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- PDB-5ln1: STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST; -

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Basic information

Entry
Database: PDB / ID: 5ln1
TitleSTRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST;
Components
  • 26S proteasome regulatory subunit RPN10
  • Polyubiquitin-B
KeywordsUBIQUITIN-BINDING PROTEIN / UBIQUITIN / VWA / UBIQUITYLATION / PROTEASOME
Function / homology
Function and homology information


proteasome regulatory particle, base subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / K48-linked polyubiquitin modification-dependent protein binding / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I ...proteasome regulatory particle, base subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / K48-linked polyubiquitin modification-dependent protein binding / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / proteasome assembly / polyubiquitin modification-dependent protein binding / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / 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 / Translesion synthesis by POLK / proteasome complex / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / neuron projection morphogenesis / 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) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / 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 / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex
Similarity search - Function
von Willebrand factor type A domain / von Willebrand factor, type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain ...von Willebrand factor type A domain / von Willebrand factor, type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / 26S proteasome regulatory subunit RPN10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsKeren-Kaplan, T. / Attali, I. / Levin-Kravets, O. / Prag, G.
Funding support Israel, 1items
OrganizationGrant numberCountry
ISF1695/08 Israel
Citation
Journal: Nat Commun / Year: 2016
Title: Structure of ubiquitylated-Rpn10 provides insight into its autoregulation mechanism.
Authors: Keren-Kaplan, T. / Zeev Peters, L. / Levin-Kravets, O. / Attali, I. / Kleifeld, O. / Shohat, N. / Artzi, S. / Zucker, O. / Pilzer, I. / Reis, N. / Glickman, M.H. / Ben-Aroya, S. / Prag, G.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012
Title: Purification and crystallization of mono-ubiquitylated ubiquitin receptor Rpn10.
Authors: Keren-Kaplan, T. / Prag, G.
History
DepositionAug 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_validate_close_contact ...diffrn_radiation_wavelength / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: 26S proteasome regulatory subunit RPN10
U: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)30,6052
Polymers30,6052
Non-polymers00
Water00
1
A: 26S proteasome regulatory subunit RPN10
U: Polyubiquitin-B

A: 26S proteasome regulatory subunit RPN10
U: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)61,2104
Polymers61,2104
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area820 Å2
ΔGint0 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.290, 49.700, 81.330
Angle α, β, γ (deg.)90.00, 130.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 26S proteasome regulatory subunit RPN10


Mass: 21624.496 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPN10, MCB1, SUN1, YHR200W / Production host: Escherichia coli (E. coli) / References: UniProt: P38886
#2: Protein Polyubiquitin-B


Mass: 8980.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 292 K / Method: evaporation, recrystallization / pH: 6.5
Details: 12% (W/V) PEG 20000, 0.1M MES PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3.14→61.8 Å / Num. obs: 5824 / % possible obs: 99.8 % / Observed criterion σ(I): 9.8 / Redundancy: 3.2 % / Rmerge(I) obs: 0.084 / Rsym value: 0.098 / Net I/σ(I): 10.2
Reflection shellResolution: 3.14→3.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 5.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X5N, 1UBQ

2x5n

1ubq


Resolution: 3.14→53.64 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.21
RfactorNum. reflection% reflection
Rfree0.248 571 4.57 %
Rwork0.19 --
obs0.193 5823 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.14→53.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 0 0 2069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012098
X-RAY DIFFRACTIONf_angle_d1.4092836
X-RAY DIFFRACTIONf_dihedral_angle_d17.541796
X-RAY DIFFRACTIONf_chiral_restr0.101337
X-RAY DIFFRACTIONf_plane_restr0.006371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.2490.31641260.21112754X-RAY DIFFRACTION100
3.249-53.64860.20991400.17632803X-RAY DIFFRACTION99

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