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- PDB-2mro: Structure of the complex of ubiquitin and the UBA domain from DNA... -

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Basic information

Entry
Database: PDB / ID: 2mro
TitleStructure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1)
Components
  • DNA damage-inducible protein 1
  • Polyubiquitin-B
KeywordsTRANSPORT PROTEIN/SIGNALING PROTEIN / DNA-damage-inducible 1 protein / Ubiquitin associated domain / Ddi1 / UBA / HYDROLASE-SIGNALING PROTEIN complex / TRANSPORT PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / female gonad development / seminiferous tubule development ...proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / polyubiquitin modification-dependent protein binding / protein secretion / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / vesicle-mediated transport / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / SNARE binding / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / positive regulation of DNA replication / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling
Similarity search - Function
DNA damage inducible protein 1 ubiquitin-like domain / Aspartic peptidase, DDI1-type / Aspartyl protease / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 ...DNA damage inducible protein 1 ubiquitin-like domain / Aspartic peptidase, DDI1-type / Aspartyl protease / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Peptidase A2A, retrovirus, catalytic / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Aspartic peptidase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polyubiquitin-B / DNA damage-inducible protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsZhang, D. / Fushman, D.
CitationJournal: Structure / Year: 2015
Title: DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin.
Authors: Nowicka, U. / Zhang, D. / Walker, O. / Krutauz, D. / Castaneda, C.A. / Chaturvedi, A. / Chen, T.Y. / Reis, N. / Glickman, M.H. / Fushman, D.
History
DepositionJul 14, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Experimental preparation
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_related.db_name / _pdbx_nmr_sample_details.contents ..._pdbx_database_related.db_name / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyubiquitin-B
B: DNA damage-inducible protein 1


Theoretical massNumber of molelcules
Total (without water)13,3222
Polymers13,3222
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-6 kcal/mol
Surface area7120 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Polyubiquitin-B / Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: Human Ubiquitin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0CG47
#2: Protein/peptide DNA damage-inducible protein 1 / v-SNARE-master 1


Mass: 4745.367 Da / Num. of mol.: 1 / Fragment: Ubiquitin associated domain, UNP residues 389-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DDI1, VSM1, YER143W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P40087

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Complex structure based on chemical shift perturbation data and spin-labeling data, calculated using Haddock program
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
NMR detailsText: Two titration experiments were conducted. Basically unlabeled ligand protein was added stepwise to N15-Labeled protein solution.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] Ub-1, 20 mM sodium phosphate-2, 7 % [U-99% 2H] D2O-3, 93 % H2O-4, 93% H2O/7% D2O93% H2O/7% D2O
21 mM [U-100% 15N] UBA-5, 20 mM sodium phosphate-6, 7 % [U-99% 2H] D2O-7, 93 % H2O-8, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMUb-1[U-100% 15N]1
20 mMsodium phosphate-21
7 %D2O-3[U-99% 2H]1
93 %H2O-41
1 mMUBA-5[U-100% 15N]2
20 mMsodium phosphate-62
7 %D2O-7[U-99% 2H]2
93 %H2O-82
Sample conditionsIonic strength: 20 / pH: 6.8 / Pressure: ambient / Temperature: 298.2 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.8.1Keller and Wuthrichchemical shift assignment
HADDOCK2.1Alexandre Bonvingeometry optimization
HADDOCK2.1Alexandre Bonvinrefinement
HADDOCK2.1Alexandre Bonvinstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 10 / Conformers submitted total number: 10

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