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- PDB-4idx: hexameric crystal structure of Schmallenberg virus nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 4idx
Titlehexameric crystal structure of Schmallenberg virus nucleoprotein
ComponentsNucleocapsid proteinVirus
KeywordsDNA BINDING PROTEIN / nucleoprotein / Protects genomic RNA / RNA replication and transcription / SBV nucleoprotein
Function / homology
Function and homology information


viral nucleocapsid / ribonucleoprotein complex / RNA binding
Similarity search - Function
Bunyavirus nucleocapsid (N) protein, C-terminal domain / Poly(ADP-ribose) Polymerase; domain 1 - #20 / Bunyavirus nucleocapsid (N) protein / Bunyavirus nucleocapsid (N) , C-terminal domain / Bunyavirus nucleocapsid (N) , N-terminal domain / Bunyavirus nucleocapsid (N) protein / Poly(ADP-ribose) Polymerase; domain 1 / Cyclin A; domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSchmallenberg virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsDong, H. / Dong, C.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of Schmallenberg orthobunyavirus nucleoprotein suggests a novel mechanism of genome encapsidation
Authors: Dong, H. / Li, P. / Elliott, R.M. / Dong, C.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Dec 4, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Nov 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Nucleocapsid protein
A: Nucleocapsid protein
C: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)78,6253
Polymers78,6253
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)26,2081
Polymers26,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)26,2081
Polymers26,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)26,2081
Polymers26,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.200, 159.200, 157.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13A
23C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHRBA17 - 22417 - 224
21THRTHRTHRTHRAB17 - 22417 - 224
12THRTHRTHRTHRBA17 - 22417 - 224
22THRTHRTHRTHRCC17 - 22417 - 224
13ALAALAGLNGLNAB16 - 22716 - 227
23ALAALAGLNGLNCC16 - 22716 - 227

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Nucleocapsid protein / Virus


Mass: 26208.291 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schmallenberg virus / Gene: N / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: H2AM13
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.075M Tris, 1.5M ammonium sulphate, 25% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9919 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 20, 2012
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 3.21→49.94 Å / Num. all: 16505 / Num. obs: 16400 / % possible obs: 99.7 % / Observed criterion σ(F): 2.08 / Observed criterion σ(I): 2.5 / Redundancy: 5.6 % / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.072 / Net I/σ(I): 2
Reflection shellResolution: 3.21→3.28 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1080 / Rsym value: 0.683 / % possible all: 99.9

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASESphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IDU

4idu


Resolution: 3.21→49.94 Å / Cor.coef. Fo:Fc: 0.837 / Cor.coef. Fo:Fc free: 0.741 / SU B: 108.953 / SU ML: 0.735 / Cross valid method: THROUGHOUT / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.37382 853 5 %RANDOM
Rwork0.32142 ---
obs0.32411 16050 99.78 %-
all-16500 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.028 Å2
Baniso -1Baniso -2Baniso -3
1--4.56 Å2-0 Å2-0 Å2
2---4.56 Å2-0 Å2
3---9.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.03 Å0.02 Å
Luzzati d res low-4 Å
Luzzati sigma a0.4 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 3.21→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5055 0 0 17 5072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.025188
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9347024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.8175637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19223.886229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.37315861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3311522
X-RAY DIFFRACTIONr_chiral_restr0.1220.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213930
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B1850.38
12A1850.38
21B1780.34
22C1780.34
31A1740.36
32C1740.36
LS refinement shellResolution: 3.21→3.291 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 62 -
Rwork0.314 1143 -
obs-1080 97.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.49420.32-0.48151.1053-0.45050.5072-0.02660.0091-0.0253-0.06820.01280.120.05520.05170.01380.22880.0112-0.04190.2543-0.03860.1028-5.6135-51.8327-50.8674
20.25220.06280.24640.4918-0.23530.50330.0740.02430.0240.0010.04440.07280.10270.0159-0.11850.2576-0.0059-0.04950.18970.01140.13936.8115-27.5678-24.5824
31.28290.05620.3010.7413-0.39640.3341-0.0882-0.0509-0.0638-0.08730.09280.02850.1108-0.019-0.00460.28440.10380.00060.1682-0.03560.122727.2448-52.2387-7.223
40.63430.15560.25350.09760.02550.1528-0.05330.00380.07120.03660.0195-0.00280.0355-0.03850.03380.2894-0.0328-0.03320.1618-0.07020.04596.3845-53.6694-30.5814
554.446289.7286-37.8408157.8069-61.933926.3184-0.333-0.81710.5278-1.68480.8931-1.39370.1140.6672-0.56010.2735-0.28260.21950.7257-0.3720.764422.5125-4.5703-3.3631
60.005-0.11490.23953.2521-6.812114.5007-0.0314-0.0110.0205-0.3286-0.2907-0.310.63260.33020.32210.1549-0.11620.14880.58830.05790.4339-23.4265-72.7405-71.4159
70.06370.8372-0.76111.5295-10.47189.5114-0.06170.03270.0722-0.65070.85480.87650.5942-0.7676-0.79310.13860.1092-0.10430.4320.08980.27016.9491-73.7672-25.2086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 219
2X-RAY DIFFRACTION2B17 - 224
3X-RAY DIFFRACTION3C16 - 223
4X-RAY DIFFRACTION4A301 - 307
5X-RAY DIFFRACTION4B301 - 303
6X-RAY DIFFRACTION4C301 - 307
7X-RAY DIFFRACTION5B225
8X-RAY DIFFRACTION6A220 - 228
9X-RAY DIFFRACTION7C224 - 228

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