.5
5.08-5.814.80.0517320.9940.0240.0561.13698.9
5.81-7.324.70.0477210.9950.0230.0531.04698.5
7.32-504.70.0437460.9940.0210.0481.12198.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SBC-Collectdata collection
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6VYO

6vyo


Resolution: 2.67→35.61 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.52
RfactorNum. reflection% reflection
Rfree0.2477 656 5.4 %
Rwork0.1973 --
obs0.2001 12158 83.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.84 Å2 / Biso mean: 47.6316 Å2 / Biso min: 0.58 Å2
Refinement stepCycle: final / Resolution: 2.67→35.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 28 37 3562
Biso mean--62.3 28.33 -
Num. residues----455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.870.358960.25191487158355
2.87-3.160.31591340.24521960209473
3.16-3.620.27741240.21112581270594
3.62-4.560.2231590.17682679283899
4.56-35.610.20791430.18342795293899
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)
10.06490.02220.00730.0683-0.01230.0067-0.15490.07250.0116-0.06070.0595-0.0120.055-0.0398-0.05990.7631-0.0361-0.02940.2598-0.06720.10376.4776-9.887732.4463
20.0508-0.0047-0.03040.00110.00410.0199-0.02680.0010.00170.0077-0.0216-0.0311-0.0311-0.0073-0.03030.4955-0.0582-0.25510.2567-0.07990.37736.17213.568741.5063
30.0160.00660.01590.0118-0.00050.0126-0.0501-0.0286-0.0586-0.0418-0.03920.1269-0.0364-0.0549-0.00160.4121-0.19050.10350.4506-0.15810.382-2.3144-8.029434.2359
40.04650.0219-0.01730.0232-0.02340.02390.0227-0.0008-0.02620.013-0.02870.00140.00480.00360.01840.7968-0.34170.38120.4228-0.09960.3118-1.3204-13.831439.6711
50.0066-0.00090.00570.0030.00280.0053-0.08770.0258-0.05290.0089-0.16880.11630.0189-0.044400.36220.0822-0.03980.4773-0.13170.3641-0.6324-0.030342.8785
60.00250.00380.0080.00480.0050.0075-0.1931-0.06840.0395-0.0963-0.08420.01590.08530.12780.00010.9515-0.02980.07820.55890.08390.350712.968-7.682430.7498
70.03-0.0334-0.02470.0340.03060.02980.00560.0183-0.01210.0047-0.11690.04580.0429-0.088-0.0911-0.04560.06340.09760.27530.05340.117710.93636.84567.0951
80.13870.02210.03760.0020.00550.0099-0.02140.04920.0437-0.027-0.0374-0.05760.00640.0359-0.0375-0.06930.0241-0.08070.15110.00140.478721.5962-0.36217.9617
90.0503-0.0123-0.02130.0175-0.00010.02090.0555-0.02-0.00930.03690.0736-0.03390.03930.06710.12520.15460.0155-0.05730.15680.04020.124613.0274-4.559612.4718
100.0004-0.001800.0058-0.00170.0018-0.00480.00920.0197-0.01750.0185-0.00210.0031-0.0137-00.41120.2059-0.090.6466-0.09170.49135.995914.1267-1.472
110.119-0.0207-0.04640.0040.00340.0219-0.07170.2894-0.0085-0.1255-0.08790.0857-0.0548-0.0532-0.17690.0484-0.0158-0.08050.2172-0.10170.273410.2735-3.56063.4742
120.00510.00690.00140.0140.0070.0047-0.06-0.0047-0.04140.045-0.001-0.04950.05930.0459-0.05040.04680.0288-0.03150.0989-0.01630.088518.5584-7.41817.9949
130.22520.13170.05190.13930.06490.07320.0492-0.05370.11890.0473-0.2699-0.04290.1319-0.1741-0.3399-0.2463-0.25930.03010.0991-0.02530.295711.13110.274613.5364
140.1944-0.07530.26560.0673-0.1190.3876-0.0922-0.0849-0.14120.0528-0.0751-0.1095-0.2626-0.1905-0.10140.27630.07660.14160.1127-0.06220.34525.536933.871821.3023
150.00180.0016-0.0010.02730.0350.0493-0.0095-0.0482-0.05960.0436-0.0335-0.0835-0.00230.0355-0.06320.20810.37880.12430.27370.01290.18529.304825.770315.1718
160.0048-0.0082-0.01990.00840.02750.0544-0.0004-0.08860.0806-0.0651-0.06750.05550.0008-0.0787-0.01740.18930.1960.05620.2295-0.20680.0051-4.564133.83223.2003
170.1557-0.10370.08580.0986-0.0190.1501-0.05420.017-0.1557-0.0544-0.13690.0255-0.1477-0.0496-0.22710.07870.4271-0.0697-0.05810.08410.10435.726629.8377.8043
180.0030.00520.00330.00580.00060.0029-0.11690.0291-0.08010.02480.0724-0.10940.0044-0.06110.00010.36320.00360.12310.335-0.0350.54911.05417.528719.5109
190.0376-0.00270.00760.0388-0.01140.00460.0602-0.0312-0.02180.0356-0.0054-0.0543-0.00650.03450.01520.4174-0.26210.02040.2902-0.16540.211912.249633.792526.1153
200.0014-0.0045-0.00870.09420.12780.1724-0.0182-0.0393-0.00220.0702-0.0420.02930.06240.0099-0.0280.16580.0302-0.09440.418-0.05060.2827-3.551217.726339.5765
210.0063-0.0062-0.00540.0761-0.02550.01960.0437-0.0277-0.0616-0.00170.02150.0032-0.04020.06810.05810.5509-0.041-0.24580.44680.12940.30881.913117.781153.4567
220.01690.0059-0.00340.09980.08640.07580.1188-0.0696-0.02730.01330.1439-0.0795-0.10810.03410.04520.25620.03130.07180.18710.03850.18741.069826.836941.1739
230.00420.0035-0.00110.0016-0.00090.001-0.0074-0.0009-0.0005-0.03030.01570.01070.01190.011800.6224-0.13520.07170.43380.17040.3536-9.4118.267748.9549
240.07470.0001-0.01380.03540.00720.00510.1023-0.009-0.01070.02630.00870.1013-0.0107-0.04420.02170.35520.06770.00010.23750.07680.1484-6.736223.309642.5409
250.02450.0203-0.06760.057-0.0030.2430.08610.04080.07160.07230.00190.00270.0694-0.02560.0060.83340.14760.13360.2760.00570.4451-8.934429.112651.2728
26-0.00010.00010.00370.0063-0.00160.010.025-0.0451-0.08270.00330.05750.0311-0.02920.0183-0.00010.5326-0.0239-0.02510.21460.01570.22591.010330.716747.0634
270.00280.0012-0.00480.0041-0.0010.00370.13910.01410.05830.06880.00310.0563-0.10690.063-0.00010.4630.19270.06210.42010.01640.4861-6.040232.016536.5158
280.1205-0.0460.07550.0604-0.06420.0938-0.04220.1119-0.15450.12560.0243-0.25660.0882-0.0066-0.03560.47970.072-0.16530.3407-0.15420.36482.882717.258439.9298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 73 )A50 - 73
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 83 )A74 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 122 )A84 - 122
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 134 )A123 - 134
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 149 )A135 - 149
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 173 )A156 - 173
7X-RAY DIFFRACTION7chain 'B' and (resid 48 through 63 )B48 - 63
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 73 )B64 - 73
9X-RAY DIFFRACTION9chain 'B' and (resid 74 through 90 )B74 - 90
10X-RAY DIFFRACTION10chain 'B' and (resid 91 through 105 )B91 - 105
11X-RAY DIFFRACTION11chain 'B' and (resid 106 through 129 )B106 - 129
12X-RAY DIFFRACTION12chain 'B' and (resid 130 through 139 )B130 - 139
13X-RAY DIFFRACTION13chain 'B' and (resid 140 through 173 )B140 - 173
14X-RAY DIFFRACTION14chain 'C' and (resid 50 through 69 )C50 - 69
15X-RAY DIFFRACTION15chain 'C' and (resid 70 through 90 )C70 - 90
16X-RAY DIFFRACTION16chain 'C' and (resid 91 through 112 )C91 - 112
17X-RAY DIFFRACTION17chain 'C' and (resid 113 through 144 )C113 - 144
18X-RAY DIFFRACTION18chain 'C' and (resid 145 through 159 )C145 - 159
19X-RAY DIFFRACTION19chain 'C' and (resid 160 through 173 )C160 - 173
20X-RAY DIFFRACTION20chain 'D' and (resid 49 through 58 )D49 - 58
21X-RAY DIFFRACTION21chain 'D' and (resid 59 through 68 )D59 - 68
22X-RAY DIFFRACTION22chain 'D' and (resid 69 through 90 )D69 - 90
23X-RAY DIFFRACTION23chain 'D' and (resid 91 through 106 )D91 - 106
24X-RAY DIFFRACTION24chain 'D' and (resid 107 through 118 )D107 - 118
25X-RAY DIFFRACTION25chain 'D' and (resid 119 through 129 )D119 - 129
26X-RAY DIFFRACTION26chain 'D' and (resid 130 through 139 )D130 - 139
27X-RAY DIFFRACTION27chain 'D' and (resid 140 through 149 )D140 - 149
28X-RAY DIFFRACTION28chain 'D' and (resid 150 through 173 )D150 - 173

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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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