1LJ2

Recognition of eIF4G by Rotavirus NSP3 reveals a basis for mRNA circularization

> Summary

Summary for 1LJ2

DescriptorNONSTRUCTURAL RNA-BINDING PROTEIN 34/eukaryotic protein synthesis initiation factor
Functional Keywordsnsp3; homodimer; eif4g; rotavirus; translation; mrna; closed loop; coiled coil, viral protein- translation complex, viral protein/ translation
Biological sourceSimian rotavirus A/SA11
More
Total number of polymer chains4
Total molecular weight32683.28
Authors
Groft, C.M.,Burley, S.K. (deposition date: 2002-04-18, release date: 2002-07-05, Last modification date: 2009-02-24)
Primary citation
Groft, C.M.,Burley, S.K.
Recognition of eIF4G by rotavirus NSP3 reveals a basis for mRNA circularization.
Mol.Cell, 9:1273-1283, 2002
PubMed: 12086624
DOI: 10.1016/S1097-2765(02)00555-5
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.38 Å)
?

Structure validation

ClashscoreRamachandran outliersSidechain outliers140.4%2.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1lj2
no rotation
Molmil generated image of 1lj2
rotated about x axis by 90°
Molmil generated image of 1lj2
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BNONSTRUCTURAL RNA-BINDING PROTEIN 34polymer11012842.52
UniProt (P03536)
Simian rotavirus A/SA11NSP3-C; NS34; NCVP4; non-structural protein NCVP4
C, Deukaryotic protein synthesis initiation factorpolymer283203.72
UniProt (Q04637)
eIF4GI
GOLD IONnon-polymer197.03
waterwater18.0196

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight32092.4
Non-Polymers*Number of molecules3
Total molecular weight590.9
All*Total molecular weight32683.3
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.38 Å)

Cell axes59.69074.04077.460
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits20.00 - 2.38
the highest resolution shell value -
R-work0.22100
R-free0.27200
RMSD bond length0.006
RMSD bond angle1.010

Data Collection Statistics

Resolution limits20.00 - 2.38
the highest resolution shell value -
Number of reflections24286 (26797*)
Number of measurements110178*
Rmerge_l_obs0.074*
the highest resolution shell value0.316*
Completeness99.9
the highest resolution shell value99.9*
I/sigma(I)1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP275 (4*)*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11reservoirPEG550 MME17 (%)
21reservoirglucose2.5 (%(w/v))
31reservoirtheophylline1.5 (mM)
41dropprotein7 (mg/ml)
Annotated Information is extracted from Literature Info*

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0016281cellular_componenteukaryotic translation initiation factor 4F complex
C0016020cellular_componentmembrane
C0005634cellular_componentnucleus
C0005844cellular_componentpolysome
C0005524molecular_functionATP binding
C0045296molecular_functioncadherin binding
C0008190molecular_functioneukaryotic initiation factor 4E binding
C0003729molecular_functionmRNA binding
C0032947molecular_functionprotein complex scaffold
C0003723molecular_functionRNA binding
C0008135molecular_functiontranslation factor activity, RNA binding
C0003743molecular_functiontranslation initiation factor activity
C0031369molecular_functiontranslation initiation factor binding
C0001662biological_processbehavioral fear response
C0002191biological_processcap-dependent translational initiation
C0034645biological_processcellular macromolecule biosynthetic process
C0032502biological_processdevelopmental process
C0007005biological_processmitochondrion organization
C0010507biological_processnegative regulation of autophagy
C1901215biological_processnegative regulation of neuron death
C0010801biological_processnegative regulation of peptidyl-threonine phosphorylation
C0000184biological_processnuclear-transcribed mRNA catabolic process, nonsense-mediated decay
C0000289biological_processnuclear-transcribed mRNA poly(A) tail shortening
C0030307biological_processpositive regulation of cell growth
C0008284biological_processpositive regulation of cell proliferation
C0032270biological_processpositive regulation of cellular protein metabolic process
C2000507biological_processpositive regulation of energy homeostasis
C1905537biological_processpositive regulation of eukaryotic translation initiation factor 4F complex assembly
C1900087biological_processpositive regulation of G1/S transition of mitotic cell cycle
C1905618biological_processpositive regulation of miRNA mediated inhibition of translation
C1905612biological_processpositive regulation of mRNA cap binding
C0045666biological_processpositive regulation of neuron differentiation
C0033138biological_processpositive regulation of peptidyl-serine phosphorylation
C0080135biological_processregulation of cellular response to stress
C0060964biological_processregulation of gene silencing by miRNA
C0043488biological_processregulation of mRNA stability
C1905696biological_processregulation of polysome binding
C1905606biological_processregulation of presynapse assembly
C0006446biological_processregulation of translational initiation
C0006412biological_processtranslation
C0006413biological_processtranslational initiation
C0016032biological_processviral process
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0016281cellular_componenteukaryotic translation initiation factor 4F complex
D0016020cellular_componentmembrane
D0005634cellular_componentnucleus
D0005844cellular_componentpolysome
D0005524molecular_functionATP binding
D0045296molecular_functioncadherin binding
D0008190molecular_functioneukaryotic initiation factor 4E binding
D0003729molecular_functionmRNA binding
D0032947molecular_functionprotein complex scaffold
D0003723molecular_functionRNA binding
D0008135molecular_functiontranslation factor activity, RNA binding
D0003743molecular_functiontranslation initiation factor activity
D0031369molecular_functiontranslation initiation factor binding
D0001662biological_processbehavioral fear response
D0002191biological_processcap-dependent translational initiation
D0034645biological_processcellular macromolecule biosynthetic process
D0032502biological_processdevelopmental process
D0007005biological_processmitochondrion organization
D0010507biological_processnegative regulation of autophagy
D1901215biological_processnegative regulation of neuron death
D0010801biological_processnegative regulation of peptidyl-threonine phosphorylation
D0000184biological_processnuclear-transcribed mRNA catabolic process, nonsense-mediated decay
D0000289biological_processnuclear-transcribed mRNA poly(A) tail shortening
D0030307biological_processpositive regulation of cell growth
D0008284biological_processpositive regulation of cell proliferation
D0032270biological_processpositive regulation of cellular protein metabolic process
D2000507biological_processpositive regulation of energy homeostasis
D1905537biological_processpositive regulation of eukaryotic translation initiation factor 4F complex assembly
D1900087biological_processpositive regulation of G1/S transition of mitotic cell cycle
D1905618biological_processpositive regulation of miRNA mediated inhibition of translation
D1905612biological_processpositive regulation of mRNA cap binding
D0045666biological_processpositive regulation of neuron differentiation
D0033138biological_processpositive regulation of peptidyl-serine phosphorylation
D0080135biological_processregulation of cellular response to stress
D0060964biological_processregulation of gene silencing by miRNA
D0043488biological_processregulation of mRNA stability
D1905696biological_processregulation of polysome binding
D1905606biological_processregulation of presynapse assembly
D0006446biological_processregulation of translational initiation
D0006412biological_processtranslation
D0006413biological_processtranslational initiation
D0016032biological_processviral process
A0003723molecular_functionRNA binding
A0006417biological_processregulation of translation
A0039657biological_processsuppression by virus of host gene expression
B0003723molecular_functionRNA binding
B0006417biological_processregulation of translation
B0039657biological_processsuppression by virus of host gene expression
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC13BINDING SITE FOR RESIDUE AU D 1
ChainResidue
AHOH1101
DGLY149
DHOH1100

AC21BINDING SITE FOR RESIDUE AU B 2
ChainResidue
BSER208

AC31BINDING SITE FOR RESIDUE AU B 3
ChainResidue
BHOH1223

?

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

site_idNumber of ResiduesDetails
?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
?

Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2017 Protein Data Bank Japan