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- PDB-5dsd: The crystal structure of the C-terminal domain of Ebola (Bundibug... -

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Basic information

Entry
Database: PDB / ID: 5dsd
TitleThe crystal structure of the C-terminal domain of Ebola (Bundibugyo) nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Filoviridae
Function / homologyP40 nucleoprotein, subdomain 2, Borna disease virus / Ebola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / Nucleoprotein
Function and homology information
Biological speciesBundibugyo virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsBaker, L. / Handing, K.B. / Utepbergenov, D. / Derewenda, U. / Derewenda, Z.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA1-14-C-0006 United States
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Molecular architecture of the nucleoprotein C-terminal domain from the Ebola and Marburg viruses.
Authors: Baker, L.E. / Ellena, J.F. / Handing, K.B. / Derewenda, U. / Utepbergenov, D. / Engel, D.A. / Derewenda, Z.S.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2014
Title: The structure of the C-terminal domain of the Zaire ebolavirus nucleoprotein.
Authors: Dziubanska, P.J. / Derewenda, U. / Ellena, J.F. / Engel, D.A. / Derewenda, Z.S.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionSep 30, 2015ID: 5CIJ
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4874
Polymers12,2681
Non-polymers2203
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleoprotein
hetero molecules

A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9758
Polymers24,5352
Non-polymers4396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+2/31
Buried area2910 Å2
ΔGint-35 kcal/mol
Surface area12490 Å2
MethodPISA
3
A: Nucleoprotein
hetero molecules

A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9758
Polymers24,5352
Non-polymers4396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area2050 Å2
ΔGint-32 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.957, 108.957, 82.736
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Nucleoprotein /


Mass: 12267.726 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 641-739)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bundibugyo virus / Gene: NP, DH33_45404gpNP / Plasmid: Parallel1-MBPHis / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: B8XCM7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 5.94 Å3/Da / Density % sol: 79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystallization solution: 1.33 M LiSO4, 0.1 M Tris pH 8.5. 1:1 ratio (250 nL: 250 nL) of precipitant to protein (at a concentration of 13.9 mg/ml). 60 mcL reservoir. Protein purification ...Details: Crystallization solution: 1.33 M LiSO4, 0.1 M Tris pH 8.5. 1:1 ratio (250 nL: 250 nL) of precipitant to protein (at a concentration of 13.9 mg/ml). 60 mcL reservoir. Protein purification buffer 50mM Tris-HCl, 150 mM NaCl; pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.99 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 14, 2014
Diffraction measurementDetails: 0.50 degrees, -1.0 sec, detector distance 350.62 mm
Method: \w scans
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionAv R equivalents: 0.084 / Number: 184210
ReflectionResolution: 2.3→80 Å / Num. obs: 12398 / % possible obs: 94.3 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.084 / Net I/av σ(I): 31.34 / Net I/σ(I): 20.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.432 / % possible all: 64.7
Cell measurementReflection used: 184210

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
REFMAC5.8.0103refinement
SBC-Collectdata collection
HKL-3000phasing
SCALEPACKdata scaling
PHENIXmodel building
HKL-3000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QB0

4qb0


Resolution: 2.31→80 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.2071 / WRfactor Rwork: 0.1698 / FOM work R set: 0.8163 / SU B: 9.71 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1436 / SU Rfree: 0.1412 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 604 4.9 %RANDOM
Rwork0.1676 ---
obs0.1692 11792 94.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 243.89 Å2 / Biso mean: 81.78 Å2 / Biso min: 46.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å2-0 Å2
3----2.2 Å2
Refinement stepCycle: final / Resolution: 2.31→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 13 113 987
Biso mean--115.8 79.01 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019908
X-RAY DIFFRACTIONr_bond_other_d0.0010.02806
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9361225
X-RAY DIFFRACTIONr_angle_other_deg0.89931866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6785104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.10224.90251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3615153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.807153
X-RAY DIFFRACTIONr_chiral_restr0.0710.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02222
X-RAY DIFFRACTIONr_mcbond_it13.6963.935413
X-RAY DIFFRACTIONr_mcbond_other13.6293.925412
X-RAY DIFFRACTIONr_mcangle_it14.3635.917515
LS refinement shellResolution: 2.312→2.372 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 27 -
Rwork0.278 534 -
all-561 -
obs--59.49 %
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)
16.9694-4.8245-5.653410.90716.152922.4559-0.2281-0.0362-0.52990.8334-0.38090.72541.9299-1.40080.6090.8102-0.13670.04810.6334-0.0990.0736-8.65266.0327.423
25.22560.835-0.347513.26045.30526.0221-0.07260.2498-0.3232-0.0731-0.21510.65020.0341-0.60760.28770.40490.0005-0.00960.4396-0.06580.0621-4.86857.11713.558
33.43090.34352.03978.38680.2656.5105-0.1390.0581-0.50160.004-0.03940.147-0.20020.08320.17840.5052-0.0008-0.0070.4583-0.03440.12313.44555.95817.46
44.0368-2.6128-1.76629.64492.15894.7331-0.6915-0.2001-0.41830.6160.18320.31460.2982-0.19340.50830.41920.04250.13370.44130.01550.08455.88846.05724.51
512.2717-3.0546-6.43579.0614-0.443115.8036-0.7594-0.7271-1.32640.76810.30450.27321.02970.19330.45480.47570.0380.3090.28580.05110.376412.66231.19522.992
65.5817-5.3055-0.77656.68941.07375.6811-0.1280.6475-1.0672-0.2807-0.21640.93180.2186-0.4450.34450.5341-0.10770.20180.4981-0.14080.33398.45138.77814.976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A637 - 645
2X-RAY DIFFRACTION2A646 - 661
3X-RAY DIFFRACTION3A662 - 671
4X-RAY DIFFRACTION4A672 - 698
5X-RAY DIFFRACTION5A699 - 715
6X-RAY DIFFRACTION6A716 - 739

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