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- PDB-7xwx: Crystal structure of SARS-CoV-2 N-CTD -

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Basic information

Entry
Database: PDB / ID: 7xwx
TitleCrystal structure of SARS-CoV-2 N-CTD
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / structural protein / drug target
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / RNA stem-loop binding / 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 / 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, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid
Similarity search - Domain/homology
PHOSPHATE ION / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLuan, X.D. / Li, X.M. / Li, Y.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS) United Kingdom
CitationJournal: Sci Bull (Beijing) / Year: 2022
Title: Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein.
Authors: Luan, X. / Li, X. / Li, Y. / Su, G. / Yin, W. / Jiang, Y. / Xu, N. / Wang, F. / Cheng, W. / Jin, Y. / Zhang, L. / Xu, H.E. / Xue, Y. / Zhang, S.
History
DepositionMay 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
G: Nucleoprotein
H: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,92111
Polymers89,6368
Non-polymers2853
Water1448
1
A: Nucleoprotein
E: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5043
Polymers22,4092
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-30 kcal/mol
Surface area11450 Å2
MethodPISA
2
B: Nucleoprotein
F: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5043
Polymers22,4092
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-31 kcal/mol
Surface area11280 Å2
MethodPISA
3
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5043
Polymers22,4092
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-35 kcal/mol
Surface area11260 Å2
MethodPISA
4
G: Nucleoprotein
H: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)22,4092
Polymers22,4092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-31 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.456, 286.665, 164.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-401-

PO4

21A-401-

PO4

31B-401-

PO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPROPROAA269 - 3652 - 98
21ASNASNPROPROBB269 - 3652 - 98
12ASNASNPROPROAA269 - 3652 - 98
22ASNASNPROPROCC269 - 3652 - 98
13ASNASNPHEPHEAA269 - 3632 - 96
23ASNASNPHEPHEDD269 - 3632 - 96
14ALAALAPHEPHEAA273 - 3636 - 96
24ALAALAPHEPHEEE273 - 3636 - 96
15ASNASNPHEPHEAA269 - 3632 - 96
25ASNASNPHEPHEFF269 - 3632 - 96
16ASNASNPROPROAA269 - 3652 - 98
26ASNASNPROPROGG269 - 3652 - 98
17ALAALALYSLYSAA273 - 3616 - 94
27ALAALALYSLYSHH273 - 3616 - 94
18GLYGLYTHRTHRBB268 - 3661 - 99
28GLYGLYTHRTHRCC268 - 3661 - 99
19ASNASNPHEPHEBB269 - 3632 - 96
29ASNASNPHEPHEDD269 - 3632 - 96
110ALAALAPHEPHEBB273 - 3636 - 96
210ALAALAPHEPHEEE273 - 3636 - 96
111ASNASNPHEPHEBB269 - 3632 - 96
211ASNASNPHEPHEFF269 - 3632 - 96
112GLYGLYTHRTHRBB268 - 3661 - 99
212GLYGLYTHRTHRGG268 - 3661 - 99
113ALAALALYSLYSBB273 - 3616 - 94
213ALAALALYSLYSHH273 - 3616 - 94
114ASNASNPHEPHECC269 - 3632 - 96
214ASNASNPHEPHEDD269 - 3632 - 96
115ALAALAPHEPHECC273 - 3636 - 96
215ALAALAPHEPHEEE273 - 3636 - 96
116ASNASNPHEPHECC269 - 3632 - 96
216ASNASNPHEPHEFF269 - 3632 - 96
117GLYGLYTHRTHRCC268 - 3661 - 99
217GLYGLYTHRTHRGG268 - 3661 - 99
118ALAALALYSLYSCC273 - 3616 - 94
218ALAALALYSLYSHH273 - 3616 - 94
119ALAALAPHEPHEDD273 - 3636 - 96
219ALAALAPHEPHEEE273 - 3636 - 96
120ASNASNPROPRODD269 - 3642 - 97
220ASNASNPROPROFF269 - 3642 - 97
121ASNASNPHEPHEDD269 - 3632 - 96
221ASNASNPHEPHEGG269 - 3632 - 96
122ALAALALYSLYSDD273 - 3616 - 94
222ALAALALYSLYSHH273 - 3616 - 94
123ALAALAPHEPHEEE273 - 3636 - 96
223ALAALAPHEPHEFF273 - 3636 - 96
124ALAALAPHEPHEEE273 - 3636 - 96
224ALAALAPHEPHEGG273 - 3636 - 96
125ALAALALYSLYSEE273 - 3616 - 94
225ALAALALYSLYSHH273 - 3616 - 94
126ASNASNPHEPHEFF269 - 3632 - 96
226ASNASNPHEPHEGG269 - 3632 - 96
127ALAALALYSLYSFF273 - 3616 - 94
227ALAALALYSLYSHH273 - 3616 - 94
128ALAALALYSLYSGG273 - 3616 - 94
228ALAALALYSLYSHH273 - 3616 - 94

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Nucleoprotein / / N / Nucleocapsid protein / NC / Protein N


Mass: 11204.461 Da / Num. of mol.: 8 / Fragment: C-terminal domain
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: NaNO3, Na2HPO4, (NH4)2SO4, Tris(base), Bicine, PEG MME500, PEG 20000, 1,8-ANS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3→19.65 Å / Num. obs: 20290 / % possible obs: 99.6 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.224 / Net I/σ(I): 12
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.856 / Num. unique obs: 3247

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJR

2cjr


Resolution: 3→19.65 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 1062 5.2 %RANDOM
Rwork0.2192 ---
obs0.2217 19205 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.35 Å2 / Biso mean: 52.403 Å2 / Biso min: 11.01 Å2
Baniso -1Baniso -2Baniso -3
1--4.95 Å2-0 Å20 Å2
2---2.69 Å2-0 Å2
3---7.64 Å2
Refinement stepCycle: final / Resolution: 3→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6109 0 15 8 6132
Biso mean--30.44 19.06 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136291
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175561
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.6568523
X-RAY DIFFRACTIONr_angle_other_deg2.3321.58312968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91623.132348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.632151003
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9031532
X-RAY DIFFRACTIONr_chiral_restr0.0590.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027102
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021370
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A28430.08
12B28430.08
21A28640.07
22C28640.07
31A26640.11
32D26640.11
41A25710.12
42E25710.12
51A26680.1
52F26680.1
61A28450.07
62G28450.07
71A24740.09
72H24740.09
81B29390.06
82C29390.06
91B26670.12
92D26670.12
101B26040.11
102E26040.11
111B26640.11
112F26640.11
121B29180.07
122G29180.07
131B24740.11
132H24740.11
141C26730.11
142D26730.11
151C25920.12
152E25920.12
161C26590.11
162F26590.11
171C29060.07
172G29060.07
181C24810.09
182H24810.09
191D25920.11
192E25920.11
201D27060.1
202F27060.1
211D26480.12
212G26480.12
221D24990.09
222H24990.09
231E25820.11
232F25820.11
241E25820.12
242G25820.12
251E24650.12
252H24650.12
261F26550.11
262G26550.11
271F24750.1
272H24750.1
281G24540.1
282H24540.1
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 83 -
Rwork0.315 1389 -
all-1472 -
obs--100 %

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