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- PDB-8ftq: Crystal structure of hRpn13 Pru domain in complex with Ubiquitin ... -

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Basic information

Entry
Database: PDB / ID: 8ftq
TitleCrystal structure of hRpn13 Pru domain in complex with Ubiquitin and XL44
Components
  • Proteasomal ubiquitin receptor ADRM1
  • Ubiquitin
KeywordsPROTEIN BINDING / Proteasome / Rpn13 / PROTAC
Function / homology
Function and homology information


proteasome regulatory particle, lid subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / molecular function inhibitor activity / proteasome binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) ...proteasome regulatory particle, lid subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / molecular function inhibitor activity / proteasome binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / endopeptidase activator activity / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / proteasome assembly / 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 / 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 / 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 / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / proteasome complex / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / SCF-beta-TrCP mediated degradation of Emi1 / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR3 signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR2 signaling / Degradation of DVL / Peroxisomal protein import / Negative regulation of FGFR4 signaling / Stabilization of p53 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Termination of translesion DNA synthesis
Similarity search - Function
RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. ...RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / Polyubiquitin-C / Proteasomal ubiquitin receptor ADRM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalters, K.J. / Lu, X. / Chandravanshi, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nat Commun / Year: 2024
Title: A structure-based designed small molecule depletes hRpn13 Pru and a select group of KEN box proteins.
Authors: Lu, X. / Chandravanshi, M. / Sabbasani, V.R. / Gaikwad, S. / Hughitt, V.K. / Gyabaah-Kessie, N. / Scroggins, B.T. / Das, S. / Myint, W. / Clapp, M.E. / Schwieters, C.D. / Dyba, M.A. / ...Authors: Lu, X. / Chandravanshi, M. / Sabbasani, V.R. / Gaikwad, S. / Hughitt, V.K. / Gyabaah-Kessie, N. / Scroggins, B.T. / Das, S. / Myint, W. / Clapp, M.E. / Schwieters, C.D. / Dyba, M.A. / Bolhuis, D.L. / Koscielniak, J.W. / Andresson, T. / Emanuele, M.J. / Brown, N.G. / Matsuo, H. / Chari, R. / Citrin, D.E. / Mock, B.A. / Swenson, R.E. / Walters, K.J.
History
DepositionJan 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Experimental preparation / Category: exptl_crystal
Item: _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasomal ubiquitin receptor ADRM1
B: Proteasomal ubiquitin receptor ADRM1
C: Ubiquitin
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3876
Polymers49,6064
Non-polymers7812
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.350, 90.283, 65.027
Angle α, β, γ (deg.)90.000, 113.240, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Proteasomal ubiquitin receptor ADRM1 / 110 kDa cell membrane glycoprotein / Gp110 / Adhesion-regulating molecule 1 / ARM-1 / Proteasome ...110 kDa cell membrane glycoprotein / Gp110 / Adhesion-regulating molecule 1 / ARM-1 / Proteasome regulatory particle non-ATPase 13 / hRpn13 / Rpn13 homolog


Mass: 16610.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1, GP110 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q16186
#2: Protein Ubiquitin


Mass: 8192.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P0CG48
#3: Chemical ChemComp-ZTO / N-(3-{[(3R)-5-fluoro-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}phenyl)-4-methoxybenzamide


Mass: 390.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H19FN2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 4.6 / Details: 0.1 M Citric acid pH 4.6 and 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.4 Å / Num. obs: 32724 / % possible obs: 98.54 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.82 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.06884 / Rpim(I) all: 0.04364 / Rrim(I) all: 0.08181 / Net I/σ(I): 9.01
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.4141 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 3183 / CC1/2: 0.915 / CC star: 0.977 / Rpim(I) all: 0.278 / Rrim(I) all: 0.5017 / % possible all: 97.07

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Processing

Software
NameVersionClassification
SERGUIdata collection
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
Coot0.8.9.2model building
PHENIX1.17.1-3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.14 Å / SU ML: 0.2593 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 28.7345
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 1661 5.09 %RANDOM
Rwork0.2201 30966 --
obs0.2215 32627 98.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.99 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 58 101 3177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02653140
X-RAY DIFFRACTIONf_angle_d1.83074234
X-RAY DIFFRACTIONf_chiral_restr0.1238456
X-RAY DIFFRACTIONf_plane_restr0.015548
X-RAY DIFFRACTIONf_dihedral_angle_d15.22921222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.33881280.29592519X-RAY DIFFRACTION96.57
2.16-2.230.32471280.29052626X-RAY DIFFRACTION99.53
2.23-2.310.40531150.32562511X-RAY DIFFRACTION96.12
2.31-2.40.27351470.25912578X-RAY DIFFRACTION99.49
2.4-2.510.28721310.25812569X-RAY DIFFRACTION98.61
2.51-2.650.25291310.23722598X-RAY DIFFRACTION98.81
2.65-2.810.27141370.25272550X-RAY DIFFRACTION97.82
2.81-3.030.28641370.24982609X-RAY DIFFRACTION99.85
3.03-3.330.29391580.23612600X-RAY DIFFRACTION99.64
3.33-3.820.20371360.20942602X-RAY DIFFRACTION98.7
3.82-4.810.21351520.16932594X-RAY DIFFRACTION98.78
4.81-45.140.20921610.19172610X-RAY DIFFRACTION98.68

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