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- PDB-5hpl: System-wide modulation of HECT E3 ligases with selective ubiquiti... -

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Basic information

Entry
Database: PDB / ID: 5hpl
TitleSystem-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: Rsp5 and UbV R5.4
Components
  • Rsp5
  • Ubiquitin variant R5.4
KeywordsLIGASE / HECT E3 / Rsp5 / Ubiquitin / Ubv
Function / homology
Function and homology information


regulation of dolichol biosynthetic process / RSP5-BUL ubiquitin ligase complex / regulation of ribosomal large subunit export from nucleus / regulation of tRNA processing / regulation of tRNA export from nucleus / regulation of ubiquinone biosynthetic process / regulation of phosphate metabolic process / regulation of ergosterol biosynthetic process / RHOQ GTPase cycle / RHOU GTPase cycle ...regulation of dolichol biosynthetic process / RSP5-BUL ubiquitin ligase complex / regulation of ribosomal large subunit export from nucleus / regulation of tRNA processing / regulation of tRNA export from nucleus / regulation of ubiquinone biosynthetic process / regulation of phosphate metabolic process / regulation of ergosterol biosynthetic process / RHOQ GTPase cycle / RHOU GTPase cycle / positive regulation of ubiquitin-dependent endocytosis / regulation of multivesicular body size / ribophagy / ubiquitin-dependent endocytosis / regulation of mRNA export from nucleus / mitochondria-associated ubiquitin-dependent protein catabolic process / regulation of rRNA processing / actin cortical patch / cellular bud tip / late endosome to vacuole transport via multivesicular body sorting pathway / nonfunctional rRNA decay / positive regulation of fatty acid biosynthetic process / regulation of nitrogen utilization / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / poly(A)+ mRNA export from nucleus / Regulation of PTEN stability and activity / Peptide chain elongation / positive regulation of endocytosis / Selenocysteine synthesis / Formation of a pool of free 40S subunits / protein K63-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / ubiquitin ligase complex / 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 / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / mitochondrion organization / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / phosphatidylinositol binding / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle
Similarity search - Function
E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. ...E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / C2 domain superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RSP5 / Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsWu, K.-P. / Kamadurai, H.B. / Schulman, B.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
CitationJournal: Mol.Cell / Year: 2016
Title: System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes.
Authors: Zhang, W. / Wu, K.P. / Sartori, M.A. / Kamadurai, H.B. / Ordureau, A. / Jiang, C. / Mercredi, P.Y. / Murchie, R. / Hu, J. / Persaud, A. / Mukherjee, M. / Li, N. / Doye, A. / Walker, J.R. / ...Authors: Zhang, W. / Wu, K.P. / Sartori, M.A. / Kamadurai, H.B. / Ordureau, A. / Jiang, C. / Mercredi, P.Y. / Murchie, R. / Hu, J. / Persaud, A. / Mukherjee, M. / Li, N. / Doye, A. / Walker, J.R. / Sheng, Y. / Hao, Z. / Li, Y. / Brown, K.R. / Lemichez, E. / Chen, J. / Tong, Y. / Harper, J.W. / Moffat, J. / Rotin, D. / Schulman, B.A. / Sidhu, S.S.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: Rsp5
B: Rsp5
C: Ubiquitin variant R5.4
D: Ubiquitin variant R5.4


Theoretical massNumber of molelcules
Total (without water)109,4824
Polymers109,4824
Non-polymers00
Water5,134285
1
A: Rsp5
C: Ubiquitin variant R5.4


Theoretical massNumber of molelcules
Total (without water)54,7412
Polymers54,7412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-14 kcal/mol
Surface area21680 Å2
MethodPISA
2
B: Rsp5
D: Ubiquitin variant R5.4


Theoretical massNumber of molelcules
Total (without water)54,7412
Polymers54,7412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-13 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.486, 92.352, 82.161
Angle α, β, γ (deg.)90.00, 101.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rsp5 / Reverses SPT-phenotype protein 5


Mass: 44864.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P39940
#2: Protein Ubiquitin variant R5.4


Mass: 9876.315 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSF-duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P62987*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Bis-Tris 0.1M, pH 5.5 ammonium acetate 0.2 M, PEG 3350 14%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.31→80.482 Å / Num. obs: 45796 / % possible obs: 98.17 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 7.72
Reflection shellResolution: 2.31→2.393 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.41 / % possible all: 98.58

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ND7

1nd7


Resolution: 2.31→80.482 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 2320 5.07 %
Rwork0.1912 --
obs0.1944 45787 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→80.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7464 0 0 285 7749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097632
X-RAY DIFFRACTIONf_angle_d1.1310296
X-RAY DIFFRACTIONf_dihedral_angle_d15.2762890
X-RAY DIFFRACTIONf_chiral_restr0.0441089
X-RAY DIFFRACTIONf_plane_restr0.0051349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.35720.3071490.25922568X-RAY DIFFRACTION98
2.3572-2.40840.33211440.25842553X-RAY DIFFRACTION99
2.4084-2.46450.32571330.24362551X-RAY DIFFRACTION100
2.4645-2.52610.3331310.25342580X-RAY DIFFRACTION99
2.5261-2.59440.31231510.24442551X-RAY DIFFRACTION99
2.5944-2.67080.33641370.24082580X-RAY DIFFRACTION99
2.6708-2.7570.29691370.23322554X-RAY DIFFRACTION99
2.757-2.85550.29591270.22952569X-RAY DIFFRACTION99
2.8555-2.96980.3291240.21482589X-RAY DIFFRACTION99
2.9698-3.1050.29661440.2172560X-RAY DIFFRACTION99
3.105-3.26870.30511320.21562573X-RAY DIFFRACTION98
3.2687-3.47350.29011280.21512531X-RAY DIFFRACTION97
3.4735-3.74170.26141270.18662558X-RAY DIFFRACTION98
3.7417-4.11820.22651590.15972511X-RAY DIFFRACTION97
4.1182-4.71410.18761320.14272517X-RAY DIFFRACTION96
4.7141-5.9390.20821280.15892517X-RAY DIFFRACTION96
5.939-80.53060.17231370.15052605X-RAY DIFFRACTION97

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