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- PDB-5xit: Crystal structure of RNF168 UDM1 in complex with Lys63-linked diu... -

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Basic information

Entry
Database: PDB / ID: 5xit
TitleCrystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II
Components
  • (Ubiquitin-40S ribosomal protein ...) x 2
  • E3 ubiquitin-protein ligase RNF168
KeywordsTRANSFERASE/RIBOSOMAL PROTEIN / protein complex / DNA repair / TRANSFERASE-RIBOSOMAL PROTEIN complex
Function / homology
Function and homology information


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 / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription ...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 / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of expression of SLITs and ROBOs / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Alpha-protein kinase 1 signaling pathway / Pexophagy / 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 / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / Formation of a pool of free 40S subunits / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / Interferon alpha/beta signaling / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / SRP-dependent cotranslational protein targeting to membrane / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / Formation of TC-NER Pre-Incision Complex / Major pathway of rRNA processing in the nucleolus and cytosol / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Downregulation of ERBB2 signaling / Dual incision in TC-NER / Oncogene Induced Senescence / PINK1-PRKN Mediated Mitophagy / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / HDR through Homologous Recombination (HRR) / Gap-filling DNA repair synthesis and ligation in TC-NER / Inactivation of CSF3 (G-CSF) signaling / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Formation of Incision Complex in GG-NER / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / EGFR downregulation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / translation at postsynapse / Autodegradation of the E3 ubiquitin ligase COP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G2/M Checkpoints / Degradation of AXIN / Regulation of FZD by ubiquitination / Regulation of TNFR1 signaling / 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 / Regulation of RAS by GAPs
Similarity search - Function
E3 ubiquitin-protein ligase RNF168 / : / Prokaryotic RING finger family 4 / 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 / : / Prokaryotic RING finger family 4 / 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
PRASEODYMIUM ION / Ubiquitin-ribosomal protein eS31 fusion protein / E3 ubiquitin-protein ligase RNF168
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 28, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,71414
Polymers53,8316
Non-polymers8838
Water1,04558
1
D: Ubiquitin-40S ribosomal protein S27a
A: E3 ubiquitin-protein ligase RNF168
B: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2847
Polymers26,9153
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: E3 ubiquitin-protein ligase RNF168
H: Ubiquitin-40S ribosomal protein S27a
F: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4307
Polymers26,9153
Non-polymers5154
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.372, 50.019, 64.407
Angle α, β, γ (deg.)73.49, 69.69, 73.82
Int Tables number1
Space group name H-MP1

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Components

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Ubiquitin-40S ribosomal protein ... , 2 types, 4 molecules DFHB

#1: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 8604.845 Da / Num. of mol.: 2 / Mutation: K63R
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: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 8691.918 Da / Num. of mol.: 2
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

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Protein , 1 types, 2 molecules EA

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


Mass: 9618.506 Da / Num. of mol.: 2 / Fragment: UNP residues 113-188
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

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Non-polymers , 3 types, 66 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pr
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsadditional C-terminal residue

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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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23% PEG MME 2000, 0.1 M Bis-Tris (pH 6.5), 10 mM Pr 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: Oct 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 21397 / % possible obs: 90.2 % / Redundancy: 3.1 % / Rsym value: 0.112 / Net I/σ(I): 20.2
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.67 / % possible all: 91.5

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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: 2.25→46.986 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.26
RfactorNum. reflection% reflection
Rfree0.2391 1099 5.14 %
Rwork0.2202 --
obs0.2213 21366 89.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→46.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3649 0 33 58 3740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033704
X-RAY DIFFRACTIONf_angle_d0.6154952
X-RAY DIFFRACTIONf_dihedral_angle_d20.5182365
X-RAY DIFFRACTIONf_chiral_restr0.046558
X-RAY DIFFRACTIONf_plane_restr0.003652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2443-2.34650.33961210.31742418X-RAY DIFFRACTION86
2.3465-2.47020.34181430.28872546X-RAY DIFFRACTION89
2.4702-2.62490.30261310.28142444X-RAY DIFFRACTION86
2.6249-2.82760.34011410.27632634X-RAY DIFFRACTION93
2.8276-3.11210.2521340.26122588X-RAY DIFFRACTION91
3.1121-3.56230.28541410.24322522X-RAY DIFFRACTION89
3.5623-4.48750.21711480.19832556X-RAY DIFFRACTION91
4.4875-46.99590.1831400.17712559X-RAY DIFFRACTION90

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