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

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Basic information

Entry
Database: PDB / ID: 5xis
TitleCrystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I
Components
  • (Ubiquitin-40S ribosomal protein ...) x 2
  • E3 ubiquitin-protein ligase RNF168
KeywordsTRANSFERASE/RIBOSOMAL PROTEIN / ubiquitin / 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 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SCF-beta-TrCP mediated degradation of Emi1 / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 ...Formation of the ternary complex, and subsequently, the 43S complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SCF-beta-TrCP mediated degradation of Emi1 / 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 / Regulation of pyruvate metabolism / 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 / E3 ubiquitin ligases ubiquitinate target proteins / Translesion synthesis by REV1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Formation of a pool of free 40S subunits / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / SRP-dependent cotranslational protein targeting to membrane / p75NTR recruits signalling complexes / Interferon alpha/beta signaling / Negative regulation of MAPK pathway / Major pathway of rRNA processing in the nucleolus and cytosol / Regulation of BACH1 activity / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / Formation of TC-NER Pre-Incision Complex / 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 / 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-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 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Dual incision in TC-NER / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Oncogene Induced Senescence / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / 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 / PINK1-PRKN Mediated Mitophagy / HDR through Homologous Recombination (HRR) / Gap-filling DNA repair synthesis and ligation in TC-NER / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SCF(Skp2)-mediated degradation of p27/p21 / 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 / Inactivation of CSF3 (G-CSF) signaling / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / Regulation of FZD by ubiquitination / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 TNFR1 signaling / Regulation of RUNX3 expression and activity / Regulation of RAS by GAPs / Regulation of PTEN stability and activity
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
beta-D-xylofuranose / 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: 1.78 Å
AuthorsTakahashi, T.S. / Sato, Y. / Fukai, S.
Funding support Japan, 7items
OrganizationGrant numberCountry
JSPS22121003 Japan
JSPS15H01175 Japan
JSPS24247014 Japan
JSPS24687012 Japan
JSPS16H04750 Japan
JSTJPMJCR1XMX5 Japan
JSPS15F15386 Japan
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 28, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,83810
Polymers54,4896
Non-polymers3494
Water5,621312
1
A: E3 ubiquitin-protein ligase RNF168
B: Ubiquitin-40S ribosomal protein S27a
C: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4436
Polymers27,2453
Non-polymers1993
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: E3 ubiquitin-protein ligase RNF168
E: Ubiquitin-40S ribosomal protein S27a
F: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3954
Polymers27,2453
Non-polymers1501
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.273, 66.291, 74.173
Angle α, β, γ (deg.)76.47, 79.29, 80.49
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 BECF

#2: 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
#3: 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

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Protein / Sugars , 2 types, 4 molecules AD

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


Mass: 9947.921 Da / Num. of mol.: 2 / Fragment: UNP residues 110-188
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
#4: Sugar ChemComp-XYZ / beta-D-xylofuranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylfbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylofuranoseCOMMON NAMEGMML 1.0
b-D-XylfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 314 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 15% PEG3350, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2

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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: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 56388 / % possible obs: 92.9 % / Redundancy: 6.3 % / Rsym value: 0.064 / Net I/σ(I): 32.7
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.667 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FID

2fid


Resolution: 1.78→43.286 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 2863 5.08 %
Rwork0.2185 --
obs0.2198 56375 92.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→43.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 22 312 4040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053766
X-RAY DIFFRACTIONf_angle_d0.925046
X-RAY DIFFRACTIONf_dihedral_angle_d11.4483607
X-RAY DIFFRACTIONf_chiral_restr0.058575
X-RAY DIFFRACTIONf_plane_restr0.005665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7799-1.81060.3581290.34142333X-RAY DIFFRACTION82
1.8106-1.84350.36891430.32872693X-RAY DIFFRACTION92
1.8435-1.8790.33381240.3122667X-RAY DIFFRACTION93
1.879-1.91730.34671430.30782671X-RAY DIFFRACTION92
1.9173-1.9590.33371630.29242730X-RAY DIFFRACTION93
1.959-2.00460.29911550.2812622X-RAY DIFFRACTION91
2.0046-2.05470.28271480.26852561X-RAY DIFFRACTION88
2.0547-2.11020.32251410.26432688X-RAY DIFFRACTION94
2.1102-2.17230.30891370.2662749X-RAY DIFFRACTION94
2.1723-2.24250.28721570.25562699X-RAY DIFFRACTION94
2.2425-2.32260.29621390.24992739X-RAY DIFFRACTION94
2.3226-2.41560.28211340.24992632X-RAY DIFFRACTION92
2.4156-2.52550.28211440.25522631X-RAY DIFFRACTION89
2.5255-2.65860.33731410.2512770X-RAY DIFFRACTION96
2.6586-2.82520.27691410.25342748X-RAY DIFFRACTION95
2.8252-3.04330.30161390.24972732X-RAY DIFFRACTION94
3.0433-3.34940.26521560.23382635X-RAY DIFFRACTION91
3.3494-3.83380.24091410.20782781X-RAY DIFFRACTION96
3.8338-4.82920.16281310.15832662X-RAY DIFFRACTION92
4.8292-43.29880.17361570.16542769X-RAY DIFFRACTION95

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