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- PDB-6bjy: VSV Nucleocapsid with Polyamide Bound -

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Basic information

Entry
Database: PDB / ID: 6bjy
TitleVSV Nucleocapsid with Polyamide Bound
Components
  • Nucleoprotein
  • RNA (45-MER)
Keywordsrna binding protein/rna / VSV / nucleocapisd / nucleocapsid-like particle / RNA BINDING PROTEIN / rna binding protein-rna complex
Function / homology
Function and homology information


RNA replication / helical viral capsid / viral transcription / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Rhabdovirus nucleoprotein-like / Nucleoprotein / Rhabdovirus nucleoprotein-like fold / Rhabdovirus nucleocapsid protein like domain / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DV4 / URANYL (VI) ION / RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 Å
AuthorsGumpper, R.H. / Luo, M.
CitationJournal: J. Virol. / Year: 2018
Title: A Polyamide Inhibits Replication of Vesicular Stomatitis Virus by Targeting RNA in the Nucleocapsid.
Authors: Gumpper, R.H. / Li, W. / Castaneda, C.H. / Scuderi, M.J. / Bashkin, J.K. / Luo, M.
History
DepositionNov 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: RNA (45-MER)
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,91522
Polymers250,3966
Non-polymers4,51916
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35190 Å2
ΔGint-252 kcal/mol
Surface area96140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.480, 165.480, 234.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: RNA chain RNA (45-MER)


Mass: 13732.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Production host: Escherichia coli (E. coli)
#2: Protein
Nucleoprotein / NP / Nucleocapsid protein / Protein N


Mass: 47332.750 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus (strain San Juan)
Strain: San Juan / Production host: Escherichia coli (E. coli) / References: UniProt: P03521
#3: Chemical ChemComp-DV4 / 4-{[4-(acetylamino)-1-methyl-1H-pyrrole-2-carbonyl]amino}-1-methyl-N-{4-[(1-methyl-1H-pyrrol-3-yl)amino]-4-oxobutyl}-1H-imidazole-2-carboxamide


Mass: 468.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N8O4
#4: Chemical
ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: O2U

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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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Sodium Acetate pH 4.5, 0.01% beta-OG, and 6% PEG 3350, 250 mM Sodium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 3.46 Å / Num. obs: 38377 / % possible obs: 97.6 % / Redundancy: 4.386 % / Biso Wilson estimate: 93.452 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.169 / Χ2: 0.904 / Net I/σ(I): 6.56 / Num. measured all: 168334 / Scaling rejects: 39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.46-3.554.3840.6662.7212368284628210.7160.75499.1
3.55-3.654.4310.5893.0312230278927600.7730.66699
3.65-3.754.4490.513.4511910271026770.820.57698.8
3.75-3.874.4380.4223.811535263425990.870.47798.7
3.87-44.4550.3624.3511289256725340.8920.40998.7
4-4.144.4270.2894.9810776247424340.9450.32698.4
4.14-4.294.4720.2355.8410483238423440.9620.26598.3
4.29-4.474.4040.2136.1610073233022870.960.24198.2
4.47-4.674.4210.1797.179584220721680.9680.20298.2
4.67-4.894.4380.167.859156211520630.970.18197.5
4.89-5.164.3790.1557.968684203219830.9730.17597.6
5.16-5.474.390.148.418311194518930.9810.15797.3
5.47-5.854.3810.1388.457706181117590.9780.15697.1
5.85-6.324.4130.1259.087237169416400.9840.14196.8
6.32-6.924.3530.1149.876612157615190.9870.12896.4
6.92-7.744.3030.10311.115874141513650.9850.11696.5
7.74-8.934.2570.09411.985160127212120.9880.10695.3
8.93-10.944.1630.09212.254363110310480.990.10395
10.94-15.474.1090.08812.133698748200.9890.09893.8
15.473.5790.111.0616145314510.9840.11384.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GIC

2gic


Resolution: 3.46→46.295 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 33.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3107 1999 5.52 %
Rwork0.2656 --
obs0.2681 36199 92.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.46→46.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16517 900 49 0 17466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317919
X-RAY DIFFRACTIONf_angle_d0.78924452
X-RAY DIFFRACTIONf_dihedral_angle_d17.26510694
X-RAY DIFFRACTIONf_chiral_restr0.052716
X-RAY DIFFRACTIONf_plane_restr0.0042991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4602-3.54670.36491310.31832252X-RAY DIFFRACTION87
3.5467-3.64250.31631320.3032259X-RAY DIFFRACTION87
3.6425-3.74970.36791350.28692297X-RAY DIFFRACTION88
3.7497-3.87060.34461350.27342307X-RAY DIFFRACTION89
3.8706-4.00890.35671390.2712365X-RAY DIFFRACTION90
4.0089-4.16930.31711390.26572397X-RAY DIFFRACTION92
4.1693-4.35890.30511430.26742436X-RAY DIFFRACTION93
4.3589-4.58850.33841450.25152468X-RAY DIFFRACTION94
4.5885-4.87570.28611460.24042526X-RAY DIFFRACTION96
4.8757-5.25170.32611480.24482538X-RAY DIFFRACTION96
5.2517-5.77930.28991490.262553X-RAY DIFFRACTION95
5.7793-6.61350.33341480.29652530X-RAY DIFFRACTION95
6.6135-8.32450.30661530.25882605X-RAY DIFFRACTION96
8.3245-46.29920.27511560.25752667X-RAY DIFFRACTION94

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