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- PDB-2wj8: Respiratory Syncitial Virus RiboNucleoProtein -

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Basic information

Entry
Database: PDB / ID: 2wj8
TitleRespiratory Syncitial Virus RiboNucleoProtein
Components
  • NUCLEOPROTEIN
  • RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN RNA COMPLEX / NUCLEOCAPSID (N) / RIBONUCLEOPROTEIN / RESPIRATORY SYNCYTIAL VIRUS (RSV) / VIRAL NUCLEOPROTEIN / TEMPLATE-LIKE ASSEMBLY / RNA / VIRION / COMPLEX / CYTOPLASM / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


Respiratory syncytial virus genome transcription / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / protein serine/threonine kinase inhibitor activity / helical viral capsid / Respiratory syncytial virus genome replication / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry ...Respiratory syncytial virus genome transcription / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / protein serine/threonine kinase inhibitor activity / helical viral capsid / Respiratory syncytial virus genome replication / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / PKR-mediated signaling / Evasion by RSV of host interferon responses / viral capsid / viral nucleocapsid / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / RNA binding
Similarity search - Function
Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
BORATE ION / RNA / Nucleoprotein
Similarity search - Component
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS A STRAIN LONG
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsTawar, R.G. / Duquerroy, S. / Vonrhein, C. / Varela, P.F. / Damier-Piolle, L. / Castagne, N. / MacLellan, K. / Bedouelle, H. / Bricogne, G. / Bhella, D. ...Tawar, R.G. / Duquerroy, S. / Vonrhein, C. / Varela, P.F. / Damier-Piolle, L. / Castagne, N. / MacLellan, K. / Bedouelle, H. / Bricogne, G. / Bhella, D. / Eleouet, J. / Rey, F.A.
Citation
Journal: Science / Year: 2009
Title: Crystal structure of a nucleocapsid-like nucleoprotein-RNA complex of respiratory syncytial virus.
Authors: Rajiv G Tawar / Stéphane Duquerroy / Clemens Vonrhein / Paloma F Varela / Laurence Damier-Piolle / Nathalie Castagné / Kirsty MacLellan / Hugues Bedouelle / Gérard Bricogne / David Bhella ...Authors: Rajiv G Tawar / Stéphane Duquerroy / Clemens Vonrhein / Paloma F Varela / Laurence Damier-Piolle / Nathalie Castagné / Kirsty MacLellan / Hugues Bedouelle / Gérard Bricogne / David Bhella / Jean-François Eléouët / Félix A Rey /
Abstract: The respiratory syncytial virus (RSV) is an important human pathogen, yet neither a vaccine nor effective therapies are available to treat infection. To help elucidate the replication mechanism of ...The respiratory syncytial virus (RSV) is an important human pathogen, yet neither a vaccine nor effective therapies are available to treat infection. To help elucidate the replication mechanism of this RNA virus, we determined the three-dimensional (3D) crystal structure at 3.3 A resolution of a decameric, annular ribonucleoprotein complex of the RSV nucleoprotein (N) bound to RNA. This complex mimics one turn of the viral helical nucleocapsid complex, which serves as template for viral RNA synthesis. The RNA wraps around the protein ring, with seven nucleotides contacting each N subunit, alternating rows of four and three stacked bases that are exposed and buried within a protein groove, respectively. Combined with electron microscopy data, this structure provides a detailed model for the RSV nucleocapsid, in which the bases are accessible for readout by the viral polymerase. Furthermore, the nucleoprotein structure highlights possible key sites for drug targeting.
#1: Journal: J.Virol. / Year: 2007
Title: The 24-Angstrom Structure of Respiratory Syncytial Virus Nucleocapsid Protein-RNA Decameric Rings.
Authors: Maclellan, K. / Loney, C. / Yeo, R.P. / Bhella, D.
History
DepositionMay 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_special_symmetry
Revision 1.3Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.5May 1, 2024Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
a: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
b: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
c: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
d: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
e: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
f: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
g: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
h: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
i: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
j: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
k: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
l: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
m: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
n: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
o: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
p: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
q: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
r: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
s: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
t: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)912,92952
Polymers911,98340
Non-polymers94612
Water12,340685
1
K: NUCLEOPROTEIN
L: NUCLEOPROTEIN
M: NUCLEOPROTEIN
N: NUCLEOPROTEIN
O: NUCLEOPROTEIN
P: NUCLEOPROTEIN
Q: NUCLEOPROTEIN
R: NUCLEOPROTEIN
S: NUCLEOPROTEIN
T: NUCLEOPROTEIN
k: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
l: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
m: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
n: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
o: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
p: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
q: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
r: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
s: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
t: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)456,46526
Polymers455,99220
Non-polymers4736
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area75970 Å2
ΔGint-455.05 kcal/mol
Surface area147400 Å2
MethodPISA
2
A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
E: NUCLEOPROTEIN
F: NUCLEOPROTEIN
G: NUCLEOPROTEIN
H: NUCLEOPROTEIN
I: NUCLEOPROTEIN
J: NUCLEOPROTEIN
a: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
b: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
c: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
d: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
e: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
f: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
g: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
h: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
i: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
j: RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)456,46526
Polymers455,99220
Non-polymers4736
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area75820 Å2
ΔGint-452.47 kcal/mol
Surface area147060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.200, 220.990, 218.100
Angle α, β, γ (deg.)90.00, 93.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-2001-

BO4

21I-2001-

BO4

31O-2001-

BO4

41T-2001-

BO4

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.898076, -0.428888, 0.097529), (0.428709, 0.804014, -0.412026), (0.098295, 0.411854, 0.905939)25.02422, 115.41074, -24.10942
2given(0.634794, -0.69275, 0.342254), (0.693488, 0.31545, -0.647746), (0.340764, 0.648534, 0.680651)-2.36447, 224.1357, 2.21694
3given(0.316302, -0.702916, 0.637077), (0.694719, -0.285672, -0.660121), (0.646003, 0.651381, 0.397972)-69.76667, 292.71124, 67.24315
4given(0.03877, -0.43665, 0.898795), (0.435356, -0.802233, -0.408518), (0.899421, 0.40714, 0.158999)-158.9149, 292.79144, 148.95276
5given(-0.066286, 0.005566, 0.997782), (-0.002468, -0.999981, 0.005415), (0.997794, -0.002103, 0.066298)-230.47574, 220.53116, 215.34981
6given(0.036404, 0.434608, 0.899884), (-0.426183, -0.807737, 0.407343), (0.903904, -0.398349, 0.155815)-255.35376, 107.21156, 238.38187
7given(0.304546, 0.692706, 0.653766), (-0.686417, -0.316251, 0.654836), (0.660364, -0.648187, 0.379173)-226.97728, -3.92357, 214.13055
8given(0.630712, 0.695352, 0.344505), (-0.68862, 0.296833, 0.661582), (0.357768, -0.654505, 0.666052)-156.30705, -72.93071, 148.8253
9given(0.895024, 0.435361, 0.096972), (-0.434082, 0.800233, 0.41376), (0.102533, -0.412414, 0.905211)-70.47168, -71.99734, 67.3136
10given(0.034091, -0.433687, 0.900421), (-0.42821, 0.807723, 0.405245), (-0.90304, -0.399381, -0.158172)-44.26447, -72.44729, 177.26276
11given(-0.07046, 0.004435, 0.997499), (0.001253, 0.999986, -0.004358), (-0.997514, 0.000943, -0.070466)-114.93875, -0.20702, 112.9248
12given(0.031241, 0.423956, 0.905148), (0.416584, 0.817658, -0.397358), (-0.908557, 0.389482, -0.151062)-139.7063, 110.68253, 89.0531
13given(0.295733, 0.695397, 0.654952), (0.690991, 0.317683, -0.649313), (-0.659596, 0.644593, -0.386569)-112.38541, 224.03156, 114.49227
14given(0.633852, 0.698281, 0.332615), (0.688383, -0.313223, -0.654236), (-0.352652, 0.643658, -0.679224)-39.53724, 294.67053, 181.32082
15given(0.897091, 0.432754, 0.089134), (0.429288, -0.805968, -0.407576), (-0.104541, 0.403902, -0.908809)46.16614, 292.36072, 260.64883
16given(0.99999, -0.001009, -0.004393), (-0.001009, -1.000004, 3.9E-5), (-0.004393, -3.5E-5, -0.999994)115.73892, 220.71881, 326.21722
17given(0.900408, -0.4248, 0.09392), (-0.426053, -0.817292, 0.387961), (-0.088048, -0.389338, -0.916879)140.13438, 110.65357, 349.66214
18given(0.632746, -0.696889, 0.337594), (-0.695018, -0.318878, 0.644411), (-0.341442, -0.642389, -0.68612)113.98705, -3.07732, 324.70236
19given(0.309955, -0.70031, 0.643033), (-0.690662, 0.29895, 0.658494), (-0.653395, -0.648222, -0.391014)44.05276, -73.81007, 258.2142

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Components

#1: Protein
NUCLEOPROTEIN / PROTEIN N / NUCLEOCAPSID PROTEIN


Mass: 43507.848 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS A STRAIN LONG
Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03418
#2: RNA chain
RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')


Mass: 2091.315 Da / Num. of mol.: 20 / Source method: isolated from a natural source
Details: NON SPECIFIC RNA FROM CELLULAR ORIGIN BOUND TO THE NUCLEOPROTEIN
Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3)
#3: Chemical
ChemComp-BO4 / BORATE ION


Mass: 78.840 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: BH4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57 %
Description: STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING 24 ANG EM MAP AND PHASES WERE EXTENDED TO 3.3 ANG BY PHASE EXTENSION USING 20-FOLD NCS
Crystal growDetails: 12%MPD, 50MM MGCL2, 100MM TRIS PH 8.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2008
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SAGITALLY FOCUSSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→80 Å / Num. obs: 384943 / % possible obs: 96.9 % / Observed criterion σ(I): -2 / Redundancy: 2.6 % / Biso Wilson estimate: 79.61 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.2
Reflection shellResolution: 3.3→3.47 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 94.7

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
AMoREphasing
MOLREPphasing
BUSTER-TNT2.7.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EMDB ENTRY EMD-1622

Resolution: 3.29→79.18 Å / Cross valid method: RESOLUTION SHELLS / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE TYPES WITHOUT IDEAL-DIST CONTACT DATA, C BO4. THE RNA MOLECULE WAS NON SPECIFICALLY INCORPORATED. EACH BASE WAS MODELED AS A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE TYPES WITHOUT IDEAL-DIST CONTACT DATA, C BO4. THE RNA MOLECULE WAS NON SPECIFICALLY INCORPORATED. EACH BASE WAS MODELED AS A CYTOSINE BUT CORRESPOND TO AN AVERAGE OF FOUR POSSIBLE BASES OF THE GENETIC CODE. C TERMINAL ENDS ARE DISORDERED. NCS RESTRAINT LSSR (-AUTONCS)
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 5094 3.4 %RANDOM
Rwork0.205 ---
obs0.2057 150167 96.65 %-
Displacement parametersBiso mean: 71.43 Å2
Baniso -1Baniso -2Baniso -3
1--12.979 Å20 Å22.6224 Å2
2--26.1085 Å20 Å2
3----13.1294 Å2
Refinement stepCycle: LAST / Resolution: 3.29→79.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58383 2800 60 685 61928
LS refinement shellResolution: 3.29→3.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2592 252 2.42 %
Rwork0.2301 10175 -
all0.2308 10427 -
obs--96.65 %

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