[English] 日本語
Yorodumi
- PDB-4idx: hexameric crystal structure of Schmallenberg virus nucleoprotein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4idx
Titlehexameric crystal structure of Schmallenberg virus nucleoprotein
ComponentsNucleocapsid protein
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: _ / 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
11THRTHRTHRTHRBA17 - 22417 - 224
21THRTHRTHRTHRAB17 - 22417 - 224
12THRTHRTHRTHRBA17 - 22417 - 224
22THRTHRTHRTHRCC17 - 22417 - 224
13ALAALAGLNGLNAB16 - 22716 - 227
23ALAALAGLNGLNCC16 - 22716 - 227

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Nucleocapsid protein


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


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more