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- PDB-2rr9: The solution structure of the K63-Ub2:tUIMs complex -

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Basic information

Entry
Database: PDB / ID: 2rr9
TitleThe solution structure of the K63-Ub2:tUIMs complex
Components
  • Putative uncharacterized protein UIMC1
  • ubiquitin
KeywordsNUCLEAR PROTEIN / Lys63-linked diubiquitin / ubiquitin-interacting motif / ubiquitin / Rap80 / DNA repair
Function / homology
Function and homology information


: / BRCA1-A complex / ubiquitin-modified histone reader activity / mitotic G2/M transition checkpoint / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / mitotic G2 DNA damage checkpoint signaling / regulation of DNA repair / Maturation of protein E ...: / BRCA1-A complex / ubiquitin-modified histone reader activity / mitotic G2/M transition checkpoint / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / mitotic G2 DNA damage checkpoint signaling / regulation of DNA repair / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of DNA repair / 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 / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / 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 / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Termination of translesion DNA synthesis / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Nonhomologous End-Joining (NHEJ) / Hedgehog ligand biogenesis
Similarity search - Function
BRCA1-A complex subunit RAP80 / RAP80, N-terminal / RAP80 N-terminal ubiquitin interaction motif / Ubiquitin-interacting motif. / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site ...BRCA1-A complex subunit RAP80 / RAP80, N-terminal / RAP80 N-terminal ubiquitin interaction motif / Ubiquitin-interacting motif. / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / Polyubiquitin-C / BRCA1-A complex subunit RAP80
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 1
AuthorsSekiyama, N. / Jee, J. / Isogai, S. / Akagi, K. / Huang, T. / Ariyoshi, M. / Tochio, H. / Shirakawa, M.
CitationJournal: To be Published
Title: The solution structure of the K63-Ub2:tUIMs complex
Authors: Sekiyama, N. / Jee, J. / Isogai, S. / Akagi, K. / Huang, T. / Ariyoshi, M. / Tochio, H. / Shirakawa, M.
History
DepositionJun 16, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ubiquitin
B: ubiquitin
C: Putative uncharacterized protein UIMC1


Theoretical massNumber of molelcules
Total (without water)22,4723
Polymers22,4723
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0CG48
#2: Protein/peptide Putative uncharacterized protein UIMC1


Mass: 5318.808 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 79-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UIMC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: C9JR12, UniProt: Q96RL1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1523D C(CO)NH
1623D H(CCO)NH
1722D 1H-13C HSQC
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11032D 1H-15N HSQC
11133D C(CO)NH
11233D H(CCO)NH
11332D 1H-13C HSQC
11433D 1H-15N NOESY
11533D 1H-13C NOESY
11642D 1H-15N HSQC
11743D C(CO)NH
11843D H(CCO)NH
11942D 1H-13C HSQC
12043D 1H-15N NOESY
12143D 1H-13C NOESY
12213D 15N-edited/15N,13C-filtered NOESY
12333D 15N-edited/15N,13C-filtered NOESY
12443D 15N-edited/15N,13C-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.4 mM ubiquitin 1-1, 2.4 mM ubiquitin 2-2, 2.4 mM [U-13C; U-15N] tandem UIMs of Rap80-3, 1 mM DTT-4, 50 mM sodium phosphate-5, 90% H2O/10% D2O90% H2O/10% D2O
22 mM ubiquitin 1-6, 2 mM ubiquitin 2-7, 2 mM [U-13C; U-15N; U-70% 2H] tandem UIMs of Rap80-8, 1 mM DTT-9, 50 mM sodium phosphate-10, 90% H2O/10% D2O90% H2O/10% D2O
32.9 mM [U-13C; U-15N] ubiquitin 1-11, 2.9 mM ubiquitin 2-12, 2.9 mM tandem UIMs of Rap80-13, 1 mM DTT-14, 50 mM sodium phosphate-15, 90% H2O/10% D2O90% H2O/10% D2O
42.9 mM ubiquitin 1-16, 2.9 mM [U-13C; U-15N] ubiquitin 2-17, 2.9 mM tandem UIMs of Rap80-18, 1 mM DTT-19, 50 mM sodium phosphate-20, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.4 mMubiquitin 1-11
2.4 mMubiquitin 2-21
2.4 mMtandem UIMs of Rap80-3[U-13C; U-15N]1
1 mMDTT-41
50 mMsodium phosphate-51
2 mMubiquitin 1-62
2 mMubiquitin 2-72
2 mMtandem UIMs of Rap80-8[U-13C; U-15N; U-70% 2H]2
1 mMDTT-92
50 mMsodium phosphate-102
2.9 mMubiquitin 1-11[U-13C; U-15N]3
2.9 mMubiquitin 2-123
2.9 mMtandem UIMs of Rap80-133
1 mMDTT-143
50 mMsodium phosphate-153
2.9 mMubiquitin 1-164
2.9 mMubiquitin 2-17[U-13C; U-15N]4
2.9 mMtandem UIMs of Rap80-184
1 mMDTT-194
50 mMsodium phosphate-204
Sample conditionsIonic strength: 0 / pH: 6.8 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX7001
Bruker AvanceBrukerAvance6002
Bruker AvanceBrukerAvance8003

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Processing

NMR software
NameDeveloperClassification
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CANDIDHerrmann, Guntert and Wuthrichchemical shift assignment
CANDIDHerrmann, Guntert and Wuthrichstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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