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- PDB-5xsq: Crystal Structure of the Marburg Virus Nucleoprotein Core Domain ... -

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Basic information

Entry
Database: PDB / ID: 5xsq
TitleCrystal Structure of the Marburg Virus Nucleoprotein Core Domain Chaperoned by a VP35 Peptide
Components
  • Nucleoprotein
  • Peptide from Polymerase cofactor VP35
KeywordsVIRAL PROTEIN / Marburg virus / Nucleoprotein / VP35 / NPBP / filovirus
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhu, T. / Song, H. / Shi, Y. / Qi, J. / Gao, G.F.
CitationJournal: J. Virol. / Year: 2017
Title: Crystal Structure of the Marburg Virus Nucleoprotein Core Domain Chaperoned by a VP35 Peptide Reveals a Conserved Drug Target for Filovirus
Authors: Zhu, T. / Song, H. / Peng, R. / Shi, Y. / Qi, J. / Gao, G.F.
History
DepositionJun 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2Sep 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.name
Revision 1.3Feb 7, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Nov 22, 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
B: Peptide from Polymerase cofactor VP35
C: Nucleoprotein
D: Peptide from Polymerase cofactor VP35
E: Nucleoprotein
F: Peptide from Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)118,4586
Polymers118,4586
Non-polymers00
Water0
1
A: Nucleoprotein
B: Peptide from Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)39,4862
Polymers39,4862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-16 kcal/mol
Surface area16710 Å2
MethodPISA
2
C: Nucleoprotein
D: Peptide from Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)39,4862
Polymers39,4862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-16 kcal/mol
Surface area16700 Å2
MethodPISA
3
E: Nucleoprotein
F: Peptide from Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)39,4862
Polymers39,4862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-15 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.320, 101.320, 96.330
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: 36365.484 Da / Num. of mol.: 3 / Fragment: UNP residues 18-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Ozolin-75)
Strain: Ozolin-75 / Gene: NP / Plasmid: pet21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6UY69
#2: Protein/peptide Peptide from Polymerase cofactor VP35 /


Mass: 3120.512 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Lake Victoria marburgvirus (strain Ozolin-75)
References: UniProt: Q6UY68

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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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium citrate tribasic monohydrate, pH 8.3, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 35200 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.061 / Net I/σ(I): 14.937
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.3 % / Rmerge(I) obs: 2.307 / Mean I/σ(I) obs: 1.209 / CC1/2: 0.457 / Rpim(I) all: 0.993 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPI

4ypi


Resolution: 2.6→34.907 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 33.86
RfactorNum. reflection% reflection
Rfree0.2442 1547 5.1 %
Rwork0.214 --
obs0.2156 30340 86.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→34.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7871 0 0 0 7871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058016
X-RAY DIFFRACTIONf_angle_d0.9910862
X-RAY DIFFRACTIONf_dihedral_angle_d16.4932901
X-RAY DIFFRACTIONf_chiral_restr0.0461276
X-RAY DIFFRACTIONf_plane_restr0.0051386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5817-2.6650.292390.2959840X-RAY DIFFRACTION27
2.665-2.76020.312800.27681376X-RAY DIFFRACTION44
2.7602-2.87060.29641240.26732593X-RAY DIFFRACTION82
2.8706-3.00120.29111370.26153022X-RAY DIFFRACTION96
3.0012-3.15930.27651590.24383009X-RAY DIFFRACTION95
3.1593-3.3570.28641760.23812971X-RAY DIFFRACTION94
3.357-3.61580.25531630.21213015X-RAY DIFFRACTION95
3.6158-3.97910.2041610.19582985X-RAY DIFFRACTION95
3.9791-4.55340.22161510.17573014X-RAY DIFFRACTION95
4.5534-5.7310.24671600.20592981X-RAY DIFFRACTION95
5.731-31.36060.231760.19932976X-RAY DIFFRACTION94
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)
10.22090.01630.08280.3555-0.01010.1218-0.0053-0.04640.0879-0.1661-0.18870.1324-0.041-0.0942-0.15280.08180.0581-0.03280.1555-0.01790.2262.448795.835921.3208
20.0147-0.0283-0.01060.11560.04340.04050.13280.0821-0.1431-0.10180.0510.03050.36380.11970.11270.51970.1149-0.01110.1779-0.0240.270459.494274.6187-8.4337
30.00230.00130.00120.00120.0010.00260.01030.0008-0.03560.0185-0.0359-0.0278-0.02180.033800.1940.12730.03630.4072-0.01340.29868.800482.8447-8.3728
40.0021-0.0011-0.00020.0024-0.00110.00280.0096-0.01630.013-0.0262-0.0175-0.0078-0.00490.028700.55480.05160.11670.550.02850.37460.854586.8627-15.7673
50.23150.12370.06950.09910.09830.1613-0.1085-0.02680.30020.12320.01130.1138-0.1494-0.0961-0.1150.28310.1751-0.01350.2386-0.01640.275783.3233117.789824.0915
60.0822-0.0195-0.05750.03520.03520.055-0.0481-0.0801-0.0033-0.0535-0.02330.0022-0.0722-0.0111-0.14890.42850.06-0.10850.24910.10130.366886.1216120.27159.7577
70.1880.07460.0990.11160.09530.1561-0.0076-0.1042-0.08810.0619-0.0117-0.11520.15270.0490.05750.18470.0909-0.00130.16440.03650.112393.1556101.895725.0944
80.0840.01710.01250.1819-0.14660.13750.0358-0.0342-0.10520.07380.0861-0.05580.31060.18420.10170.3840.2096-0.07920.2911-0.02860.1906108.3119102.818951.7751
90.00610.004-0.00070.01630.01830.0269-0.0202-0.0148-0.03430.0218-0.0329-0.01760.0625-0.0125-0.00840.47980.1794-0.07860.2370.01370.469196.550498.861851.7637
100.00420.0009-0.0020.0033-0.00170.0027-0.07420.01460.00040.02730.0069-0.02050.0512-0.059400.49480.02850.04180.2762-0.03660.458296.9391107.662559.2982
110.02170.02630.03550.03720.0340.0785-0.1206-0.00040.16050.0963-0.0797-0.1248-0.24970.0689-0.20580.31690.0441-0.24360.10410.14110.3763100.271475.833434.3104
120.0470.02270.01560.10280.11910.1684-0.1525-0.01540.00920.08630.01130.15180.1267-0.42-0.03370.1998-0.00390.03510.3141-0.03020.277888.339259.460651.3642
130.018-0.01660.00610.0153-0.01090.0425-0.0086-0.0185-0.0419-0.07290.05040.00480.0834-0.06390.03170.281-0.11280.16530.2669-0.11030.517882.862439.767268.2771
140.0086-0.00540.00310.0086-0.00740.00640.01920.02240.0149-0.00830.02890.05580.0265-0.03580.00060.61710.21540.09270.5209-0.1220.4582.889960.255566.5783
150.0006-0.0001-0.00310.0312-0.00150.02240.0018-0.02520.00420.0017-0.0323-0.025-0.0281-0.00040.00880.4130.0856-0.2650.3783-0.04640.491191.687860.94874.0205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 205 )
2X-RAY DIFFRACTION2chain 'A' and (resid 206 through 320 )
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 16 )
4X-RAY DIFFRACTION4chain 'B' and (resid 17 through 27 )
5X-RAY DIFFRACTION5chain 'C' and (resid 5 through 76 )
6X-RAY DIFFRACTION6chain 'C' and (resid 77 through 111 )
7X-RAY DIFFRACTION7chain 'C' and (resid 112 through 205 )
8X-RAY DIFFRACTION8chain 'C' and (resid 206 through 320 )
9X-RAY DIFFRACTION9chain 'D' and (resid 5 through 16 )
10X-RAY DIFFRACTION10chain 'D' and (resid 17 through 27 )
11X-RAY DIFFRACTION11chain 'E' and (resid 5 through 111 )
12X-RAY DIFFRACTION12chain 'E' and (resid 112 through 279 )
13X-RAY DIFFRACTION13chain 'E' and (resid 280 through 320 )
14X-RAY DIFFRACTION14chain 'F' and (resid 5 through 16 )
15X-RAY DIFFRACTION15chain 'F' and (resid 17 through 27 )

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