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- PDB-6wzq: Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P21 form -

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Basic information

Entry
Database: PDB / ID: 6wzq
TitleStructure of SARS-CoV-2 Nucleocapsid dimerization domain, P21 form
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / COVID-19 / nucleocapsid / RNA binding
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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...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 / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / 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 / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / 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 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: 1.45 Å
AuthorsYe, Q. / Corbett, K.D.
Citation
Journal: Protein Sci. / Year: 2020
Title: Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.
Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D.
#1: Journal: Biorxiv / Year: 2020
Title: Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.
Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D.
#2: Journal: Protein Sci. / Year: 2020
Title: Architecture and self-assembly of the SARS-CoV-2 ucleocapsid protein
Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D.
History
DepositionMay 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Sep 9, 2020Group: Database references / Category: citation / citation_author
Revision 1.4Apr 7, 2021Group: Database references / Category: citation / citation_author
Revision 1.5Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)62,93810
Polymers62,3624
Non-polymers5766
Water8,881493
1
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4695
Polymers31,1812
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-61 kcal/mol
Surface area12070 Å2
MethodPISA
2
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4695
Polymers31,1812
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-51 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.146, 43.546, 74.233
Angle α, β, γ (deg.)90.000, 94.870, 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
Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 15590.458 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 1.84 Å3/Da / Density % sol: 33.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 50 mM Ammonium Sulfate, and 38% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→74 Å / Num. obs: 80163 / % possible obs: 98.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Net I/σ(I): 16
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2 / Num. unique obs: 3906 / CC1/2: 0.796 / Rrim(I) all: 0.877

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WXO

6wxo


Resolution: 1.45→73.97 Å / SU ML: 0.144 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 20.7015
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1802 3919 4.89 %
Rwork0.1673 76201 -
obs0.168 80120 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.5 Å2
Refinement stepCycle: LAST / Resolution: 1.45→73.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3637 0 30 493 4160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093785
X-RAY DIFFRACTIONf_angle_d0.9225127
X-RAY DIFFRACTIONf_chiral_restr0.0804527
X-RAY DIFFRACTIONf_plane_restr0.0081675
X-RAY DIFFRACTIONf_dihedral_angle_d21.70181401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.460.30961170.28882404X-RAY DIFFRACTION88.89
1.46-1.480.29921370.26322689X-RAY DIFFRACTION97.55
1.48-1.50.26641250.25022698X-RAY DIFFRACTION97.08
1.5-1.520.26931370.2362577X-RAY DIFFRACTION96.34
1.52-1.550.28171550.22362764X-RAY DIFFRACTION99.56
1.55-1.570.22491150.21812710X-RAY DIFFRACTION99.65
1.57-1.590.24551230.20572751X-RAY DIFFRACTION99.76
1.59-1.620.20631320.19212768X-RAY DIFFRACTION99.62
1.62-1.650.2321410.19012707X-RAY DIFFRACTION99.41
1.65-1.680.21431450.18932757X-RAY DIFFRACTION99.83
1.68-1.710.221240.18592736X-RAY DIFFRACTION99.51
1.71-1.740.26231470.19272722X-RAY DIFFRACTION99.38
1.74-1.780.21051180.18992722X-RAY DIFFRACTION99.51
1.78-1.820.19691410.1862768X-RAY DIFFRACTION99.22
1.82-1.870.23381510.17452681X-RAY DIFFRACTION99.02
1.87-1.920.19561300.17182733X-RAY DIFFRACTION99.1
1.92-1.980.18921490.16642715X-RAY DIFFRACTION98.59
1.98-2.040.19891500.1672722X-RAY DIFFRACTION98.93
2.04-2.110.18961480.16292673X-RAY DIFFRACTION98.46
2.11-2.20.17681220.16452803X-RAY DIFFRACTION99.83
2.2-2.30.16991360.15712771X-RAY DIFFRACTION99.9
2.3-2.420.17841550.1592726X-RAY DIFFRACTION99.83
2.42-2.570.19411480.16822769X-RAY DIFFRACTION99.93
2.57-2.770.19531560.17092754X-RAY DIFFRACTION99.79
2.77-3.050.18841240.16512756X-RAY DIFFRACTION99.55
3.05-3.490.16961360.16472773X-RAY DIFFRACTION98.78
3.49-4.390.13451550.13842726X-RAY DIFFRACTION97.07
4.39-73.970.15762020.1622826X-RAY DIFFRACTION99.61
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)
11.01576948675-0.0941243664726-0.2949170118163.998942038440.3629217316171.390133265830.0642687264618-0.130679751902-0.05158593450920.604098270551-0.090859416885-0.3384830079130.1470468583580.07661234200970.009571119727910.206504227629-0.0274869832256-0.0792741180310.1927289401230.01741459671590.1662721300237.221511991014.1320229875424.3224027882
20.6546413687440.2912192802980.2394699920762.906811476330.1023638642371.693246921870.02220829154730.02804411861020.0413881381806-0.218335696102-0.0841535767024-0.0798322691966-0.1275944087140.06067097794770.06219146935630.1464795777780.00721182967641-0.01080382363050.1706747305820.007318717792710.1459175766365.5639046316314.814556066511.0529991376
30.4543765885770.0922926193934-0.3500138700363.399135552130.08093636156750.8950344130080.01201247867070.0752505484510.0171716598769-0.350341410811-0.0369446395428-0.0848344433507-0.073814156328-0.0717942624280.02991736023290.1544885364310.004674343376260.01463665286290.1964885917290.0005246038114290.176592807651-34.415070225920.282053843425.2684199618
41.30473023224-0.2479339865220.1439691099292.69605643183-0.03339147988211.45704923325-0.02082733561270.192374807353-0.0800662312043-0.9704506421950.0130373896529-0.659273595031-0.02956821069030.2058709079580.02558803572650.381662224673-0.003253139153390.2256499513410.233953740601-0.02439911585810.293965686468-25.26413823379.7284673714815.1021751224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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