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- PDB-5vkd: Crystal structure of C-terminal domain of Ebola (Bundibugyo) nucl... -

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Basic information

Entry
Database: PDB / ID: 5vkd
TitleCrystal structure of C-terminal domain of Ebola (Bundibugyo) nucleoprotein in complex with Fab fragment
Components
  • Fab Heavy Chain
  • Fab light chain
  • Nucleoprotein
KeywordsIMMUNE SYSTEM / Ebolavirus / Nucleoprotein / Fab / antibody fragment
Function / homology
Function and homology information


viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
P40 nucleoprotein, subdomain 2, Borna disease virus / Ebola nucleoprotein / Ebola nucleoprotein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesBundibugyo ebolavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å
AuthorsRadwanska, M.J. / Derewenda, U. / Kossiakoff, 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
DepositionApr 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 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 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
H: Fab Heavy Chain
L: Fab light chain


Theoretical massNumber of molelcules
Total (without water)60,7433
Polymers60,7433
Non-polymers00
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-39 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.407, 87.485, 130.399
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: Protein Nucleoprotein


Mass: 12267.726 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fragment: C-terminal domain (UNP residues 641-739) Gene Name(s): NP DH33_45404gpNP
Source: (gene. exp.) Bundibugyo ebolavirus / Production host: Escherichia coli (E. coli) / References: UniProt: R4QJ68, UniProt: B8XCM7*PLUS
#2: Antibody Fab Heavy Chain


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)
#3: Antibody Fab light chain


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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium formate, 10% w/v Polyvinylpyrrolidone, 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: AREA DETECTOR / Date: Apr 17, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.749→42.88 Å / Num. obs: 53300 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 27.5 Å2 / Net I/σ(I): 1.69

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data collection
HKL-3000data processing
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
BALBESmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.749→41.471 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 1064 2 %Random selection
Rwork0.1761 ---
obs0.1767 53228 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.749→41.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 0 567 4762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034343
X-RAY DIFFRACTIONf_angle_d0.6495917
X-RAY DIFFRACTIONf_dihedral_angle_d10.2192611
X-RAY DIFFRACTIONf_chiral_restr0.046650
X-RAY DIFFRACTIONf_plane_restr0.004755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7493-1.8290.23881300.2436342X-RAY DIFFRACTION99
1.829-1.92540.2711310.21786421X-RAY DIFFRACTION100
1.9254-2.0460.22881310.19586461X-RAY DIFFRACTION100
2.046-2.2040.2051320.18356467X-RAY DIFFRACTION100
2.204-2.42580.20841330.18656508X-RAY DIFFRACTION100
2.4258-2.77670.2551330.18726507X-RAY DIFFRACTION100
2.7767-3.49810.20231350.18066617X-RAY DIFFRACTION100
3.4981-41.4830.16991390.15356841X-RAY DIFFRACTION100

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