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

+
Open data


ID or keywords:

Loading...

-
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


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 pyruvate metabolism / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription ...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 pyruvate metabolism / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / 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 / Termination of translesion DNA synthesis / 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) / 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 / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Oncogene Induced Senescence / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Ubiquitin-dependent degradation of Cyclin D / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / 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 / Regulation of TNFR1 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of necroptotic cell death / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Degradation of AXIN / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Asymmetric localization of PCP proteins
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. ...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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Details

Sequence detailsadditional C-terminal residue

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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://pdbjlc1.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