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- PDB-2d3g: Double sided ubiquitin binding of Hrs-UIM -

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Basic information

Entry
Database: PDB / ID: 2d3g
TitleDouble sided ubiquitin binding of Hrs-UIM
Components
  • ubiquitin
  • ubiquitin interacting motif from hepatocyte growth factor-regulated tyrosine kinase substrate
KeywordsPROTEIN TRANSPORT / protein-protein complex / uim and ubiquitin
Function / homology
Function and homology information


Inhibition of membrane repair / ESCRT-0 complex / : / membrane invagination / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling ...Inhibition of membrane repair / ESCRT-0 complex / : / membrane invagination / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Negative regulation of FLT3 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of pyruvate metabolism / SCF-beta-TrCP mediated degradation of Emi1 / Termination of translesion DNA synthesis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Ovarian tumor domain proteases / Cyclin D associated events in G1 / Negative regulators of DDX58/IFIH1 signaling / Regulation of BACH1 activity / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Inactivation of CSF3 (G-CSF) signaling / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / DNA Damage Recognition in GG-NER / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6
Similarity search - Function
Hepatocyte growth factor-regulated tyrosine kinase substrate, helical domain / Hepatocyte growth factor-regulated tyrosine kinase substrate / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / VHS domain / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM ...Hepatocyte growth factor-regulated tyrosine kinase substrate, helical domain / Hepatocyte growth factor-regulated tyrosine kinase substrate / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / VHS domain / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / ENTH/VHS / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger, FYVE/PHD-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor-regulated tyrosine kinase substrate / Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHirano, S. / Kawasaki, M. / Kato, R. / Wakatsuki, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting
Authors: Hirano, S. / Kawasaki, M. / Ura, H. / Kato, R. / Raiborg, C. / Stenmark, H. / Wakatsuki, S.
History
DepositionSep 28, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: ubiquitin
B: ubiquitin
P: ubiquitin interacting motif from hepatocyte growth factor-regulated tyrosine kinase substrate


Theoretical massNumber of molelcules
Total (without water)19,5423
Polymers19,5423
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.244, 73.244, 169.636
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-125-

HOH

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Components

#1: Protein ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P62990, UniProt: P0CH28*PLUS
#2: Protein/peptide ubiquitin interacting motif from hepatocyte growth factor-regulated tyrosine kinase substrate


Mass: 2388.556 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in human HRS and was synthesized by standard peptide synthesis methods.
References: UniProt: O14964
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG400, CHES, pH 9.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 19706 / Num. obs: 19682 / % possible obs: 99.8 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 8.45 / Num. unique all: 1931 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UBQ

1ubq


Resolution: 1.7→36.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.038 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 992 5.1 %RANDOM
Rwork0.197 ---
all0.1989 19706 --
obs0.1989 19418 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0.29 Å20 Å2
2---0.58 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1287 0 0 105 1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221301
X-RAY DIFFRACTIONr_bond_other_d0.0020.021219
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9951750
X-RAY DIFFRACTIONr_angle_other_deg0.78832870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5945159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021401
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02209
X-RAY DIFFRACTIONr_nbd_refined0.2080.2214
X-RAY DIFFRACTIONr_nbd_other0.2450.21419
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0790.2814
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1371.5808
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.10621313
X-RAY DIFFRACTIONr_scbond_it3.1453493
X-RAY DIFFRACTIONr_scangle_it5.4554.5437
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.27 80
Rwork0.228 1277

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