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- PDB-5f5o: Crystal structure of Marburg virus nucleoprotein core domain boun... -

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Basic information

Entry
Database: PDB / ID: 5f5o
TitleCrystal structure of Marburg virus nucleoprotein core domain bound to VP35 regulation peptide
Components
  • Nucleoprotein
  • Peptide from Polymerase cofactor VP35
KeywordsNUCLEAR PROTEIN/PEPTIDE / Filovirus / Marburg virus / Nucleocapsid / nucleoprotein / complex / VP35 peptide / NPBP / NUCLEAR PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


viral RNA genome packaging / helical viral capsid / viral budding via host ESCRT complex / virion component / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Ebola nucleoprotein / Ebola nucleoprotein / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile.
Similarity search - Domain/homology
Polymerase cofactor VP35 / Nucleoprotein
Similarity search - Component
Biological speciesLake Victoria marburgvirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsGuo, Y. / Liu, B.C. / Liu, X. / Li, G.B. / Wang, W.M. / Dong, S.S. / Wang, W.J.
CitationJournal: J. Virol. / Year: 2017
Title: Structural Insight into Nucleoprotein Conformation Change Chaperoned by VP35 Peptide in Marburg Virus
Authors: Liu, B. / Dong, S. / Li, G. / Wang, W. / Liu, X. / Wang, Y. / Yang, C. / Rao, Z. / Guo, Y.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Peptide from Polymerase cofactor VP35
C: Nucleoprotein
D: Peptide from Polymerase cofactor VP35
E: Nucleoprotein
F: Peptide from Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0159
Polymers134,7276
Non-polymers2883
Water4,179232
1
A: Nucleoprotein
B: Peptide from Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0053
Polymers44,9092
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-32 kcal/mol
Surface area16240 Å2
MethodPISA
2
C: Nucleoprotein
D: Peptide from Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1014
Polymers44,9092
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-52 kcal/mol
Surface area16820 Å2
MethodPISA
3
E: Nucleoprotein
F: Peptide from Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)44,9092
Polymers44,9092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-18 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.396, 98.396, 95.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein


Mass: 41691.367 Da / Num. of mol.: 3 / Fragment: UNP residues 19-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Ozolin-75)
Strain: Ozolin-75 / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: Q6UY69
#2: Protein/peptide Peptide from Polymerase cofactor VP35


Mass: 3217.626 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Lake Victoria marburgvirus (strain Ozolin-75)
References: UniProt: Q6UY68
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 1.99 Å3/Da / Density % sol: 38.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM Ammonium sulfate, 100 mM Tris pH 8.5, 18% (wt/vol) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.631
11K, H, -L20.369
ReflectionResolution: 2.2→50 Å / Num. obs: 52682 / % possible obs: 100 % / Redundancy: 10.3 % / Net I/σ(I): 36.78

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALEPACKdata reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.2→31.91 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.865 / SU B: 8.283 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27733 2482 4.9 %RANDOM
Rwork0.21411 ---
obs0.21722 47813 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.403 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2--1.04 Å20 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8001 0 15 232 8248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198164
X-RAY DIFFRACTIONr_bond_other_d0.0020.027949
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.95711067
X-RAY DIFFRACTIONr_angle_other_deg1.084318234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.74451021
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12424.54359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.183151404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5761537
X-RAY DIFFRACTIONr_chiral_restr0.110.21294
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029231
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021886
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5683.1764105
X-RAY DIFFRACTIONr_mcbond_other2.5683.1764104
X-RAY DIFFRACTIONr_mcangle_it3.8524.7495119
X-RAY DIFFRACTIONr_mcangle_other3.8524.7495120
X-RAY DIFFRACTIONr_scbond_it2.3893.3634059
X-RAY DIFFRACTIONr_scbond_other2.3813.364048
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6374.9675931
X-RAY DIFFRACTIONr_long_range_B_refined5.93224.9199520
X-RAY DIFFRACTIONr_long_range_B_other5.89124.9129470
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 120 -
Rwork0.296 2220 -
obs--60.5 %

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