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- PDB-7dyd: Crystal structure of MERS-CoV N-NTD complexed with ligand P4-2 -

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Basic information

Entry
Database: PDB / ID: 7dyd
TitleCrystal structure of MERS-CoV N-NTD complexed with ligand P4-2
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Middle East respiratory syndrome coronavirus / nucleocapsid protein / N-terminal domain
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / RNA binding
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
5-propan-2-yloxy-1H-indole / Nucleoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsHou, M.H. / Lin, S.M. / Hsu, J.N.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2311-B-005-007-MY3 Taiwan
CitationJournal: Front Mol Biosci / Year: 2022
Title: Targeting the N-Terminus Domain of the Coronavirus Nucleocapsid Protein Induces Abnormal Oligomerization via Allosteric Modulation.
Authors: Hsu, J.N. / Chen, J.S. / Lin, S.M. / Hong, J.Y. / Chen, Y.J. / Jeng, U.S. / Luo, S.Y. / Hou, M.H.
History
DepositionJan 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: 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
Revision 1.2Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2635
Polymers57,0874
Non-polymers1751
Water2,504139
1
A: Nucleoprotein
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)28,5442
Polymers28,5442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7193
Polymers28,5442
Non-polymers1751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.638, 109.370, 92.179
Angle α, β, γ (deg.)90.000, 101.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 14271.826 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2I2MQD0
#2: Chemical ChemComp-EY3 / 5-propan-2-yloxy-1H-indole


Mass: 175.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.09 Å3/Da / Density % sol: 60.16 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein 5 mg/mL, Tris-HCl (pH=7.5) 25 mM, NaCl 75 mM, MES (pH=5.5) 140 mM ,(NH4)2SO4 75 mM, PEG 3350 29 %, NaBr 2 mM, ligands 2 mM

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Data collection

DiffractionMean temperature: 273.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→30 Å / Num. obs: 43168 / % possible obs: 98.8 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.036 / Rrim(I) all: 0.098 / Χ2: 0.954 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.38-2.477.10.45426300.8830.1830.490.83498.2
2.47-2.567.60.37627370.9190.1470.4040.87797.9
2.56-2.687.80.27926690.9590.1080.2990.92798.2
2.68-2.827.70.21927030.9710.0850.2350.94398.7
2.82-37.70.16227280.9840.0630.1741.01298.7
3-3.237.70.1227310.9870.0460.1291.20199
3.23-3.557.70.09927330.990.0380.1060.83199
3.55-4.077.60.07827170.9920.0310.0840.95199.2
4.07-5.127.50.06227600.9950.0240.0671.0899.4
3-5.127.40.05327880.9960.0210.0570.87399.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J3K

4j3k


Resolution: 2.39→29.55 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 34.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2952 3183 7.37 %
Rwork0.2578 39985 -
obs0.2607 43168 79.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.99 Å2 / Biso mean: 40.0932 Å2 / Biso min: 15.33 Å2
Refinement stepCycle: final / Resolution: 2.39→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 0 13 139 3909
Biso mean--54.1 35.46 -
Num. residues----483
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.420.43880.3251045113348
2.42-2.460.3636900.32571079116951
2.46-2.50.3707900.31521135122551
2.5-2.540.3808900.3121181127153
2.54-2.590.3495910.30541167125855
2.59-2.640.3314980.30891228132657
2.64-2.690.29471080.30171364147261
2.69-2.750.38671070.3071401150863
2.75-2.820.3131090.29331450155968
2.82-2.890.35671400.28971665180576
2.89-2.960.3491440.28741857200184
2.96-3.050.29871580.28521910206890
3.05-3.150.2921620.28542096225896
3.15-3.260.30281730.26792141231496
3.26-3.390.32891490.27242002215193
3.39-3.550.33491720.26482135230796
3.55-3.730.31261770.252113229098
3.73-3.970.28491720.24242224239699
3.97-4.270.24091740.23592075224999
4.27-4.70.2741800.2192162234299
4.7-5.380.27961720.21662170234299
5.38-6.760.27221770.229222012378100
6.76-29.550.2371620.25742184234699

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