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- PDB-6lz8: Crystal structure of MERS-CoV N-NTD complexed with ligand P4-4 -

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Basic information

Entry
Database: PDB / ID: 6lz8
TitleCrystal structure of MERS-CoV N-NTD complexed with ligand P4-4
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 endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / 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-(2-methoxyethoxy)-1H-indole / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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
DepositionFeb 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 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
C: Nucleoprotein
B: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2795
Polymers57,0874
Non-polymers1911
Water2,234124
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)28,7353
Polymers28,5442
Non-polymers1911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.154, 111.028, 92.261
Angle α, β, γ (deg.)90.000, 100.970, 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-EY9 / 5-(2-methoxyethoxy)-1H-indole


Mass: 191.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.1 Å3/Da / Density % sol: 60.28 %
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: 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: 2.58→30 Å / Num. obs: 34259 / % possible obs: 97.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Χ2: 0.945 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.58-2.677.30.42820830.930.170.4610.88895.9
2.67-2.787.30.36920400.9450.1460.3980.91695.8
2.78-2.917.20.26420850.9730.1050.2850.93696
2.91-3.067.20.20820520.9780.0830.2250.99395.9
3.06-3.2570.14721190.9870.060.1591.01998.4
3.25-3.56.90.11821460.990.0490.1280.98998.5
3.5-3.856.80.09121400.9930.0380.0990.96399.1
3.85-4.416.20.06421410.9950.0290.070.81899.4
4.41-5.556.10.05321560.9960.0240.0590.98799.5

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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: 2.59→26.653 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 30.63
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2869 3275 9.56 %
Rwork0.2369 --
obs0.2416 34259 80.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.93 Å2 / Biso mean: 42.2462 Å2 / Biso min: 16.69 Å2
Refinement stepCycle: final / Resolution: 2.59→26.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3731 0 14 124 3869
Biso mean--64.18 37.97 -
Num. residues----480
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5903-2.6290.3277800.300278146
2.629-2.670.366980.281990254
2.67-2.71380.4255980.295795156
2.7138-2.76050.35031040.294794158
2.7605-2.81060.32421020.306599560
2.8106-2.86460.34051170.2922110365
2.8646-2.9230.32391250.2752115268
2.923-2.98650.3791310.2967116570
2.9865-3.05590.35091210.2644123076
3.0559-3.13220.31791420.2587135481
3.1322-3.21680.35251480.25147486
3.2168-3.31120.31611510.2499146189
3.3112-3.41790.27871600.2621154391
3.4179-3.53980.29981720.2569160194
3.5398-3.68120.29741660.2356154296
3.6812-3.84830.3261800.2207165597
3.8483-4.05050.25561670.2262158396
4.0505-4.30330.25141710.2045163797
4.3033-4.63390.24961760.2002162896
4.6339-5.09730.2161670.2003160395
5.0973-5.82820.24541620.2184157395
5.8282-7.31770.27761700.2167156895

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