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- PDB-8t48: The N4BP1 CUE-like domain in complex with linear di-Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 8t48
TitleThe N4BP1 CUE-like domain in complex with linear di-Ubiquitin
Components
  • Di-Ubiquitin
  • NEDD4-binding protein 1
KeywordsPROTEIN BINDING / N4BP1 / Ubiquitin / CUE-like
Function / homology
Function and homology information


negative regulation of cytokine production / negative regulation of viral genome replication / regulation of innate immune response / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / RNA nuclease activity / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion ...negative regulation of cytokine production / negative regulation of viral genome replication / regulation of innate immune response / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / RNA nuclease activity / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / SCF-beta-TrCP mediated degradation of Emi1 / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR3 signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR2 signaling / Degradation of DVL / Peroxisomal protein import / Negative regulation of FGFR4 signaling / Stabilization of p53 / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR1 signaling / EGFR downregulation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Termination of translesion DNA synthesis / Degradation of AXIN / Regulation of TNFR1 signaling / Hh mutants are degraded by ERAD / ubiquitin binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
Similarity search - Function
: / N4BP1, UBA-like domain / : / : / : / N4BP1, first type I KH-domain / N4BP1, second type I KH-domain / N4BP1, C-terminal UBA domain / Ribonuclease Zc3h12a-like, NYN domain / : ...: / N4BP1, UBA-like domain / : / : / : / N4BP1, first type I KH-domain / N4BP1, second type I KH-domain / N4BP1, C-terminal UBA domain / Ribonuclease Zc3h12a-like, NYN domain / : / Zc3h12a-like Ribonuclease NYN domain / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / NEDD4-binding protein 1 / Polyubiquitin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchubert, A.F. / Harris, S.F.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: Immunity / Year: 2024
Title: N4BP1 coordinates ubiquitin-dependent crosstalk within the I kappa B kinase family to limit Toll-like receptor signaling and inflammation.
Authors: Gitlin, A.D. / Maltzman, A. / Kanno, Y. / Heger, K. / Reja, R. / Schubert, A.F. / Wierciszewski, L.J. / Pantua, H. / Kapadia, S.B. / Harris, S.F. / Webster, J.D. / Newton, K. / Dixit, V.M.
History
DepositionJun 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 29, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Di-Ubiquitin
B: Di-Ubiquitin
C: NEDD4-binding protein 1
D: NEDD4-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1786
Polymers54,0794
Non-polymers992
Water7,746430
1
A: Di-Ubiquitin
D: NEDD4-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1323
Polymers27,0402
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-9 kcal/mol
Surface area11020 Å2
MethodPISA
2
B: Di-Ubiquitin
C: NEDD4-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0473
Polymers27,0402
Non-polymers71
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-11 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.789, 118.716, 50.695
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Di-Ubiquitin


Mass: 19307.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Linear di-Ubiquitin / Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein NEDD4-binding protein 1 / N4BP1


Mass: 7732.659 Da / Num. of mol.: 2 / Fragment: CUE-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: N4BP1, KIAA0615 / Production host: Escherichia coli (E. coli)
References: UniProt: O75113, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH 8.5, 30% (w/v) PEG 4K, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→46.6 Å / Num. obs: 28171 / % possible obs: 97.18 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.08698 / Net I/σ(I): 11.52
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 0.4762 / Num. unique obs: 2751

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.6 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 1277 4.6 %
Rwork0.1603 --
obs0.1629 27741 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 7 430 3709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073675
X-RAY DIFFRACTIONf_angle_d0.8644997
X-RAY DIFFRACTIONf_dihedral_angle_d7.9353387
X-RAY DIFFRACTIONf_chiral_restr0.055568
X-RAY DIFFRACTIONf_plane_restr0.006674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.28291700.20822920X-RAY DIFFRACTION98
2.0801-2.17480.26961510.1832942X-RAY DIFFRACTION98
2.1748-2.28940.23281450.16812922X-RAY DIFFRACTION98
2.2894-2.43290.21621100.17153016X-RAY DIFFRACTION98
2.4329-2.62070.23751330.16742961X-RAY DIFFRACTION98
2.6207-2.88450.25571050.17552957X-RAY DIFFRACTION97
2.8845-3.30180.22361420.16462957X-RAY DIFFRACTION98
3.3018-4.15980.2011690.13152876X-RAY DIFFRACTION96
4.1598-46.60.17261520.14892913X-RAY DIFFRACTION95

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