5H07

TNIP2-Ub complex, C2 form

> Summary

Summary for 5H07

DescriptorPolyubiquitin-C, TNFAIP3-interacting protein 2
Functional Keywordscoiled-coil, complex, signal transduction, signaling protein
Biological sourceHomo sapiens (Human)
Cellular locationUbiquitin: Cytoplasm  P0CG48
Cytoplasm  Q8NFZ5
Total number of polymer chains3
Total molecular weight47128.51
Authors
Lo, Y.C.,Lin, S.C. (deposition date: 2016-10-04, release date: 2017-03-08)
Primary citation
Lin, S.M.,Lin, S.C.,Hong, J.Y.,Su, T.W.,Kuo, B.J.,Chang, W.H.,Tu, Y.F.,Lo, Y.C.
Structural Insights into Linear Tri-ubiquitin Recognition by A20-Binding Inhibitor of NF-kappa B, ABIN-2
Structure, 25:66-78, 2017
PubMed: 27916521
DOI: 10.1016/j.str.2016.11.005
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.586 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.272901.5%9.3%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5h07
no rotation
Molmil generated image of 5h07
rotated about x axis by 90°
Molmil generated image of 5h07
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
APolyubiquitin-Cpolymer22825694.51
UniProt (P0CG48)
Pfam (PF00240)
Homo sapiens (Human)
D, CTNFAIP3-interacting protein 2polymer9110717.02
UniProt (Q8NFZ5)
Homo sapiens (Human)A20-binding inhibitor of NF-kappa-B activation 2,ABIN-2,Fetal liver LKB1-interacting protein
waterwater18.098

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight47128.5
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight47128.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.586 Å)

Cell axes98.76580.97265.352
Cell angles90.00114.2890.00
SpacegroupC 1 2 1
Resolution limits19.86 - 2.59
the highest resolution shell value2.689 - 2.586
R-factor0.2177
R-work0.21130
the highest resolution shell value0.230
R-free0.27340
the highest resolution shell value0.283
RMSD bond length0.002
RMSD bond angle0.517

Data Collection Statistics

Resolution limits30.00 - 2.59
the highest resolution shell value -
Number of reflections12803
Completeness99.2
Redundancy3.5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP298

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
C0005829cellular_componentcytosol
C0005634cellular_componentnucleus
C0046872molecular_functionmetal ion binding
C0031593molecular_functionpolyubiquitin binding
C0019901molecular_functionprotein kinase binding
C0006915biological_processapoptotic process
C0023035biological_processCD40 signaling pathway
C0071222biological_processcellular response to lipopolysaccharide
C0007249biological_processI-kappaB kinase/NF-kappaB signaling
C0006954biological_processinflammatory response
C0070498biological_processinterleukin-1-mediated signaling pathway
C2000352biological_processnegative regulation of endothelial cell apoptotic process
C0050871biological_processpositive regulation of B cell activation
C0043123biological_processpositive regulation of I-kappaB kinase/NF-kappaB signaling
C0043032biological_processpositive regulation of macrophage activation
C0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
C0016579biological_processprotein deubiquitination
C0050821biological_processprotein stabilization
C0051403biological_processstress-activated MAPK cascade
C0034134biological_processtoll-like receptor 2 signaling pathway
C0034138biological_processtoll-like receptor 3 signaling pathway
C0034162biological_processtoll-like receptor 9 signaling pathway
C0006351biological_processtranscription, DNA-templated
D0005829cellular_componentcytosol
D0005634cellular_componentnucleus
D0046872molecular_functionmetal ion binding
D0031593molecular_functionpolyubiquitin binding
D0019901molecular_functionprotein kinase binding
D0006915biological_processapoptotic process
D0023035biological_processCD40 signaling pathway
D0071222biological_processcellular response to lipopolysaccharide
D0007249biological_processI-kappaB kinase/NF-kappaB signaling
D0006954biological_processinflammatory response
D0070498biological_processinterleukin-1-mediated signaling pathway
D2000352biological_processnegative regulation of endothelial cell apoptotic process
D0050871biological_processpositive regulation of B cell activation
D0043123biological_processpositive regulation of I-kappaB kinase/NF-kappaB signaling
D0043032biological_processpositive regulation of macrophage activation
D0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
D0016579biological_processprotein deubiquitination
D0050821biological_processprotein stabilization
D0051403biological_processstress-activated MAPK cascade
D0034134biological_processtoll-like receptor 2 signaling pathway
D0034138biological_processtoll-like receptor 3 signaling pathway
D0034162biological_processtoll-like receptor 9 signaling pathway
D0006351biological_processtranscription, DNA-templated
A0005829cellular_componentcytosol
A0030666cellular_componentendocytic vesicle membrane
A0044322cellular_componentendoplasmic reticulum quality control compartment
A0010008cellular_componentendosome membrane
A0070062cellular_componentextracellular exosome
A0005615cellular_componentextracellular space
A0005741cellular_componentmitochondrial outer membrane
A0043209cellular_componentmyelin sheath
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0005886cellular_componentplasma membrane
A0031982cellular_componentvesicle
A0002020molecular_functionprotease binding
A0003723molecular_functionRNA binding
A0000187biological_processactivation of MAPK activity
A0031145biological_processanaphase-promoting complex-dependent catabolic process
A0044267biological_processcellular protein metabolic process
A0042769biological_processDNA damage response, detection of DNA damage
A0006977biological_processDNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
A1904380biological_processendoplasmic reticulum mannose trimming
A0016197biological_processendosomal transport
A0035635biological_processentry of bacterium into host cell
A0038128biological_processERBB2 signaling pathway
A0070987biological_processerror-free translesion synthesis
A0042276biological_processerror-prone translesion synthesis
A0038095biological_processFc-epsilon receptor signaling pathway
A0008543biological_processfibroblast growth factor receptor signaling pathway
A0000086biological_processG2/M transition of mitotic cell cycle
A0070911biological_processglobal genome nucleotide-excision repair
A0005978biological_processglycogen biosynthetic process
A0007249biological_processI-kappaB kinase/NF-kappaB signaling
A0045087biological_processinnate immune response
A0036297biological_processinterstrand cross-link repair
A0075733biological_processintracellular transport of virus
A0034220biological_procession transmembrane transport
A0007254biological_processJNK cascade
A0016236biological_processmacroautophagy
A0000165biological_processMAPK cascade
A0061024biological_processmembrane organization
A0002755biological_processMyD88-dependent toll-like receptor signaling pathway
A0002756biological_processMyD88-independent toll-like receptor signaling pathway
A0043066biological_processnegative regulation of apoptotic process
A0090090biological_processnegative regulation of canonical Wnt signaling pathway
A0042059biological_processnegative regulation of epidermal growth factor receptor signaling pathway
A0010972biological_processnegative regulation of G2/M transition of mitotic cell cycle
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0030512biological_processnegative regulation of transforming growth factor beta receptor signaling pathway
A0032480biological_processnegative regulation of type I interferon production
A0051436biological_processnegative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle
A0038061biological_processNIK/NF-kappaB signaling
A0007219biological_processNotch signaling pathway
A0070423biological_processnucleotide-binding oligomerization domain containing signaling pathway
A0000715biological_processnucleotide-excision repair, DNA damage recognition
A0000717biological_processnucleotide-excision repair, DNA duplex unwinding
A0006297biological_processnucleotide-excision repair, DNA gap filling
A0033683biological_processnucleotide-excision repair, DNA incision
A0006296biological_processnucleotide-excision repair, DNA incision, 5'-to lesion
A0006294biological_processnucleotide-excision repair, preincision complex assembly
A0043065biological_processpositive regulation of apoptotic process
A0090263biological_processpositive regulation of canonical Wnt signaling pathway
A0045742biological_processpositive regulation of epidermal growth factor receptor signaling pathway
A0043123biological_processpositive regulation of I-kappaB kinase/NF-kappaB signaling
A0051092biological_processpositive regulation of NF-kappaB transcription factor activity
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0051437biological_processpositive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition
A0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
A0016579biological_processprotein deubiquitination
A0006457biological_processprotein folding
A0000209biological_processprotein polyubiquitination
A0016567biological_processprotein ubiquitination
A0042787biological_processprotein ubiquitination involved in ubiquitin-dependent protein catabolic process
A0043488biological_processregulation of mRNA stability
A0060544biological_processregulation of necroptotic process
A1901796biological_processregulation of signal transduction by p53 class mediator
A0061418biological_processregulation of transcription from RNA polymerase II promoter in response to hypoxia
A0010803biological_processregulation of tumor necrosis factor-mediated signaling pathway
A0032479biological_processregulation of type I interferon production
A0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
A0002223biological_processstimulatory C-type lectin receptor signaling pathway
A0051403biological_processstress-activated MAPK cascade
A0050852biological_processT cell receptor signaling pathway
A0006283biological_processtranscription-coupled nucleotide-excision repair
A0007179biological_processtransforming growth factor beta receptor signaling pathway
A0019985biological_processtranslesion synthesis
A0055085biological_processtransmembrane transport
A0035666biological_processTRIF-dependent toll-like receptor signaling pathway
A0033209biological_processtumor necrosis factor-mediated signaling pathway
A0010992biological_processubiquitin homeostasis
A0019058biological_processviral life cycle
A0019068biological_processvirion assembly
A0016055biological_processWnt signaling pathway
A0060071biological_processWnt signaling pathway, planar cell polarity pathway
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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
SWS_FT_FI12Activating enzyme.
ChainResidueDetails
AARG54
AARG72

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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