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- PDB-5ukb: VSV N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1004 -

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Basic information

Entry
Database: PDB / ID: 5ukb
TitleVSV N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1004
Components
  • Anti-vesicular stomatitis virus N VHH
  • NucleocapsidCapsid
  • RNA (45-MER)
KeywordsViral Protein/RNA/Immune System / VESICULAR STOMATITIS VIRUS / NUCLEOPROTEIN / INHIBITORY VHH / ANTIVIRAL / Viral Protein-RNA-Immune System complex
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / cytoplasm
Similarity search - Function
Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Anti-vesicular stomatitis virus N VHH / Nucleoprotein
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Vesicular stomatitis Indiana virus
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.473 Å
AuthorsHanke, L. / Knockenhauer, K.E. / Ploegh, H.L. / Schwartz, T.U.
CitationJournal: EMBO Rep. / Year: 2017
Title: Vesicular stomatitis virus N protein-specific single-domain antibody fragments inhibit replication.
Authors: Hanke, L. / Schmidt, F.I. / Knockenhauer, K.E. / Morin, B. / Whelan, S.P. / Schwartz, T.U. / Ploegh, H.L.
History
DepositionJan 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Feb 26, 2020Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / pdbx_validate_symm_contact ...pdbx_validate_close_contact / pdbx_validate_symm_contact / reflns / reflns_shell / struct_conn / struct_conn_type
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.4Oct 4, 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
d: Anti-vesicular stomatitis virus N VHH
D: Nucleocapsid
c: Anti-vesicular stomatitis virus N VHH
C: Nucleocapsid
b: Anti-vesicular stomatitis virus N VHH
B: Nucleocapsid
a: Anti-vesicular stomatitis virus N VHH
A: Nucleocapsid
e: Anti-vesicular stomatitis virus N VHH
E: Nucleocapsid
R: RNA (45-MER)


Theoretical massNumber of molelcules
Total (without water)326,88111
Polymers326,88111
Non-polymers00
Water0
1
d: Anti-vesicular stomatitis virus N VHH
D: Nucleocapsid
c: Anti-vesicular stomatitis virus N VHH
C: Nucleocapsid
b: Anti-vesicular stomatitis virus N VHH
B: Nucleocapsid
a: Anti-vesicular stomatitis virus N VHH
A: Nucleocapsid
e: Anti-vesicular stomatitis virus N VHH
E: Nucleocapsid
R: RNA (45-MER)

d: Anti-vesicular stomatitis virus N VHH
D: Nucleocapsid
c: Anti-vesicular stomatitis virus N VHH
C: Nucleocapsid
b: Anti-vesicular stomatitis virus N VHH
B: Nucleocapsid
a: Anti-vesicular stomatitis virus N VHH
A: Nucleocapsid
e: Anti-vesicular stomatitis virus N VHH
E: Nucleocapsid
R: RNA (45-MER)


Theoretical massNumber of molelcules
Total (without water)653,76222
Polymers653,76222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Unit cell
Length a, b, c (Å)240.117, 335.497, 75.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsComplex confirmed by Gel filtration

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Components

#1: Antibody
Anti-vesicular stomatitis virus N VHH


Mass: 15094.652 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: GGLPETGGHHHHHH Sortase A recognition motif and HIS tag.
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A192B6J5
#2: Protein
Nucleocapsid / Capsid / Nucleocapsid protein


Mass: 47535.027 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Production host: Escherichia coli (E. coli) / References: UniProt: A6H4P1
#3: RNA chain RNA (45-MER)


Mass: 13732.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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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: 4.68 Å3/Da / Density % sol: 73.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium acetate pH 5.0 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 5.47→195.26 Å / Num. obs: 20655 / % possible obs: 99.7 % / Redundancy: 11 % / CC1/2: 0.99 / Rpim(I) all: 0.052 / Rsym value: 0.166 / Net I/σ(I): 16.2
Reflection shellResolution: 5.47→5.7 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 0.86 / CC1/2: 0.556 / Rpim(I) all: 0.46 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UK4, 4KRL

5uk4

4krl


Resolution: 5.473→137.515 Å / SU ML: 1.06 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3375 1997 9.7 %
Rwork0.3364 --
obs0.3365 20583 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.473→137.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21310 900 0 0 22210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422784
X-RAY DIFFRACTIONf_angle_d0.85131051
X-RAY DIFFRACTIONf_dihedral_angle_d22.0468562
X-RAY DIFFRACTIONf_chiral_restr0.0583420
X-RAY DIFFRACTIONf_plane_restr0.0043855

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