[English] 日本語
Yorodumi
- PDB-4un2: Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4un2
TitleCrystal structure of the UBA domain of Dsk2 in complex with Ubiquitin
Components
  • UBIQUITIN
  • UBIQUITIN DOMAIN-CONTAINING PROTEIN DSK2
KeywordsPROTEIN BINDING / UBIQUITIN-ASSOCIATED DOMAIN / PROTEIN DEGRADATION
Function / homology
Function and homology information


Cargo recognition for clathrin-mediated endocytosis / spindle pole body duplication / protein localization to vacuole / K48-linked polyubiquitin modification-dependent protein binding / polyubiquitin modification-dependent protein binding / ERAD pathway / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora ...Cargo recognition for clathrin-mediated endocytosis / spindle pole body duplication / protein localization to vacuole / K48-linked polyubiquitin modification-dependent protein binding / polyubiquitin modification-dependent protein binding / ERAD pathway / 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 / 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 / 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 / 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 / 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 / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Hh mutants are degraded by ERAD / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / EGFR downregulation / Termination of translesion DNA synthesis / Degradation of GLI1 by the proteasome
Similarity search - Function
Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / Ubiquitin-associated (UBA) domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / : ...Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / Ubiquitin-associated (UBA) domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin domain-containing protein DSK2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsMichielssens, S. / Peters, J.H. / Ban, D. / Pratihar, S. / Seeliger, D. / Sharma, M. / Giller, K. / Sabo, T.M. / Becker, S. / Lee, D. ...Michielssens, S. / Peters, J.H. / Ban, D. / Pratihar, S. / Seeliger, D. / Sharma, M. / Giller, K. / Sabo, T.M. / Becker, S. / Lee, D. / Griesinger, C. / de Groot, B.L.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: A Designed Conformational Shift to Control Protein Binding Specificity.
Authors: Michielssens, S. / Peters, J.H. / Ban, D. / Pratihar, S. / Seeliger, D. / Sharma, M. / Giller, K. / Sabo, T.M. / Becker, S. / Lee, D. / Griesinger, C. / De Groot, B.L.
History
DepositionMay 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UBIQUITIN
B: UBIQUITIN DOMAIN-CONTAINING PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)13,9222
Polymers13,9222
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-5.2 kcal/mol
Surface area6260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.971, 77.972, 49.485
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein UBIQUITIN


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG48
#2: Protein/peptide UBIQUITIN DOMAIN-CONTAINING PROTEIN DSK2


Mass: 5344.805 Da / Num. of mol.: 1 / Fragment: UBA DOMAIN, RESIDUES 328-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48510
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH 8.5, 20% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2011 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→67.5 Å / Num. obs: 27296 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 8.07 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 27.78
Reflection shellResolution: 1.52→1.62 Å / Redundancy: 7.93 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.55 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1UBQ AND 2BWB

1ubq

2bwb


Resolution: 1.51→67.52 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.316 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19615 1359 5 %RANDOM
Rwork0.15722 ---
obs0.15921 27090 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.51→67.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms893 0 0 109 1002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02926
X-RAY DIFFRACTIONr_bond_other_d0.0030.02637
X-RAY DIFFRACTIONr_angle_refined_deg2.0871.9771251
X-RAY DIFFRACTIONr_angle_other_deg1.09731564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9045119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83725.22744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68615173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.616156
X-RAY DIFFRACTIONr_chiral_restr0.160.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02174
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.47731563
X-RAY DIFFRACTIONr_sphericity_free30.19530
X-RAY DIFFRACTIONr_sphericity_bonded19.0951632
LS refinement shellResolution: 1.515→1.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 83 -
Rwork0.209 1695 -
obs--93.88 %

+
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