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- PDB-5xiu: Crystal structure of RNF168 UDM2 in complex with Lys63-linked diu... -

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Basic information

Entry
Database: PDB / ID: 5xiu
TitleCrystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin
Components
  • E3 ubiquitin-protein ligase RNF168
  • Ubiquitin-40S ribosomal protein S27a
KeywordsTRANSFERASE/RIBOSOMAL PROTEIN / ubiquitin / TRANSFERASE-RIBOSOMAL PROTEIN complex
Function / homology
Function and homology information


translation at postsynapse / Formation of the ternary complex, and subsequently, the 43S complex / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex ...translation at postsynapse / Formation of the ternary complex, and subsequently, the 43S complex / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / Formation of a pool of free 40S subunits / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / SRP-dependent cotranslational protein targeting to membrane / Regulation of BACH1 activity / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Major pathway of rRNA processing in the nucleolus and cytosol / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Regulation of innate immune responses to cytosolic DNA / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / PINK1-PRKN Mediated Mitophagy / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Termination of translesion DNA synthesis / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Inactivation of CSF3 (G-CSF) signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Senescence-Associated Secretory Phenotype (SASP) / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR1-induced NF-kappa-B signaling pathway / Josephin domain DUBs / Dual Incision in GG-NER / Downregulation of ERBB2 signaling / Regulation of FZD by ubiquitination / Dual incision in TC-NER / IKK complex recruitment mediated by RIP1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Oncogene Induced Senescence / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Translation initiation complex formation / Ribosomal scanning and start codon recognition / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Metalloprotease DUBs / Gap-filling DNA repair synthesis and ligation in TC-NER / Degradation of AXIN / Regulation of TNFR1 signaling / EGFR downregulation / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G2/M Checkpoints / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity
Similarity search - Function
E3 ubiquitin-protein ligase RNF168 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type ...E3 ubiquitin-protein ligase RNF168 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eS31 fusion protein / E3 ubiquitin-protein ligase RNF168
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTakahashi, T.S. / Sato, Y. / Fukai, S.
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.
Authors: Takahashi, T.S. / Hirade, Y. / Toma, A. / Sato, Y. / Yamagata, A. / Goto-Ito, S. / Tomita, A. / Nakada, S. / Fukai, S.
History
DepositionApr 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Author supporting evidence / Derived calculations / Structure summary
Category: pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence ...pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct
Item: _struct.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF168
B: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8137
Polymers14,5032
Non-polymers3105
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint6 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.442, 78.548, 31.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase RNF168 / hRNF168 / RING finger protein 168 / RING-type E3 ubiquitin transferase RNF168


Mass: 5925.677 Da / Num. of mol.: 1 / Fragment: UNP residues 419-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF168 / Plasmid: pCOLD-GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: Q8IYW5, RING-type E3 ubiquitin transferase
#2: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rps27a, Uba80, Ubcep1 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P62983
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG3350, 0.1 M Tris-HCl (pH8.5), 0.2 M Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: CMOS / Date: Jun 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 14042 / % possible obs: 99.3 % / Redundancy: 7.7 % / Rsym value: 0.137 / Net I/σ(I): 20.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.523 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FID

2fid


Resolution: 1.8→50 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.23
RfactorNum. reflection% reflection
Rfree0.2069 722 5.14 %
Rwork0.1693 --
obs0.1713 14039 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 20 151 1156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061010
X-RAY DIFFRACTIONf_angle_d0.7411344
X-RAY DIFFRACTIONf_dihedral_angle_d11.786631
X-RAY DIFFRACTIONf_chiral_restr0.048155
X-RAY DIFFRACTIONf_plane_restr0.004173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7934-1.93190.2441350.19192540X-RAY DIFFRACTION96
1.9319-2.12630.19831350.15762634X-RAY DIFFRACTION99
2.1263-2.43390.21361480.16562630X-RAY DIFFRACTION99
2.4339-3.06640.21441460.17442692X-RAY DIFFRACTION99
3.0664-47.41590.19521580.1672821X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.8914 Å / Origin y: 21.94 Å / Origin z: 8.4131 Å
111213212223313233
T0.085 Å20.0057 Å20.0011 Å2-0.0806 Å2-0.0118 Å2--0.079 Å2
L0.3761 °2-0.1184 °20.2084 °2-0.0711 °2-0.0632 °2--0.1432 °2
S0.0475 Å °0.1047 Å °-0.0199 Å °0.0244 Å °-0.0326 Å °0.0083 Å °0.0476 Å °0.0188 Å °0.0029 Å °
Refinement TLS groupSelection details: all

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