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

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Entry
Database: PDB / ID: 5ydk
TitleCrystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form
Components
  • (Ubiquitin-40S ribosomal protein S27a) x 2
  • E3 ubiquitin-protein ligase RNF168
KeywordsSIGNALING PROTEIN / ubiquitin
Function / homology
Function and homology information


histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / double-strand break repair via classical nonhomologous end joining / isotype switching / Formation of the ternary complex, and subsequently, the 43S complex / K63-linked polyubiquitin modification-dependent protein binding / Ribosomal scanning and start codon recognition / response to ionizing radiation / Translation initiation complex formation / DNA repair-dependent chromatin remodeling ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / double-strand break repair via classical nonhomologous end joining / isotype switching / Formation of the ternary complex, and subsequently, the 43S complex / K63-linked polyubiquitin modification-dependent protein binding / Ribosomal scanning and start codon recognition / response to ionizing radiation / Translation initiation complex formation / DNA repair-dependent chromatin remodeling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / negative regulation of transcription elongation by RNA polymerase II / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein K63-linked ubiquitination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / ubiquitin ligase complex / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / interstrand cross-link repair / SUMOylation of DNA damage response and repair proteins / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / nucleosome binding / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / cytosolic ribosome / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / positive regulation of DNA repair / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / epigenetic regulation of gene expression / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / ubiquitin binding / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling
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
Ubiquitin-ribosomal protein eS31 fusion protein / E3 ubiquitin-protein ligase RNF168
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.505 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
DepositionSep 13, 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 1.2Nov 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Ubiquitin-40S ribosomal protein S27a
G: E3 ubiquitin-protein ligase RNF168
H: Ubiquitin-40S ribosomal protein S27a
J: Ubiquitin-40S ribosomal protein S27a
F: E3 ubiquitin-protein ligase RNF168
E: Ubiquitin-40S ribosomal protein S27a
C: Ubiquitin-40S ribosomal protein S27a
L: E3 ubiquitin-protein ligase RNF168
K: Ubiquitin-40S ribosomal protein S27a
I: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,39214
Polymers110,20812
Non-polymers1842
Water5,008278
1
A: E3 ubiquitin-protein ligase RNF168
B: Ubiquitin-40S ribosomal protein S27a
D: Ubiquitin-40S ribosomal protein S27a


Theoretical massNumber of molelcules
Total (without water)27,5523
Polymers27,5523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: E3 ubiquitin-protein ligase RNF168
H: Ubiquitin-40S ribosomal protein S27a
J: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6444
Polymers27,5523
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: E3 ubiquitin-protein ligase RNF168
E: Ubiquitin-40S ribosomal protein S27a
C: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6444
Polymers27,5523
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
L: E3 ubiquitin-protein ligase RNF168
K: Ubiquitin-40S ribosomal protein S27a
I: Ubiquitin-40S ribosomal protein S27a


Theoretical massNumber of molelcules
Total (without water)27,5523
Polymers27,5523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.344, 64.120, 117.464
Angle α, β, γ (deg.)90.00, 109.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 10255.224 Da / Num. of mol.: 4 / Fragment: UNP residues 113-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF168 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IYW5, RING-type E3 ubiquitin transferase
#2: Protein
Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 8604.845 Da / Num. of mol.: 4 / Fragment: UNP residues 1-76 / Mutation: K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62979
#3: Protein
Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 8691.918 Da / Num. of mol.: 4 / Fragment: UNP residues 1-76 / Mutation: D77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62979
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 7.6 21% PEG3350

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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: PIXEL / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 40288 / % possible obs: 97.2 % / Redundancy: 5.1 % / Rsym value: 0.128 / Net I/σ(I): 6.875
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.25 / Rsym value: 0.673 / % possible all: 97.4

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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: 2.505→42.654 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 2017 5.02 %
Rwork0.2295 --
obs0.231 40207 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.505→42.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7481 0 12 278 7771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047558
X-RAY DIFFRACTIONf_angle_d0.58710120
X-RAY DIFFRACTIONf_dihedral_angle_d20.8454818
X-RAY DIFFRACTIONf_chiral_restr0.0421136
X-RAY DIFFRACTIONf_plane_restr0.0031343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.505-2.56770.41221410.3612697X-RAY DIFFRACTION96
2.5677-2.63710.36531420.3452657X-RAY DIFFRACTION97
2.6371-2.71470.36191260.32792722X-RAY DIFFRACTION96
2.7147-2.80230.34771320.31512732X-RAY DIFFRACTION96
2.8023-2.90240.3281360.30772627X-RAY DIFFRACTION94
2.9024-3.01860.31261640.27862711X-RAY DIFFRACTION98
3.0186-3.15590.28271650.24822716X-RAY DIFFRACTION98
3.1559-3.32230.31881460.24112745X-RAY DIFFRACTION98
3.3223-3.53030.2461460.2232755X-RAY DIFFRACTION98
3.5303-3.80270.26571370.21532676X-RAY DIFFRACTION95
3.8027-4.18510.21681380.18522797X-RAY DIFFRACTION99
4.1851-4.790.19171300.1652813X-RAY DIFFRACTION99
4.79-6.03220.21211550.19552717X-RAY DIFFRACTION96
6.0322-42.66010.19571590.18682825X-RAY DIFFRACTION96

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