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- PDB-6lnn: Crystal structure of MERS-CoV N-NTD complexed with ligand P4-1 -

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Basic information

Entry
Database: PDB / ID: 6lnn
TitleCrystal structure of MERS-CoV N-NTD complexed with ligand P4-1
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Middle East respiratory syndrome coronavirus / nucleocapsid protein / N-terminal domain
Function / homology
Function and homology information


viral RNA genome packaging / negative regulation of interferon-beta production / viral capsid / host cell / viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / RNA binding
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
5-propoxy-1H-indole / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.634 Å
AuthorsHou, M.H. / Lin, S.M. / Hsu, J.N.
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
DepositionDec 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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
Water1,928107
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)35.395, 108.721, 91.364
Angle α, β, γ (deg.)90.000, 101.060, 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) / Strain (production host): BL21 / References: UniProt: A0A2I2MQD0, UniProt: K9N4V7*PLUS
#2: Chemical ChemComp-EJC / 5-propoxy-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.: 107 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
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: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 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: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.634→30 Å / Num. obs: 19852 / % possible obs: 98.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.046 / Rrim(I) all: 0.112 / Χ2: 1.027 / 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
2.64-2.695.60.37610170.9150.1710.4140.86698.3
2.69-2.735.70.38110010.9150.1720.4190.83398.7
2.73-2.795.90.3619430.9290.1620.3970.8698.3
2.79-2.845.90.3039840.9480.1350.3320.97998.6
2.84-2.9160.269750.9670.1150.285198.8
2.91-2.9760.2410080.970.1070.2631.09698.9
2.97-3.0560.2259520.9660.10.2471.09898.1
3.05-3.135.90.1869940.9790.0820.2041.07699
3.13-3.225.90.1710160.9830.0760.1871.06799
3.22-3.335.90.1489650.9860.0660.1621.09998.7
3.33-3.445.90.1429690.9890.0630.1561.08299
3.44-3.585.90.12510210.9890.0560.1371.0798.8
3.58-3.745.80.1099830.9910.0490.121.0398.8
3.74-3.945.70.09310290.9920.0420.1021.04399.3
3.94-4.195.70.0899690.9920.040.0971.04798.9
4.19-4.515.70.089980.9930.0360.0881.07599.3
4.51-4.965.60.0779980.9950.0350.0851.03999.5
4.96-5.685.80.0749920.9950.0330.0811.07399.1
5.68-7.145.70.06710260.9960.030.0741.01699.4
7.14-305.50.06110120.9960.0290.0681.08198.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J3K

4j3k


Resolution: 2.634→29.889 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 26.68
RfactorNum. reflection% reflection
Rfree0.2416 1984 10.01 %
Rwork0.2054 --
obs0.2091 19829 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.68 Å2 / Biso mean: 52.5 Å2 / Biso min: 26.03 Å2
Refinement stepCycle: final / Resolution: 2.634→29.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 13 107 3882
Biso mean--70.44 47.67 -
Num. residues----482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6345-2.70030.29971340.2509122595
2.7003-2.77330.31731390.2565126798
2.7733-2.85480.31691370.2612125599
2.8548-2.94690.33591450.2379131299
2.9469-3.05210.29451390.2395123399
3.0521-3.17420.30141450.2333128899
3.1742-3.31850.30741350.2279125999
3.3185-3.49320.23491430.2129130199
3.4932-3.71170.26161360.2065126299
3.7117-3.99760.20021450.1894128499
3.9976-4.39880.19771420.1781128799
4.3988-5.03270.21241450.1637129599
5.0327-6.33080.17411420.1869128299
6.3308-29.8890.25011570.212129599

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