[English] 日本語
Yorodumi
- PDB-5ydk: Crystal structure of RNF168 UDM1 in complex with Lys63-linked diu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 / response to ionizing radiation / Ribosomal scanning and start codon recognition / 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 / response to ionizing radiation / Ribosomal scanning and start codon recognition / Translation initiation complex formation / DNA repair-dependent chromatin remodeling / negative regulation of transcription elongation by RNA polymerase II / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / protein K63-linked ubiquitination / Viral mRNA Translation / 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 / cytosolic ribosome / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / 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 / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / positive regulation of DNA repair / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / epigenetic regulation of gene expression / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / ubiquitin binding / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more