4IDX

hexameric crystal structure of Schmallenberg virus nucleoprotein

> Summary

Summary for 4IDX

Related4IDU
DescriptorNucleocapsid protein
Functional Keywordsnucleoprotein, protects genomic rna, rna replication and transcription, sbv nucleoprotein, dna binding protein
Biological sourceSchmallenberg virus (SBV)
Cellular locationVirion H2AM13
Total number of polymer chains3
Total molecular weight78625.44
Authors
Dong, H.H.,Dong, C.J. (deposition date: 2012-12-13, release date: 2013-04-24, modification date: 2013-10-02)
Primary citation
Dong, H.,Li, P.,Elliott, R.M.,Dong, C.
Structure of Schmallenberg orthobunyavirus nucleoprotein suggests a novel mechanism of genome encapsidation
J.Virol., 87:5593-5601, 2013
PubMed: 23468499
DOI: 10.1128/JVI.00223-13
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.21 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.373326.8%12.2%8.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4idx
no rotation
Molmil generated image of 4idx
rotated about x axis by 90°
Molmil generated image of 4idx
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
B, A, CNucleocapsid proteinpolymer23326208.53
UniProt (H2AM13)
Schmallenberg virus (SBV)
waterwater18.017

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight78625.4
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight78625.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3.21 Å)
Cell axes159.200159.200157.800
Cell angles90.0090.0090.00
SpacegroupI 4 2 2
Resolution limits49.94 - 3.21
the highest resolution shell value3.291 - 3.210
R-factor0.32411
R-work0.32142
the highest resolution shell value0.314
R-free0.37382
the highest resolution shell value0.337
RMSD bond length0.007
RMSD bond angle1.707

Data Collection Statistics

Resolution limits49.94 - 3.21
the highest resolution shell value -
Number of reflections16400
Rmerge_l_obs0.073
the highest resolution shell value0.073
Completeness99.7
Redundancy5.6
the highest resolution shell value5.6
I/sigma(I)2.5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP8.5293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0030529cellular_componentintracellular ribonucleoprotein complex
A0019013cellular_componentviral nucleocapsid
A0003723molecular_functionRNA binding
B0030529cellular_componentintracellular ribonucleoprotein complex
B0019013cellular_componentviral nucleocapsid
B0003723molecular_functionRNA binding
C0030529cellular_componentintracellular ribonucleoprotein complex
C0019013cellular_componentviral nucleocapsid
C0003723molecular_functionRNA binding
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb4idx.ent.gz (217.41 KB)
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all (no-compress)pdb4idx.ent (868.61 KB)
header onlypdb4idx.ent.gz (9.67 KB)
Display
PDBx/mmCIF4idx.cif.gz (258.51 KB)
PDBMLall4idx.xml.gz (396.62 KB)
Display
no-atom4idx-noatom.xml.gz (31.18 KB)
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ext-atom4idx-extatom.xml.gz (118.78 KB)
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PDBMLplusall4idx-plus.xml.gz (397.61 KB)
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no-atom4idx-plus-noatom.xml.gz (32.16 KB)
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add only4idx-add.xml.gz (1006 B)
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RDF4idx.rdf.gz (62.6 KB)
Display
Structure factorsr4idxsf.ent.gz (268.17 KB)
Biological unit (PDB format)4idx.pdb1.gz (209.71 KB) (B,A,C)
*author defined assembly, 3 molecule(s) (trimeric)
Display
4idx.pdb2.gz (69.22 KB) (B)
*software defined assembly, 1 molecule(s) (monomeric)
Display
4idx.pdb3.gz (72.98 KB) (A)
*software defined assembly, 1 molecule(s) (monomeric)
Display
4idx.pdb4.gz (72.5 KB) (C)
*software defined assembly, 1 molecule(s) (monomeric)
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Validation reportsPDF4idx​_validation.pdf.gz (271.56 KB)
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PDF-full4idx​_full​_validation.pdf.gz (312.31 KB)
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XML4idx​_validation.xml.gz (30.42 KB)
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PNG4idx​_multipercentile​_validation.png.gz (149.89 KB)
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SVG4idx​_multipercentile​_validation.svg.gz (943 B)
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Sequence (fasta)4idx​_seq.txt
Display

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