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- PDB-5uk4: VESICULAR STOMATITS VIRUS N PROTEIN IN COMPLEX WITH INHIBITORY NA... -

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Basic information

Entry
Database: PDB / ID: 5uk4
TitleVESICULAR STOMATITS VIRUS N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1307
Components
  • Anti-vesicular stomatitis virus N VHH
  • Nucleoprotein
  • 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


RNA replication / helical viral capsid / viral transcription / immunoglobulin mediated immune response / immunoglobulin complex / antigen binding / viral nucleocapsid / blood microparticle / 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 / : ...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 / : / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Anti-vesicular stomatitis virus N VHH / Nucleoprotein
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.204 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 19, 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 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.5Oct 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
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Nucleoprotein
p: Anti-vesicular stomatitis virus N VHH
B: Nucleoprotein
b: Anti-vesicular stomatitis virus N VHH
Q: Nucleoprotein
q: Anti-vesicular stomatitis virus N VHH
C: Nucleoprotein
c: Anti-vesicular stomatitis virus N VHH
R: Nucleoprotein
r: Anti-vesicular stomatitis virus N VHH
D: Nucleoprotein
d: Anti-vesicular stomatitis virus N VHH
S: Nucleoprotein
s: Anti-vesicular stomatitis virus N VHH
E: Nucleoprotein
e: Anti-vesicular stomatitis virus N VHH
T: Nucleoprotein
t: Anti-vesicular stomatitis virus N VHH
K: Nucleoprotein
k: Anti-vesicular stomatitis virus N VHH
L: Nucleoprotein
l: Anti-vesicular stomatitis virus N VHH
N: Nucleoprotein
n: Anti-vesicular stomatitis virus N VHH
M: Nucleoprotein
m: Anti-vesicular stomatitis virus N VHH
F: Nucleoprotein
f: Anti-vesicular stomatitis virus N VHH
G: Nucleoprotein
g: Anti-vesicular stomatitis virus N VHH
H: Nucleoprotein
h: Anti-vesicular stomatitis virus N VHH
I: Nucleoprotein
i: Anti-vesicular stomatitis virus N VHH
O: Nucleoprotein
o: Anti-vesicular stomatitis virus N VHH
J: Nucleoprotein
j: Anti-vesicular stomatitis virus N VHH
A: Nucleoprotein
a: Anti-vesicular stomatitis virus N VHH
u: RNA (45-MER)
v: RNA (45-MER)
w: RNA (45-MER)
x: RNA (45-MER)


Theoretical massNumber of molelcules
Total (without water)1,309,76744
Polymers1,309,76744
Non-polymers00
Water00
1
P: Nucleoprotein
p: Anti-vesicular stomatitis virus N VHH
Q: Nucleoprotein
q: Anti-vesicular stomatitis virus N VHH
R: Nucleoprotein
r: Anti-vesicular stomatitis virus N VHH
S: Nucleoprotein
s: Anti-vesicular stomatitis virus N VHH
T: Nucleoprotein
t: Anti-vesicular stomatitis virus N VHH
K: Nucleoprotein
k: Anti-vesicular stomatitis virus N VHH
L: Nucleoprotein
l: Anti-vesicular stomatitis virus N VHH
N: Nucleoprotein
n: Anti-vesicular stomatitis virus N VHH
M: Nucleoprotein
m: Anti-vesicular stomatitis virus N VHH
O: Nucleoprotein
o: Anti-vesicular stomatitis virus N VHH
u: RNA (45-MER)
v: RNA (45-MER)


Theoretical massNumber of molelcules
Total (without water)654,88422
Polymers654,88422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
b: Anti-vesicular stomatitis virus N VHH
C: Nucleoprotein
c: Anti-vesicular stomatitis virus N VHH
D: Nucleoprotein
d: Anti-vesicular stomatitis virus N VHH
E: Nucleoprotein
e: Anti-vesicular stomatitis virus N VHH
F: Nucleoprotein
f: Anti-vesicular stomatitis virus N VHH
G: Nucleoprotein
g: Anti-vesicular stomatitis virus N VHH
H: Nucleoprotein
h: Anti-vesicular stomatitis virus N VHH
I: Nucleoprotein
i: Anti-vesicular stomatitis virus N VHH
J: Nucleoprotein
j: Anti-vesicular stomatitis virus N VHH
A: Nucleoprotein
a: Anti-vesicular stomatitis virus N VHH
w: RNA (45-MER)
x: RNA (45-MER)


Theoretical massNumber of molelcules
Total (without water)654,88422
Polymers654,88422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.555, 156.008, 217.450
Angle α, β, γ (deg.)79.24, 75.66, 62.27
Int Tables number1
Space group name H-MP1
DetailsComplex confirmed by Gel filtration

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Components

#1: Protein
Nucleoprotein / NP / Nucleocapsid protein / Protein N


Mass: 47463.949 Da / Num. of mol.: 20
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
#2: Antibody
Anti-vesicular stomatitis virus N VHH


Mass: 15277.912 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Details: GGLPETGGHHHHHH Sortase A recognition mofiv and HIS TAG
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A192B6J6
#3: RNA chain
RNA (45-MER)


Mass: 13732.498 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
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: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M sodium acetate, 0.1 M tri-sodium citrate pH 5.5, 5% (w/v) polyethylene glycol 4000

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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 PILATUS3 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: 3.2→128.45 Å / Num. obs: 250547 / % possible obs: 92.4 % / Redundancy: 2.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.152 / Net I/σ(I): 5.1
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.619 / Rpim(I) all: 0.502 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GIC (VSV N) and 5TJW (VHH)

2gic

5tjw


Resolution: 3.204→128.352 Å / SU ML: 0.47 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 31.16
RfactorNum. reflection% reflection
Rfree0.2877 1990 0.8 %
Rwork0.2365 --
obs0.237 250312 91.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.204→128.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms85486 3600 0 0 89086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291358
X-RAY DIFFRACTIONf_angle_d0.525124378
X-RAY DIFFRACTIONf_dihedral_angle_d11.27354162
X-RAY DIFFRACTIONf_chiral_restr0.04113680
X-RAY DIFFRACTIONf_plane_restr0.00315376

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