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- PDB-4wlr: Crystal Structure of mUCH37-hRPN13 CTD-hUb complex -

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Basic information

Entry
Database: PDB / ID: 4wlr
TitleCrystal Structure of mUCH37-hRPN13 CTD-hUb complex
Components
  • Polyubiquitin-B
  • Proteasomal ubiquitin receptor ADRM1
  • Ubiquitin carboxyl-terminal hydrolase isozyme L5
KeywordsPROTEIN BINDING / UCH37 RPN13 Proteasome INO80 DUB
Function / homology
Function and homology information


lateral ventricle development / UCH proteinases / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / positive regulation of smoothened signaling pathway / hypothalamus gonadotrophin-releasing hormone neuron development ...lateral ventricle development / UCH proteinases / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / positive regulation of smoothened signaling pathway / hypothalamus gonadotrophin-releasing hormone neuron development / protein deubiquitination / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / midbrain development / endopeptidase inhibitor activity / molecular function inhibitor activity / proteasome binding / regulation of chromosome organization / female gonad development / seminiferous tubule development / male meiosis I / regulation of DNA replication / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of embryonic development / endopeptidase activator activity / proteasome assembly / positive regulation of DNA repair / regulation of DNA repair / neuron projection morphogenesis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / telomere maintenance / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / proteasome complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / 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 / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / positive regulation of protein ubiquitination
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Proteasomal ubiquitin receptor ADRM1 / Ubiquitin carboxyl-terminal hydrolase isozyme L5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.997 Å
AuthorsHemmis, C.W. / Hill, C.P. / VanderLinden, R. / Whitby, F.G.
Funding support United States, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM059135 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM082545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM098401 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM097452 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA042014 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR001209 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Mol.Cell / Year: 2015
Title: Structural Basis for the Activation and Inhibition of the UCH37 Deubiquitylase.
Authors: VanderLinden, R.T. / Hemmis, C.W. / Schmitt, B. / Ndoja, A. / Whitby, F.G. / Robinson, H. / Cohen, R.E. / Yao, T. / Hill, C.P.
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references / Structure summary
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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 carboxyl-terminal hydrolase isozyme L5
B: Proteasomal ubiquitin receptor ADRM1
C: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)56,8303
Polymers56,8303
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-51 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.120, 99.610, 99.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L5 / UCH-L5 / Ubiquitin C-terminal hydrolase UCH37 / Ubiquitin thioesterase L5


Mass: 37533.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Uchl5, Uch37 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WUP7, ubiquitinyl hydrolase 1
#2: 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: 10719.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1, GP110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16186
#3: Protein Polyubiquitin-B


Mass: 8576.831 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 25% PEG 3350, 220 mM MgCl2,100 mM Bis-Tris / Temp details: constant temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: single wavelength
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→38.42 Å / Num. obs: 41390 / % possible obs: 99.7 % / Redundancy: 14.5 % / Biso Wilson estimate: 39.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.024 / Net I/σ(I): 17.7 / Num. measured all: 600550 / Scaling rejects: 553
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.0513.72.0061.53985229070.5890.55696.2
8.93-38.4212.70.04258.768805410.9980.01299

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
ADSC0.1.26data collection
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.997→38.422 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 1999 4.84 %
Rwork0.1806 --
obs0.1828 41279 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.997→38.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3719 0 0 201 3920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083782
X-RAY DIFFRACTIONf_angle_d1.0745106
X-RAY DIFFRACTIONf_dihedral_angle_d14.0861437
X-RAY DIFFRACTIONf_chiral_restr0.041575
X-RAY DIFFRACTIONf_plane_restr0.005670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9974-2.04730.42481340.33232639X-RAY DIFFRACTION95
2.0473-2.10260.34381400.27122767X-RAY DIFFRACTION100
2.1026-2.16450.30451390.24452772X-RAY DIFFRACTION100
2.1645-2.23440.25321430.21922780X-RAY DIFFRACTION100
2.2344-2.31420.26211430.21452794X-RAY DIFFRACTION100
2.3142-2.40690.26621420.1982772X-RAY DIFFRACTION100
2.4069-2.51640.24011470.19432800X-RAY DIFFRACTION100
2.5164-2.6490.26731410.2012785X-RAY DIFFRACTION100
2.649-2.81490.23561420.19112789X-RAY DIFFRACTION100
2.8149-3.03220.25461430.20092826X-RAY DIFFRACTION100
3.0322-3.33720.25331450.1922839X-RAY DIFFRACTION100
3.3372-3.81970.21721410.16872832X-RAY DIFFRACTION100
3.8197-4.8110.18461430.14312874X-RAY DIFFRACTION100
4.811-38.42890.18331560.15953011X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.47971.3567-0.15793.7583-0.33392.7178-0.0808-0.1546-0.1147-0.04560.039-0.38730.10810.2594-0.00870.31990.0382-0.0150.22860.00710.258717.1819-1.298125.0027
22.8651.9411.07446.91390.67013.4754-0.16240.1878-0.1074-0.36180.2144-0.04570.1735-0.2045-0.07740.2629-0.0329-0.00080.27150.03740.22835.4839-9.770320.7616
35.1336-0.0289-4.51851.642-1.13694.5563-0.31370.8779-0.1832-0.63990.455-0.35920.3873-0.4808-0.14990.7144-0.19130.08340.502-0.0370.435417.9143-2.8395.7761
42.99751.9499-0.22013.6634-0.96513.20280.1047-0.3074-0.3560.1077-0.2253-0.59180.14210.49820.05310.2520.0421-0.04440.30140.05280.308618.781-5.928531.7864
57.3482-2.5895-1.27926.7386-0.74475.93480.0257-0.5114-0.26610.9420.19180.3788-0.3311-0.3585-0.24930.44410.0547-0.04060.29170.07230.30322.646323.534634.9811
65.8582-5.3441-6.06855.50625.83046.0056-0.4071-0.3760.17980.26480.5168-0.31450.32240.5472-0.01490.51830.02580.01210.28610.0310.395314.190319.898923.0244
74.8197-0.36662.17253.85560.4321.20730.05170.13310.23420.09750.1502-0.6258-0.61151.26570.10920.4242-0.1990.00270.8601-0.16650.375639.552311.7486-4.2904
85.2453-3.9621.3034.6603-4.10036.9937-0.4076-1.8190.32842.01950.666-0.796-1.03441.0869-0.13850.8279-0.3598-0.14711.7390.11460.767941.046613.24663.024
93.7575-0.14680.20533.59390.77897.40810.18790.05430.06630.09820.0492-0.2109-0.76090.8788-0.20280.3401-0.0918-0.01550.4461-0.02310.314530.382711.5306-2.3607
100.78750.23480.76168.22162.19533.5434-0.40440.1925-0.2950.41761.3297-2.34460.40552.0219-0.86730.69110.3313-0.01431.5374-0.36980.891744.31762.6248-11.3491
116.2756-1.16161.42293.1561-1.09248.0390.6408-1.4743-0.6010.5905-0.9535-1.8813-0.34381.81110.11750.5086-0.1062-0.1940.75930.02620.623538.381410.217330.1877
122.57721.99960.85132.349-0.3337.7291-0.22850.0638-0.0828-0.09250.085-0.9917-0.50361.28770.08180.4993-0.0560.06210.5626-0.05030.652437.800411.077619.3329
136.46784.0160.51862.95181.62995.51660.18250.82521.1119-1.0586-0.23030.5629-1.6942-0.0191-0.06210.9926-0.01480.06570.4634-0.06370.704329.372618.80221.0585
149.11555.01921.79835.38391.15546.16140.2628-0.44190.1324-0.0962-0.2771-0.3687-0.71830.1952-0.05370.5656-0.03080.01270.4407-0.03090.492931.783613.248824.6268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 226 )
5X-RAY DIFFRACTION5chain 'A' and (resid 227 through 254 )
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 288 )
7X-RAY DIFFRACTION7chain 'A' and (resid 289 through 318 )
8X-RAY DIFFRACTION8chain 'B' and (resid 286 through 299 )
9X-RAY DIFFRACTION9chain 'B' and (resid 300 through 362 )
10X-RAY DIFFRACTION10chain 'B' and (resid 363 through 384 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 16 )
12X-RAY DIFFRACTION12chain 'C' and (resid 17 through 44 )
13X-RAY DIFFRACTION13chain 'C' and (resid 45 through 56 )
14X-RAY DIFFRACTION14chain 'C' and (resid 57 through 76 )

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