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- PDB-4wlq: Crystal structure of mUCH37-hRPN13 CTD complex -

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Basic information

Entry
Database: PDB / ID: 4wlq
TitleCrystal structure of mUCH37-hRPN13 CTD complex
Components
  • 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 / cytosolic proteasome complex / Ino80 complex / positive regulation of smoothened signaling pathway / proteasome regulatory particle, lid subcomplex / Regulation of ornithine decarboxylase (ODC) ...lateral ventricle development / UCH proteinases / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / cytosolic proteasome complex / Ino80 complex / positive regulation of smoothened signaling pathway / proteasome regulatory particle, lid subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / endopeptidase inhibitor activity / molecular function inhibitor activity / proteasome binding / regulation of chromosome organization / midbrain development / regulation of DNA replication / regulation of embryonic development / protein deubiquitination / endopeptidase activator activity / proteasome assembly / regulation of DNA repair / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / telomere maintenance / proteasome complex / positive regulation of DNA repair / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / transcription elongation by RNA polymerase II / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / protease binding / ubiquitin-dependent protein catabolic process / DNA recombination / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / DNA repair / positive regulation of DNA-templated transcription / nucleolus / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / UCH37-like (ULD) domain profile. / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / UCH37-like (ULD) domain profile. / 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 / Ubiquitin carboxyl-terminal hydrolase (UCH) catalytic domain profile. / 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 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Proteasomal ubiquitin receptor ADRM1 / Ubiquitin carboxyl-terminal hydrolase isozyme L5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.85 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
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 / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
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_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
B: Proteasomal ubiquitin receptor ADRM1


Theoretical massNumber of molelcules
Total (without water)47,9242
Polymers47,9242
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-36 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.935, 96.843, 98.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 10390.718 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

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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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 20% PEG 3350, 200 mM Mg(OAC)2,100 mM HEPES / Temp details: constant temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: single wavelength
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 2, 2010
RadiationMonochromator: VariMax-HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→38.26 Å / Num. obs: 14095 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 86.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.042 / Net I/σ(I): 12.2 / Num. measured all: 110961 / Scaling rejects: 173
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
2.85-37.61.0032.41529920110.8610.375100
9.01-38.266.80.07726.535045150.9960.03199

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Processing

Software
NameVersionClassification
CrystalClear0.1.26data collection
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.85→38.144 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 1253 8.98 %
Rwork0.1918 12699 -
obs0.1996 13952 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 358.99 Å2 / Biso mean: 112.4345 Å2 / Biso min: 41.99 Å2
Refinement stepCycle: final / Resolution: 2.85→38.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 0 0 3082
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093139
X-RAY DIFFRACTIONf_angle_d1.2124243
X-RAY DIFFRACTIONf_chiral_restr0.041474
X-RAY DIFFRACTIONf_plane_restr0.006558
X-RAY DIFFRACTIONf_dihedral_angle_d15.9711179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8501-2.96420.41121320.292213721504
2.9642-3.09910.32521380.25413751513
3.0991-3.26240.33351330.232713921525
3.2624-3.46660.3261400.20513861526
3.4666-3.73410.2911370.190614131550
3.7341-4.10950.27831390.187113911530
4.1095-4.70320.27051400.163914271567
4.7032-5.92190.29191450.185514261571
5.9219-38.14760.23291490.187815171666
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)
18.16571.6642.67777.0775-1.91978.18130.07390.4384-0.7753-0.9442-0.01050.52430.3122-0.56-0.05021.1960.02890.03170.5953-0.09250.5772-14.9355-1.995716.6563
27.7802-0.2731.78334.75970.1067.1469-0.3881-1.23150.40881.37450.12261.07580.1097-1.1190.13961.03370.09430.1811.1003-0.02270.6448-19.32874.922331.9257
38.7166-0.18383.69788.57662.89833.22540.42580.0677-0.2324-0.7427-0.0510.2802-0.05590.1559-0.62120.9894-0.06460.1920.58110.01070.6386-8.66715.764324.3209
45.49045.87130.87258.83850.49279.6638-0.05260.3030.0504-1.0017-0.0954-0.71790.03180.56250.23390.88550.14820.21310.5457-0.03840.5589-4.85017.83919.4336
59.1598-1.7636.73756.70963.83929.13590.55391.9325-0.52420.1849-0.54490.30440.46110.74260.08641.7366-0.1112-0.07110.88330.01520.6097-17.9142.9995.4254
68.46754.20012.18849.47041.88429.0420.0743-0.80250.26760.6997-0.54960.94990.2227-1.39540.4620.56730.00920.25310.715-0.10340.5539-13.17099.450332.3857
76.6380.3314-1.44472.6551-0.24614.8690.8838-1.31740.1850.7464-0.28170.73790.1248-1.4937-0.08840.6840.02450.32161.0885-0.17750.6538-24.38033.475732.3344
89.1043-3.65793.13153.5721-4.49946.1044-0.01890.17171.67261.1913-0.0033-1.2372-0.49850.60230.19131.5953-0.0118-0.06820.5438-0.08150.6703-2.6278-22.812934.8944
97.9579-6.69875.55188.2034-5.86214.4105-0.8542-0.43170.0868-0.16720.0495-0.02360.8167-1.35450.39461.276-0.1156-0.01950.6175-0.01750.696-14.9686-19.55723.5563
102.71890.6699-2.08644.196-3.04363.17590.28572.24260.0191-0.39030.67641.77450.0352-0.869-1.10740.9052-0.01610.0841.27880.08651.1519-38.726-11.0839-5.5113
118.2897-0.83184.42251.2454-1.27052.94750.2628-1.3685-1.68880.46450.49540.24210.0319-2.4306-0.39721.8143-0.69790.34892.049-0.21951.0198-41.7068-14.86391.9769
127.8558-1.83291.85158.0193-0.23889.4379-0.1647-0.49640.7551.1281-0.45270.4208-0.8876-0.71870.42340.9630.03830.03350.701-0.1930.6232-31.993-9.0058-3.468
130.7739-0.6381-1.41040.54661.15776.8720.78210.218-2.1818-1.2232-1.46532.6694-0.6798-2.79111.00070.92230.1988-0.13691.8368-0.10291.9619-45.4334-2.777-10.4203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 35 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 71 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 85 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 133 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 162 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 196 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 197 through 226 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 227 through 254 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 255 through 288 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 289 through 314 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 286 through 303 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 304 through 370 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 371 through 384 )B0

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