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- PDB-8ffr: Revised structure of the rabies virus nucleoprotein-RNA complex -

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Basic information

Entry
Database: PDB / ID: 8ffr
TitleRevised structure of the rabies virus nucleoprotein-RNA complex
Components
  • (RNA (99-MER)) x 2
  • Nucleoprotein
KeywordsVIRAL PROTEIN / PROTEIN-RNA COMPLEX / RABIES VIRUS / NUCLEOPROTEIN / RNA BINDING PROTEIN
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesRabies virus CVS-11
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsLeyrat, C. / Bourhis, J.M. / Albertini, A.A.V. / Wernimont, A.K. / Muziol, T. / Ravelli, R.B.G. / Weissenhorn, W. / Ruigrok, R.W.H. / Jamin, M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)BSV8-2012 France
Citation
Journal: Viruses / Year: 2022
Title: Structure and Dynamics of the Unassembled Nucleoprotein of Rabies Virus in Complex with Its Phosphoprotein Chaperone Module.
Authors: Gerard, F.C.A. / Bourhis, J.M. / Mas, C. / Branchard, A. / Vu, D.D. / Varhoshkova, S. / Leyrat, C. / Jamin, M.
#1: Journal: Science / Year: 2006
Title: Crystal structure of the rabies virus nucleoprotein-RNA complex.
Authors: Albertini, A.A. / Wernimont, A.K. / Muziol, T. / Ravelli, R.B. / Clapier, C.R. / Schoehn, G. / Weissenhorn, W. / Ruigrok, R.W.
History
DepositionDec 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
G: Nucleoprotein
H: Nucleoprotein
I: Nucleoprotein
J: Nucleoprotein
K: Nucleoprotein
L: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
O: Nucleoprotein
P: Nucleoprotein
Q: Nucleoprotein
R: Nucleoprotein
S: Nucleoprotein
T: Nucleoprotein
U: Nucleoprotein
V: Nucleoprotein
W: RNA (99-MER)
X: RNA (99-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,176,43626
Polymers1,176,24624
Non-polymers1902
Water00
1
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
G: Nucleoprotein
H: Nucleoprotein
I: Nucleoprotein
J: Nucleoprotein
K: Nucleoprotein
W: RNA (99-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)588,30213
Polymers588,20712
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
O: Nucleoprotein
P: Nucleoprotein
Q: Nucleoprotein
R: Nucleoprotein
S: Nucleoprotein
T: Nucleoprotein
U: Nucleoprotein
V: Nucleoprotein
X: RNA (99-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)588,13413
Polymers588,03912
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)270.430, 281.000, 236.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 6 through 448)
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1(chain "K" and resid 6 through 448)
d_12ens_1(chain "L" and resid 6 through 448)
d_13ens_1(chain "M" and resid 6 through 448)
d_14ens_1chain "N"
d_15ens_1(chain "O" and resid 6 through 448)
d_16ens_1(chain "P" and resid 6 through 448)
d_17ens_1chain "Q"
d_18ens_1chain "R"
d_19ens_1chain "S"
d_20ens_1chain "T"
d_21ens_1chain "U"
d_22ens_1(chain "V" and resid 6 through 448)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILESERA1 - 418
d_21ens_1ILESERB2 - 419
d_31ens_1ILESERC1 - 418
d_41ens_1ILESERD1 - 418
d_51ens_1ILESERE1 - 418
d_61ens_1ILESERF1 - 418
d_71ens_1ILESERG1 - 418
d_81ens_1ILESERH1 - 418
d_91ens_1ILESERI1 - 418
d_101ens_1ILESERJ1 - 418
d_111ens_1ILESERK3 - 420
d_121ens_1ILESERL2 - 419
d_131ens_1ILESERM3 - 420
d_141ens_1ILESERN1 - 418
d_151ens_1ILESERO2 - 419
d_161ens_1ILESERP3 - 420
d_171ens_1ILESERQ1 - 418
d_181ens_1ILESERR1 - 418
d_191ens_1ILESERS1 - 418
d_201ens_1ILESERT1 - 418
d_211ens_1ILESERU1 - 418
d_221ens_1ILESERV2 - 419

NCS oper:
IDCodeMatrixVector
1given(0.834805138764, -0.549593548816, 0.0323621907855), (0.549324794746, 0.835426105766, 0.0174783203189), (-0.0366421911134, 0.00318636219164, 0.999323369549)135.961416511, -81.1616737224, 6.32057229292
2given(0.410485806203, -0.910650761794, 0.0470807067712), (0.909868017995, 0.412456503079, 0.0449424398333), (-0.0603456107484, 0.024388995708, 0.997879543909)288.967737643, -75.4946756829, 6.44347484973
3given(-0.102173275882, -0.994246729004, 0.0321568586841), (0.991562104717, -0.0991982986512, 0.0834523219254), (-0.0797822924306, 0.040412119589, 0.995992794354)409.120194273, 0.269264871947, 7.73055782386
4given(-0.610152425638, -0.792176331363, -0.0130643605461), (0.787404399361, -0.608139356516, 0.100800966877), (-0.0877970919542, 0.0512170194777, 0.994820831889)477.946820284, 136.614280814, 8.14847195993
5given(-0.946821021661, -0.313646046482, -0.071806061484), (0.309067358644, -0.948596699735, 0.0681297957789), (-0.0894836340384, 0.0423138130875, 0.995089051523)460.105834209, 303.468130264, 11.7845258087
6given(-0.946967656321, 0.308509575222, -0.0898559952292), (-0.309408470434, -0.950920398577, -0.00409804756346), (-0.086710185711, 0.0239214875465, 0.995946336972)339.907731793, 438.374962097, 16.4232236525
7given(-0.670138674052, 0.733328062717, -0.114647764791), (-0.74101929754, -0.669851126885, 0.0467960306357), (-0.042480091951, 0.116316036051, 0.992303391884)208.086725752, 465.272553401, -13.8673974494
8given(-0.168042917166, 0.980340966304, -0.103407774254), (-0.985765156709, -0.16768275412, 0.012229055085), (-0.00535105670529, 0.103990786883, 0.994563865438)58.2279284629, 422.224318583, -19.2084059452
9given(0.429511446622, 0.903017270993, -0.00892891426815), (-0.903060076147, 0.429472796825, -0.00596788546653), (-0.00155437786423, 0.0106266211189, 0.999942327753)-59.1303286011, 290.841103219, 0.643732805975
10given(0.82571244095, 0.561603855104, -0.0529157329434), (-0.563981571947, 0.82376145943, -0.0578086884697), (0.0111243590932, 0.0775768515106, 0.996924310439)-67.6891702393, 154.986117979, -19.0237008353
11given(-0.988128256137, 0.151612213716, -0.0248251097901), (0.152082036148, 0.988199028594, -0.0182683925434), (0.0217624379448, -0.0218269681108, -0.999524877008)376.693848069, -31.8725796776, 115.957971177
12given(-0.790352806585, 0.610871868179, -0.0466690667439), (0.612651858757, 0.788009527138, -0.0608168159461), (-0.000375612756889, -0.0766586316576, -0.997057326891)254.152781322, -80.5736956464, 134.439141825
13given(-0.289415856738, 0.957199431621, -0.00277668382998), (0.957201298315, 0.289407822257, -0.00296427394706), (-0.00203380731697, -0.00351575325106, -0.999991751519)79.6664525892, -59.7677387286, 119.278696226
14given(0.277563378188, 0.960691501326, -0.00551455978869), (0.960479280527, -0.27736785757, 0.023379975752), (0.0209313823721, -0.0117860454699, -0.999711441549)-35.0864238573, 45.7853037851, 117.414977086
15given(0.767862842762, 0.635533002195, 0.0805261313278), (0.637390162679, -0.770533851014, 0.00337119591409), (0.0641906163395, 0.0487379478688, -0.996746796941)-80.863841933, 209.3589762, 93.9804672996
16given(0.984293417833, 0.161683985429, 0.0708855166176), (0.160259425058, -0.986748561346, 0.0253809645543), (0.0740498770459, -0.013622244211, -0.997161496535)-33.5204766402, 343.13363624, 106.510861689
17given(0.919297218894, -0.382816480178, 0.0913464057212), (-0.384306818116, -0.923204406826, -0.00137577837815), (0.0848580749458, -0.0338402972922, -0.995818227085)81.0204851564, 443.930121867, 108.069840501
18given(0.0275967869986, -0.997354858076, 0.0672436199196), (-0.996250711141, -0.032959237457, -0.0799888068193), (0.0819935235094, -0.0647840701006, -0.994525055674)381.525759799, 404.806776596, 113.390672407
19given(-0.578845647868, -0.815195837723, -0.0198358791742), (-0.81218026009, 0.578535062129, -0.0752356764288), (0.0728075618635, -0.0274395343584, -0.996968470359)479.501398118, 245.767012883, 106.038248253
20given(-0.89479693904, -0.446371621841, -0.00952959076477), (-0.444385149932, 0.892470945636, -0.0775722225753), (0.0431309216821, -0.0651765786941, -0.996941190434)472.475112392, 115.069250894, 120.931266015
21given(0.578244118792, -0.809776918611, 0.0994740225775), (-0.810788366145, -0.583938359558, -0.0404749003761), (0.0908623376702, -0.0572480071383, -0.994216626934)230.010083174, 469.394663098, 110.939703282

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Components

#1: Protein ...
Nucleoprotein


Mass: 50641.289 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabies virus CVS-11 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A8VR20
#2: RNA chain RNA (99-MER)


Mass: 31153.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (99-MER)


Mass: 30984.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN

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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: 3.83 Å3/Da / Density % sol: 67.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 60% TACSIMATE, 10% L-CYSTEIN, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 25, 2005
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 3.49→49.75 Å / Num. obs: 226498 / % possible obs: 99.9 % / Redundancy: 1 % / Biso Wilson estimate: 103.61 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.15
Reflection shellResolution: 3.49→3.63 Å / Mean I/σ(I) obs: 3.36 / Num. unique obs: 21091 / Rsym value: 0.457

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
BUSTERrefinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.49→49.75 Å / SU ML: 0.4048 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.7461
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 11055 4.88 %
Rwork0.2237 215443 -
obs0.2253 226498 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.1 Å2
Refinement stepCycle: LAST / Resolution: 3.49→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms73171 4103 10 0 77284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012879511
X-RAY DIFFRACTIONf_angle_d1.3464108344
X-RAY DIFFRACTIONf_chiral_restr0.075711997
X-RAY DIFFRACTIONf_plane_restr0.011613191
X-RAY DIFFRACTIONf_dihedral_angle_d13.545412454
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.03713343265
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.39191104661
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.39793975962
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.28656426339
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS1.21525619101
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS1.27465287969
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS1.49754258061
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS1.12927288833
ens_1d_10AX-RAY DIFFRACTIONTorsion NCS1.15027308195
ens_1d_11AX-RAY DIFFRACTIONTorsion NCS1.4290615434
ens_1d_12AX-RAY DIFFRACTIONTorsion NCS1.12496771739
ens_1d_13AX-RAY DIFFRACTIONTorsion NCS1.57902576876
ens_1d_14AX-RAY DIFFRACTIONTorsion NCS0.950556727271
ens_1d_15AX-RAY DIFFRACTIONTorsion NCS1.1792334758
ens_1d_16AX-RAY DIFFRACTIONTorsion NCS1.08377693245
ens_1d_17AX-RAY DIFFRACTIONTorsion NCS1.41981700661
ens_1d_18AX-RAY DIFFRACTIONTorsion NCS1.1954308707
ens_1d_19AX-RAY DIFFRACTIONTorsion NCS1.43441438373
ens_1d_20AX-RAY DIFFRACTIONTorsion NCS1.26886127925
ens_1d_21AX-RAY DIFFRACTIONTorsion NCS1.53334912821
ens_1d_22AX-RAY DIFFRACTIONTorsion NCS1.18078348888
LS refinement shellResolution: 10.81→49.75 Å
RfactorNum. reflection% reflection
Rfree0.2374 379 -
Rwork0.2311 7464 -
obs--97.6 %
Refinement TLS params.Method: refined / Origin x: 202.620831295 Å / Origin y: 190.11480652 Å / Origin z: 59.4626671576 Å
111213212223313233
T0.846386352269 Å2-0.0187468718448 Å20.0213609611108 Å2-0.761484664636 Å2-0.00807108645615 Å2--0.667045037956 Å2
L0.0509553720839 °2-0.0068919853765 °20.0212251483112 °2-0.0748887927249 °2-0.0767334950694 °2--0.160741692111 °2
S-0.014181492141 Å °-0.0422436101718 Å °-0.0386472205158 Å °0.0607978135913 Å °0.00123730028194 Å °0.0139711461895 Å °0.071666529637 Å °-0.041834922266 Å °0.0114970655449 Å °
Refinement TLS groupSelection details: all

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