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- PDB-4ud1: Structure of the N Terminal domain of the MERS CoV nucleocapsid -

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Basic information

Entry
Database: PDB / ID: 4ud1
TitleStructure of the N Terminal domain of the MERS CoV nucleocapsid
ComponentsN PROTEIN
KeywordsVIRAL PROTEIN / RNA BINDING DOMAIN
Function / homology
Function and homology information


viral nucleocapsid / ribonucleoprotein complex / RNA binding
Similarity search - Function
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, N-terminal / Coronavirus nucleocapsid
Similarity search - Domain/homology
IMIDAZOLE / AMMONIUM ION / N protein
Similarity search - Component
Biological speciesMIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsPapageorgiou, N. / Lichiere, J. / Ferron, F. / Canard, B. / Coutard, B.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural characterization of the N-terminal part of the MERS-CoV nucleocapsid by X-ray diffraction and small-angle X-ray scattering.
Authors: Nicolas Papageorgiou / Julie Lichière / Amal Baklouti / François Ferron / Marion Sévajol / Bruno Canard / Bruno Coutard /
Abstract: The N protein of coronaviruses is a multifunctional protein that is organized into several domains. The N-terminal part is composed of an intrinsically disordered region (IDR) followed by a ...The N protein of coronaviruses is a multifunctional protein that is organized into several domains. The N-terminal part is composed of an intrinsically disordered region (IDR) followed by a structured domain called the N-terminal domain (NTD). In this study, the structure determination of the N-terminal region of the MERS-CoV N protein via X-ray diffraction measurements is reported at a resolution of 2.4 Å. Since the first 30 amino acids were not resolved by X-ray diffraction, the structural study was completed by a SAXS experiment to propose a structural model including the IDR. This model presents the N-terminal region of the MERS-CoV as a monomer that displays structural features in common with other coronavirus NTDs.
History
DepositionDec 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Data collection
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Mar 2, 2016Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N PROTEIN
B: N PROTEIN
C: N PROTEIN
D: N PROTEIN
E: N PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,53014
Polymers89,0445
Non-polymers4879
Water91951
1
A: N PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8272
Polymers17,8091
Non-polymers181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9884
Polymers17,8091
Non-polymers1793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: N PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9884
Polymers17,8091
Non-polymers1793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: N PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9012
Polymers17,8091
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: N PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8272
Polymers17,8091
Non-polymers181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)208.648, 67.021, 60.940
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
N PROTEIN / NUCLEOCAPSID


Mass: 17808.729 Da / Num. of mol.: 5 / Fragment: N-TERMINAL DOMAIN (NTD), RESIDUES 1-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS
Plasmid: PMCOX20A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): T7 EXPRESS (NEW ENGLAND BIOLABS) / References: UniProt: T2B9R0
#2: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.8 % / Description: NONE
Crystal growpH: 5 / Details: NAACETATE 0.1M, AMS04 2M, pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.48→48.26 Å / Num. obs: 32509 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 55.82 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.23
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.9 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
PHENIXdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BXX

2bxx


Resolution: 2.48→48.26 Å / SU ML: 0.4 / σ(F): 1.33 / Phase error: 33.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2738 3291 6 %
Rwork0.2281 --
obs0.2308 29457 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.82 Å2
Refinement stepCycle: LAST / Resolution: 2.48→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4839 0 32 51 4922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055046
X-RAY DIFFRACTIONf_angle_d0.8566905
X-RAY DIFFRACTIONf_dihedral_angle_d11.3661792
X-RAY DIFFRACTIONf_chiral_restr0.035708
X-RAY DIFFRACTIONf_plane_restr0.004917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.51550.43741320.38992139X-RAY DIFFRACTION93
2.5155-2.5530.40811400.37252160X-RAY DIFFRACTION93
2.553-2.59290.43061260.35362121X-RAY DIFFRACTION93
2.5929-2.63540.39641330.36832150X-RAY DIFFRACTION94
2.6354-2.68080.36221280.35522153X-RAY DIFFRACTION92
2.6808-2.72960.45541270.37552088X-RAY DIFFRACTION93
2.7296-2.78210.39721330.35792193X-RAY DIFFRACTION94
2.7821-2.83890.34661370.34522111X-RAY DIFFRACTION93
2.8389-2.90060.36571460.3262171X-RAY DIFFRACTION93
2.9006-2.9680.38971340.32872051X-RAY DIFFRACTION92
2.968-3.04230.28011290.29182127X-RAY DIFFRACTION91
3.0423-3.12450.30361260.28062021X-RAY DIFFRACTION90
3.1245-3.21640.35911500.27272173X-RAY DIFFRACTION92
3.2164-3.32020.33241310.26672040X-RAY DIFFRACTION92
3.3202-3.43880.32721410.25132206X-RAY DIFFRACTION96
3.4388-3.57650.2711410.23042230X-RAY DIFFRACTION97
3.5765-3.73920.27841390.20432218X-RAY DIFFRACTION97
3.7392-3.93630.21611550.18992266X-RAY DIFFRACTION97
3.9363-4.18280.22121460.18092199X-RAY DIFFRACTION98
4.1828-4.50550.23871460.17262233X-RAY DIFFRACTION98
4.5055-4.95850.21891330.16832204X-RAY DIFFRACTION96
4.9585-5.6750.17771450.17422213X-RAY DIFFRACTION96
5.675-7.14620.23151280.18562168X-RAY DIFFRACTION95
7.1462-48.26920.26631450.21372284X-RAY DIFFRACTION99
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)
10.12620.5040.38661.33570.00240.3397-0.0312-1.57750.6796-0.1799-0.7884-0.8140.129-1.991-0.11980.62560.17710.00640.7234-0.34690.804652.919-56.432266.5057
21.69980.12970.94061.7761-0.26810.64-0.096-0.20990.0820.13710.1483-0.167-0.0545-0.332600.45810.0301-0.06470.51430.10520.473944.1943-28.727567.1995
3-0.2475-0.19520.1737-0.022-0.81130.2813-0.116-0.1761-0.13110.08960.2527-0.17260.1597-0.20370.00050.57770.0113-0.09880.42450.03020.492350.6533-38.061176.246
42.0827-1.2504-0.01641.92360.75732.9763-0.10370.09060.37030.19940.1096-0.01660.2595-0.11590.00030.3469-0.0104-0.03010.3720.03010.373543.231-32.833565.8092
50.1715-0.0562-0.08530.30130.56090.1772-1.0449-1.13280.79340.94690.3280.11170.5563-0.35780.00230.8507-0.06540.05260.746-0.21770.903255.8567-19.912691.0555
62.9958-0.7755-0.42931.8394-0.39720.67450.1626-0.06190.4594-0.0059-0.04980.247-0.0769-0.279400.4364-0.0335-0.0210.30920.00630.447526.6648-18.950491.4947
7-0.18150.02270.96110.171-0.2880.27560.5386-0.0227-0.04531.1513-0.5379-0.06331.13220.5687-0.05580.5777-0.1025-0.12620.5586-0.00440.395438.0164-17.1795100.0934
80.1766-0.049-0.1965-0.00270.02190.15490.2694-0.90080.1350.5614-0.9383-0.47230.90640.0334-0.00520.7273-0.1775-0.05110.95680.14740.638442.2032-9.7026111.314
92.50130.2081-0.29162.9994-0.69442.17310.0005-0.26990.0287-0.0696-0.15440.0418-0.0322-0.02850.00030.38040.039-0.0210.2567-0.03220.359130.7558-20.788390.7223
100.077-0.08140.07120.1025-0.0890.2538-0.01890.6812-0.2983-0.3897-0.19040.1215-0.87250.5323-0.00140.64730.0147-0.03810.90050.07960.72-2.5667-33.760778.9035
110.8187-0.07010.30990.00390.46660.49320.02050.1943-0.13620.0230.08080.017-0.3790.11540.00020.5532-0.10640.06120.4920.03220.49520.4865-51.207479.2709
120.64670.60430.3952-0.7612-0.32790.185-0.265-0.1090.0576-0.00020.06210.0556-0.1638-0.27840.00020.5220.00090.09250.5116-0.01620.429211.1498-45.496586.1628
132.94990.4657-0.11830.76751.19651.6446-0.14610.1849-0.1770.1118-0.0687-0.1241-0.2073-0.0874-0.00040.3909-0.08410.01160.426-0.02210.409119.2499-48.837978.1273
144.70841.4503-2.17791.04030.78415.08671.5075-1.47780.0118-1.36660.73870.622-1.05610.87490.37180.91240.39250.07220.21740.2691.024836.8092-56.9024100.0002
15-00.04440.03920.09040.02630.01630.1852-0.6922-0.23921.4441-0.0207-0.6612-0.47060.8667-0.00031.19710.1294-0.04841.0349-0.05930.620440.9311-51.5923117.606
161.6650.37380.17041.40741.18931.05350.11710.0131-0.00890.21170.0131-0.2562-0.15450.085-0.00010.42190.10710.02620.35530.0610.462238.6468-46.289101.682
170.6567-0.68430.2960.76350.8370.0543-0.0535-0.1979-0.00250.1986-0.19180.18890.0719-0.1957-0.00020.4730.01880.08250.4545-0.00230.422231.2855-48.7052106.0301
180.90781.0568-0.85631.7424-2.35813.92160.92520.4496-0.57870.1077-0.8857-0.0247-0.8866-0.0353-0.12630.320.07780.10520.37-0.05770.582934.1517-40.913494.4009
19-0.132-0.21550.27270.4922-0.50810.1576-0.14840.8659-0.6453-0.02630.4051-0.62470.59020.6036-0.00030.75310.1684-0.03380.5538-0.02810.930838.2341-59.471496.3437
200.5507-0.2931-0.42870.29220.47560.8595-0.2649-0.41980.27551.21360.1879-0.81010.03890.80560.01040.72920.1223-0.17450.55650.12750.844446.815-48.6973110.2399
210.2001-0.0731-0.17060.0686-0.04480.11820.40520.79460.49770.04470.72340.0656-0.5201-0.25810.00230.6276-0.02010.0420.8669-0.1230.7339.978-23.9101112.0334
220.3595-0.0204-0.0751.86020.94491.5226-0.0941-1.03430.54521.66630.68370.52491.41331.24811.12071.06010.28910.28281.394-0.24370.67199.8439-30.3642129.5667
230.1131-0.5896-0.07151.1190.33680.49730.18990.0111-0.0607-0.1634-0.01660.24450.4499-0.0615-0.00010.4077-0.00740.0070.7395-0.05620.479514.5177-35.4895112.1601
240.9953-0.5324-0.30170.19180.07810.8363-0.2629-0.0132-0.08710.4873-0.1991-0.2416-0.30690.188-0.00030.514-0.008-0.02940.6206-0.04440.460719.3793-26.1483118.0076
250.521-0.58460.47190.4462-0.71371.00080.1698-0.0340.0780.2298-0.2579-0.15470.3077-0.4697-0.00070.3467-0.0441-0.02890.6399-0.02510.486321.201-34.3802111.2797
260.3694-0.6324-0.69110.35430.39520.4220.18550.60660.1023-0.1648-0.10410.4604-0.0434-0.5119-0.00110.44450.0765-0.02860.84770.00950.71867.3493-22.802108.3205
270.2915-0.00140.0150.3485-0.56430.7259-0.5949-1.0627-0.49570.51441.04641.09920.2992-0.08920.04560.55160.0580.12880.7921-0.07070.70526.8568-36.2621122.3184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 31 THROUGH 40 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 41 THROUGH 74 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 75 THROUGH 102 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 103 THROUGH 163 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 31 THROUGH 40 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 41 THROUGH 74 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 75 THROUGH 87 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 88 THROUGH 95 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 96 THROUGH 163 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 31 THROUGH 40 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 41 THROUGH 74 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 75 THROUGH 112 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 113 THROUGH 163 )
14X-RAY DIFFRACTION14CHAIN D AND (RESID 40 THROUGH 46 )
15X-RAY DIFFRACTION15CHAIN D AND (RESID 47 THROUGH 54 )
16X-RAY DIFFRACTION16CHAIN D AND (RESID 55 THROUGH 81 )
17X-RAY DIFFRACTION17CHAIN D AND (RESID 82 THROUGH 124 )
18X-RAY DIFFRACTION18CHAIN D AND (RESID 125 THROUGH 134 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 135 THROUGH 149 )
20X-RAY DIFFRACTION20CHAIN D AND (RESID 150 THROUGH 163 )
21X-RAY DIFFRACTION21CHAIN E AND (RESID 40 THROUGH 46 )
22X-RAY DIFFRACTION22CHAIN E AND (RESID 47 THROUGH 54 )
23X-RAY DIFFRACTION23CHAIN E AND (RESID 55 THROUGH 78 )
24X-RAY DIFFRACTION24CHAIN E AND (RESID 80 THROUGH 118 )
25X-RAY DIFFRACTION25CHAIN E AND (RESID 119 THROUGH 134 )
26X-RAY DIFFRACTION26CHAIN E AND (RESID 135 THROUGH 149 )
27X-RAY DIFFRACTION27CHAIN E AND (RESID 150 THROUGH 163 )

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