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- PDB-3zla: Crystal structure of the nucleocapsid protein from Bunyamwera vir... -

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Basic information

Entry
Database: PDB / ID: 3zla
TitleCrystal structure of the nucleocapsid protein from Bunyamwera virus bound to RNA
Components
  • NUCLEOPROTEIN
  • RNA
KeywordsVIRAL PROTEIN/RNA / VIRAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


helical viral capsid / symbiont-mediated suppression of host gene expression / 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
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesBUNYAMWERA VIRUS
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAriza, A. / Tanner, S.J. / Walter, C.T. / Dent, K.C. / Shepherd, D.A. / Wu, W. / Matthews, S.V. / Hiscox, J.A. / Green, T.J. / Luo, M. ...Ariza, A. / Tanner, S.J. / Walter, C.T. / Dent, K.C. / Shepherd, D.A. / Wu, W. / Matthews, S.V. / Hiscox, J.A. / Green, T.J. / Luo, M. / Elliot, R.M. / Ashcroft, A.E. / Stonehouse, N.J. / Ranson, N.A. / Barr, J.N. / Edwards, T.A.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Nucleocapsid Protein Structures from Orthobunyaviruses Reveal Insight Into Ribonucleoprotein Architecture and RNA Polymerization.
Authors: Ariza, A. / Tanner, S.J. / Walter, C.T. / Dent, K.C. / Shepherd, D.A. / Wu, W. / Matthews, S.V. / Hiscox, J.A. / Green, T.J. / Luo, M. / Elliott, R.M. / Fooks, A.R. / Ashcroft, A.E. / ...Authors: Ariza, A. / Tanner, S.J. / Walter, C.T. / Dent, K.C. / Shepherd, D.A. / Wu, W. / Matthews, S.V. / Hiscox, J.A. / Green, T.J. / Luo, M. / Elliott, R.M. / Fooks, A.R. / Ashcroft, A.E. / Stonehouse, N.J. / Ranson, N.A. / Barr, J.N. / Edwards, T.A.
History
DepositionJan 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Dec 17, 2014Group: Data collection
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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
A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
E: NUCLEOPROTEIN
F: NUCLEOPROTEIN
G: NUCLEOPROTEIN
H: NUCLEOPROTEIN
I: RNA
J: RNA


Theoretical massNumber of molelcules
Total (without water)241,59610
Polymers241,59610
Non-polymers00
Water00
1
E: NUCLEOPROTEIN
F: NUCLEOPROTEIN
G: NUCLEOPROTEIN
H: NUCLEOPROTEIN
J: RNA


Theoretical massNumber of molelcules
Total (without water)120,7985
Polymers120,7985
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20560 Å2
ΔGint-181.9 kcal/mol
Surface area44490 Å2
MethodPISA
2
A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
I: RNA


Theoretical massNumber of molelcules
Total (without water)120,7985
Polymers120,7985
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20050 Å2
ΔGint-184.7 kcal/mol
Surface area44900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)382.240, 88.724, 88.790
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H
129I
229J

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASNASNAA-1 - 2321 - 234
21GLYGLYASNASNBB-1 - 2321 - 234
12GLYGLYASNASNAA-1 - 2321 - 234
22GLYGLYASNASNCC-1 - 2321 - 234
13GLYGLYASNASNAA-1 - 2321 - 234
23GLYGLYASNASNDD-1 - 2321 - 234
14GLYGLYASNASNAA-1 - 2321 - 234
24GLYGLYASNASNEE-1 - 2321 - 234
15GLYGLYASNASNAA-1 - 2321 - 234
25GLYGLYASNASNFF-1 - 2321 - 234
16GLYGLYASNASNAA-1 - 2321 - 234
26GLYGLYASNASNGG-1 - 2321 - 234
17GLYGLYASNASNAA-1 - 2321 - 234
27GLYGLYASNASNHH-1 - 2321 - 234
18GLYGLYASNASNBB-1 - 2321 - 234
28GLYGLYASNASNCC-1 - 2321 - 234
19GLYGLYASNASNBB-1 - 2321 - 234
29GLYGLYASNASNDD-1 - 2321 - 234
110GLYGLYASNASNBB-1 - 2321 - 234
210GLYGLYASNASNEE-1 - 2321 - 234
111GLYGLYASNASNBB-1 - 2321 - 234
211GLYGLYASNASNFF-1 - 2321 - 234
112GLYGLYASNASNBB-1 - 2321 - 234
212GLYGLYASNASNGG-1 - 2321 - 234
113GLYGLYASNASNBB-1 - 2321 - 234
213GLYGLYASNASNHH-1 - 2321 - 234
114GLYGLYASNASNCC-1 - 2321 - 234
214GLYGLYASNASNDD-1 - 2321 - 234
115GLYGLYASNASNCC-1 - 2321 - 234
215GLYGLYASNASNEE-1 - 2321 - 234
116GLYGLYASNASNCC-1 - 2321 - 234
216GLYGLYASNASNFF-1 - 2321 - 234
117GLYGLYASNASNCC-1 - 2321 - 234
217GLYGLYASNASNGG-1 - 2321 - 234
118GLYGLYASNASNCC-1 - 2321 - 234
218GLYGLYASNASNHH-1 - 2321 - 234
119GLYGLYASNASNDD-1 - 2321 - 234
219GLYGLYASNASNEE-1 - 2321 - 234
120GLYGLYASNASNDD-1 - 2321 - 234
220GLYGLYASNASNFF-1 - 2321 - 234
121GLYGLYASNASNDD-1 - 2321 - 234
221GLYGLYASNASNGG-1 - 2321 - 234
122GLYGLYASNASNDD-1 - 2321 - 234
222GLYGLYASNASNHH-1 - 2321 - 234
123GLYGLYASNASNEE-1 - 2321 - 234
223GLYGLYASNASNFF-1 - 2321 - 234
124GLYGLYASNASNEE-1 - 2321 - 234
224GLYGLYASNASNGG-1 - 2321 - 234
125GLYGLYASNASNEE-1 - 2321 - 234
225GLYGLYASNASNHH-1 - 2321 - 234
126GLYGLYASNASNFF-1 - 2321 - 234
226GLYGLYASNASNGG-1 - 2321 - 234
127GLYGLYASNASNFF-1 - 2321 - 234
227GLYGLYASNASNHH-1 - 2321 - 234
128GLYGLYASNASNGG-1 - 2321 - 234
228GLYGLYASNASNHH-1 - 2321 - 234
129UUUUII1 - 441 - 44
229UUUUJJ1 - 441 - 44

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29

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Components

#1: Protein
NUCLEOPROTEIN / NUCLEOCAPSID PROTEIN / PROTEIN N / BUNV NUCLEOCAPSID PROTEIN


Mass: 26842.889 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BUNYAMWERA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: P16495
#2: RNA chain RNA


Mass: 13426.333 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE SINGLE-STRANDED RNA CHAINS WERE SEQUESTRED BY THE NUCLEOCAPSID PROTEIN FROM THE E. COLI EXPRESSION ORGANISM. AS A RESULT THEY DISPLAY RANDOM SEQUENCES AND WERE THEREFORE BUILT AS POLY-U CHAINS.
Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: CODONPLUS-RIL / Strain: BL21(DE3)
Sequence detailsTHE INITIAL TWO AMINO ACIDS (GS) ARE THE REMNANTS OF CUTTING AN N-TERMINAL 6-HIS TAG OFF VIA A ...THE INITIAL TWO AMINO ACIDS (GS) ARE THE REMNANTS OF CUTTING AN N-TERMINAL 6-HIS TAG OFF VIA A THROMBIN CLEAVAGE SITE.

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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: 3.55 Å3/Da / Density % sol: 65.37 %
Description: THE MOLECULAR REPLACEMENT MODEL WAS THE SBV NUCLEOCAPSID PROTEIN DETERMINED USING SAD FROM SELENOMETHIONINE-SUBSTITUTED PROTEIN
Crystal growpH: 5.7
Details: CRYSTALLISATION CONDITION: 11% PEG6000, 0.1 M SODIUM CITRATE PH 5.7, 4 M NACL, 4 MM ZINC ACETATE. CRYO CONDITION: 10% GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.12667
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2011 / Details: SLITS AND COLLIMATOR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12667 Å / Relative weight: 1
ReflectionResolution: 3.2→190.58 Å / Num. obs: 47586 / % possible obs: 96.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SBV NUCLEOCAPSID PROTEIN

Resolution: 3.2→88.7 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 38.404 / SU ML: 0.589 / Cross valid method: THROUGHOUT / ESU R Free: 0.597 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29676 2383 5.1 %RANDOM
Rwork0.24681 ---
obs0.24939 44762 95.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 136.886 Å2
Baniso -1Baniso -2Baniso -3
1--8.88 Å20 Å20.94 Å2
2--2.81 Å20 Å2
3---5.93 Å2
Refinement stepCycle: LAST / Resolution: 3.2→88.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14811 1760 0 0 16571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01917097
X-RAY DIFFRACTIONr_bond_other_d0.0030.0215475
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.88123457
X-RAY DIFFRACTIONr_angle_other_deg0.991335797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.22651815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.63223.333672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.109152728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3641596
X-RAY DIFFRACTIONr_chiral_restr0.0810.22591
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217529
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023839
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A142250.02
12B142250.02
21A142230.02
22C142230.02
31A141370.03
32D141370.03
41A142230.02
42E142230.02
51A142240.03
52F142240.03
61A142350.02
62G142350.02
71A141970.02
72H141970.02
81B142140.03
82C142140.03
91B141440.03
92D141440.03
101B142220.02
102E142220.02
111B142240.02
112F142240.02
121B142350.01
122G142350.01
131B142010.01
132H142010.01
141C141450.02
142D141450.02
151C142170.02
152E142170.02
161C142260.02
162F142260.02
171C142150.03
172G142150.03
181C141790.03
182H141790.03
191D141410.02
192E141410.02
201D141540.02
202F141540.02
211D141420.03
212G141420.03
221D141070.03
222H141070.03
231E142340.02
232F142340.02
241E142310.02
242G142310.02
251E141970.02
252H141970.02
261F142370.02
262G142370.02
271F142000.02
272H142000.02
281G142090
282H142090
291I33540.11
292J33540.11
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 149 -
Rwork0.407 3435 -
obs--98.84 %

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