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- PDB-5w2b: Crystal structure of C-terminal domain of Ebola (Reston) nucleopr... -

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Basic information

Entry
Database: PDB / ID: 5w2b
TitleCrystal structure of C-terminal domain of Ebola (Reston) nucleoprotein in complex with Fab fragment
Components
  • Fab Heavy ChainFragment antigen-binding
  • Fab Light ChainFragment antigen-binding
  • Nucleoprotein
Keywordsviral protein/immune system / Ebola virus / nucleoprotein / Fab / antibody-antigen interaction / VIRAL PROTEIN / viral protein-immune system complex
Function / homology
Function and homology information


viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / RNA binding
Similarity search - Function
Ebola nucleoprotein / Ebola nucleoprotein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Reston ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRadwanska, M.J. / Derewenda, U. / Kossiakoff, A.A. / Derewenda, Z.S.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: The structure of the C-terminal domain of the nucleoprotein from the Bundibugyo strain of the Ebola virus in complex with a pan-specific synthetic Fab.
Authors: Radwanska, M.J. / Jaskolowski, M. / Davydova, E. / Derewenda, U. / Miyake, T. / Engel, D.A. / Kossiakoff, A.A. / Derewenda, Z.S.
History
DepositionJun 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2Oct 18, 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
H: Fab Heavy Chain
L: Fab Light Chain
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)60,9383
Polymers60,9383
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-34 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.508, 88.516, 137.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab Heavy Chain / Fragment antigen-binding


Mass: 25216.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab Light Chain / Fragment antigen-binding


Mass: 23258.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Nucleoprotein / / Nucleocapsid protein / Protein N


Mass: 12462.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reston ebolavirus / Strain: Reston-89 / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: Q8JPY1
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mM xylitol, 20 mM myo-Inositol, 20 mM D-Fructose, 20 mM L-Rhamnose monohydrate, 20 mM D-Sorbitol, 0.1 M BES pH 7.5, 0.1 M triethanolamine (TEA) pH 7.5, 10% w/v PEG 8000, 20% w/v 1,5-Pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 14, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 28393 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 50.8 Å2 / Rpim(I) all: 0.034 / Χ2: 1.173 / Net I/σ(I): 3.21
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 5 % / Num. unique obs: 1835 / CC1/2: 0.836 / Rpim(I) all: 0.249

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
HKL-3000data processing
HKL-3000data scaling
PHENIX1.9_1692phasing
PHENIX1.9_1692model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VKD

5vkd


Resolution: 2.25→40.623 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.45
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 1417 5 %Random selection
Rwork0.1979 ---
obs0.2007 28332 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→40.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4131 0 0 111 4242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074242
X-RAY DIFFRACTIONf_angle_d1.0145762
X-RAY DIFFRACTIONf_dihedral_angle_d14.7581516
X-RAY DIFFRACTIONf_chiral_restr0.04633
X-RAY DIFFRACTIONf_plane_restr0.005732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.246-2.32630.36521370.26462600X-RAY DIFFRACTION98
2.3263-2.41940.34261390.25492636X-RAY DIFFRACTION100
2.4194-2.52950.29541400.23672667X-RAY DIFFRACTION100
2.5295-2.66290.3031410.23612664X-RAY DIFFRACTION100
2.6629-2.82970.31391400.23612666X-RAY DIFFRACTION100
2.8297-3.04810.31711400.22862675X-RAY DIFFRACTION100
3.0481-3.35470.28261420.2252690X-RAY DIFFRACTION100
3.3547-3.83980.2431420.20022702X-RAY DIFFRACTION100
3.8398-4.83650.21751450.16922746X-RAY DIFFRACTION100
4.8365-40.62930.21781510.17122869X-RAY DIFFRACTION100

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