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- PDB-1p3q: Mechanism of Ubiquitin Recognition by the CUE Domain of VPS9 -

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Basic information

Entry
Database: PDB / ID: 1p3q
TitleMechanism of Ubiquitin Recognition by the CUE Domain of VPS9
Components
  • Ubiquitin
  • Vacuolar protein sorting-associated protein VPS9
KeywordsTRANSLATION / Trafficking / Post Translational Modification / Mono-Ubiquitination
Function / homology
Function and homology information


: / RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / 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 ...: / RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / 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 / SCF-beta-TrCP mediated degradation of Emi1 / 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 / PINK1-PRKN Mediated Mitophagy / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / Cyclin D associated events in G1 / 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 / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / 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 / 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 / DNA Damage Recognition in GG-NER / Activation of NF-kappaB in B cells / 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 / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome
Similarity search - Function
Vacuolar protein sorting-associated protein 9, CUE domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / CUE domain ...Vacuolar protein sorting-associated protein 9, CUE domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ubiquitin-associated (UBA) domain / UBA-like superfamily / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase, Ruva Protein; domain 3 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Vacuolar protein sorting-associated protein 9 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsPrag, G. / Misra, S. / Jones, E.A. / Ghirlando, R. / Davies, B.A. / Horazdovsky, B.F. / Hurley, J.H.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: Mechanism of Ubiquitin Recognition by the CUE Domain of Vps9p.
Authors: Prag, G. / Misra, S. / Jones, E.A. / Ghirlando, R. / Davies, B.A. / Horazdovsky, B.F. / Hurley, J.H.
#1: Journal: Embo J. / Year: 2003
Title: A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain
Authors: Shih, S.C. / Prag, G. / Francis, S.A. / Sutanto, M.A. / Hurley, J.H. / Hicke, L.
History
DepositionApr 18, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Q: Vacuolar protein sorting-associated protein VPS9
R: Vacuolar protein sorting-associated protein VPS9
U: Ubiquitin
V: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)29,2234
Polymers29,2234
Non-polymers00
Water3,171176
1
Q: Vacuolar protein sorting-associated protein VPS9
R: Vacuolar protein sorting-associated protein VPS9
V: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)20,6463
Polymers20,6463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-33 kcal/mol
Surface area8780 Å2
MethodPISA
2
U: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,5771
Polymers8,5771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.607, 45.887, 57.802
Angle α, β, γ (deg.)90.00, 96.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vacuolar protein sorting-associated protein VPS9 / VPS9P


Mass: 6034.562 Da / Num. of mol.: 2 / Fragment: CUE DOMAIN / Mutation: K435A, K436A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS9 / Plasmid: pET-PARALLEL.HIS-CUE / Production host: Escherichia coli (E. coli) / Strain (production host): B834 pLys / References: UniProt: P54787
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Red blood cells / References: UniProt: P62990, UniProt: P0CH28*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.44 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 3350, magnesium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 mg/mlprotein1drop
250 mM1dropNaCl
320 mMTris1droppH7.7
410 mMdithiothreitol1drop
51.9-2.1 Mammonium sulfate1reservoir
6100 mMTris-HCl1reservoirpH8.2-8.8

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979174, 0.979311, 0.95645
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 24, 2002
RadiationMonochromator: Ni FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791741
20.9793111
30.956451
ReflectionResolution: 1.7→50 Å / Num. all: 55378 / Num. obs: 28955 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.3 / % possible all: 89.6
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 89.6 % / Num. unique obs: 2626

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→28.71 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The structure was also refined with REFMAC 5.1
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2777 10 %RANDOM
Rwork0.26 ---
all0.26 55378 --
obs-27772 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.6478 Å2 / ksol: 0.366048 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 0 176 1958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 418 10.6 %
Rwork0.304 3536 -
obs--81.5 %
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06

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