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- PDB-9e7k: Crystal structure of the UCH37 RPN13 DEUBAD complex bound to an i... -

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Basic information

Entry
Database: PDB / ID: 9e7k
TitleCrystal structure of the UCH37 RPN13 DEUBAD complex bound to an inhibitory nanobody in the canonical ubiquitin binding site
Components
  • Isoform 3 of Ubiquitin carboxyl-terminal hydrolase isozyme L5
  • Nb-cS1
  • Proteasomal ubiquitin receptor ADRM1
KeywordsHYDROLASE / Ubiquitin C-terminal Hydrolase / nanobody inhibitor / UCH37 / RPN13
Function / homology
Function and homology information


lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / 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) ...lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / 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) / endopeptidase inhibitor activity / Somitogenesis / 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 / regulation of proteasomal protein catabolic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / telomere maintenance / proteasome complex / positive regulation of DNA repair / Downregulation of TGF-beta receptor signaling / 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 / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / transcription elongation by RNA polymerase II / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / G2/M Checkpoints / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Regulation of RUNX3 expression and activity / Vif-mediated degradation of APOBEC3G / 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 / FCERI mediated NF-kB activation / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / 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 / RNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
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 / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. ...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 / 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. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Proteasomal ubiquitin receptor ADRM1 / Ubiquitin carboxyl-terminal hydrolase isozyme L5
Similarity search - Component
Biological speciesHomo sapiens (human)
Camelidae mixed library (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsPatel, R. / Li, Y. / Strieter, E. / Das, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149532 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM126296 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F31CA275390 United States
CitationJournal: Biorxiv / Year: 2025
Title: Site-Specific Nanobody Inhibitors of the Proteasomal Deubiquitinase UCH37.
Authors: Li, Y. / Chang, L.H. / Patel, R. / Shestoperova, E.I. / Du, J. / Das, C. / Strieter, E.R.
History
DepositionNov 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 3 of Ubiquitin carboxyl-terminal hydrolase isozyme L5
C: Nb-cS1
B: Proteasomal ubiquitin receptor ADRM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5907
Polymers65,4483
Non-polymers1424
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-61 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.634, 190.732, 45.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-401-

CL

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Components

#1: Protein Isoform 3 of Ubiquitin carboxyl-terminal hydrolase isozyme L5 / UCH-L5 / Ubiquitin C-terminal hydrolase UCH37 / Ubiquitin thioesterase L5


Mass: 37523.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL5, UCH37, AD-019, CGI-70 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5K5, ubiquitinyl hydrolase 1
#2: Antibody Nb-cS1


Mass: 14970.704 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae mixed library (mammal) / Production host: Escherichia coli (E. coli)
#3: 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: 12953.653 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
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 2% v/v Tacsimate pH 5.0, 16% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→37.31 Å / Num. obs: 29105 / % possible obs: 94.51 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.043 / Rrim(I) all: 0.079 / Net I/σ(I): 14.72
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.831 / Num. unique obs: 2823 / CC1/2: 0.532 / Rpim(I) all: 0.508 / Rrim(I) all: 0.978

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→37.31 Å / SU ML: 0.42 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 31.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 1368 4.71 %
Rwork0.2346 --
obs0.2363 29072 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→37.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 4 65 3752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033769
X-RAY DIFFRACTIONf_angle_d0.5845114
X-RAY DIFFRACTIONf_dihedral_angle_d4.095515
X-RAY DIFFRACTIONf_chiral_restr0.042576
X-RAY DIFFRACTIONf_plane_restr0.005674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.490.43691260.35772645X-RAY DIFFRACTION92
2.49-2.590.36011570.32032854X-RAY DIFFRACTION100
2.59-2.710.35131430.30852905X-RAY DIFFRACTION100
2.71-2.860.3441310.29112886X-RAY DIFFRACTION99
2.86-3.030.32631500.2872882X-RAY DIFFRACTION99
3.03-3.270.28631490.25762844X-RAY DIFFRACTION98
3.27-3.60.3011320.25032880X-RAY DIFFRACTION98
3.6-4.120.30151030.22952610X-RAY DIFFRACTION87
4.12-5.180.23061550.19822422X-RAY DIFFRACTION83
5.19-37.310.2271220.20712776X-RAY DIFFRACTION88
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)
15.3965-0.7065-0.71024.56910.57452.38990.0093-0.00740.23390.1126-0.08850.038-0.37780.04720.07150.50890.0375-0.04210.42350.01370.450368.35919.55755.1813
280.44043.96935.21110.07697.05160.30740.89-1.2523-0.17920.0312-0.89230.59680.4924-0.31640.59250.06010.02260.5599-0.10510.823777.7296.98712.195
31.60942.1601-1.82138.6913-2.87082.5879-0.0311-0.17280.271-0.1404-0.0787-0.4986-0.55610.27120.12720.7069-0.0725-0.05180.70370.04150.88180.840124.46682.6359
48.0313-0.0637-0.70916.9731-1.28676.60070.054-0.0806-0.64330.5891-0.08890.2410.2974-0.26420.04550.53990.07050.06160.4119-0.00310.492163.429713.852215.718
51.45230.48111.96936.38015.31017.46720.09880.158-0.36960.3021-0.06560.57620.6189-0.1283-0.0790.51830.07150.060.5732-0.07460.775154.920810.1776-6.7803
62.08541.58920.24726.94360.82720.21980.00780.37230.2308-0.3421-0.03550.03060.026-0.02760.04520.71580.18490.00490.79260.03490.802561.311433.9862-11.2518
78.47465.40854.10696.17773.28085.53430.0904-1.00853.18730.1127-0.25581.2203-0.5544-0.76970.57841.14920.4321-0.00840.9099-0.03550.987140.826839.94833.6418
89.57055.18731.46689.05561.68975.2607-0.61861.34672.162-0.9369-0.14661.90120.75030.310.54630.81440.2514-0.23530.9603-0.26681.325831.153930.9001-2.4783
93.78154.0506-3.61846.8943-4.62453.90220.5186-0.42891.7083-0.283-0.7570.5076-0.6930.66430.03050.78720.1516-0.08050.832-0.00151.03947.202832.05593.2924
108.7408-6.3832-0.41385.25971.32667.20950.0768-0.4778-0.6423-0.10710.39340.61740.29040.7586-0.35240.7060.08070.03570.7847-0.07630.961443.921924.10214.0144
115.32695.89861.95856.5422.27136.451-0.32490.0724-1.98231.0552-1.18871.11950.86070.49691.45380.74540.1560.06841.1536-0.31271.599937.874117.6061-0.6271
129.0067-3.5996-2.35774.0265.34778.44220.11012.14311.6939-0.60410.63640.1459-1.80670.1134-0.8871.15310.1332-0.08240.91070.20050.889845.741432.1492-6.5754
131.2101-0.56980.95758.572-2.30163.81010.19190.3276-0.0486-0.068-0.251.1085-0.1726-0.69310.03150.80120.2877-0.09050.8071-0.17590.975936.607328.58061.2474
149.8193-2.1893.29144.5521-1.19472.9134-0.6732-0.05480.87630.5260.26680.9137-0.5346-0.39160.4010.75170.17480.00970.6229-0.10810.703343.555631.87638.0179
152.79880.85392.641.0431-0.81415.6657-3.4979-2.5780.1661.60.72780.74810.172-0.23471.97151.5080.77470.07561.3653-0.14481.10763.525352.9036-4.376
166.02663.8851.69215.9359-3.23276.5831-0.62981.22120.5289-1.06040.42790.635-0.7194-0.36120.20330.74340.18460.08931.05110.05040.928263.886251.8033-19.2234
176.0849-0.33091.25175.4442-0.98594.08390.0362-0.38050.14210.3458-0.6001-0.60630.3083-0.0750.51630.68420.12590.07890.62510.02580.795866.290441.9335-10.3217
185.78895.62211.77125.71993.10046.6985-1.21270.27620.3582-1.09350.2779-2.89820.22690.90870.81291.04190.387-0.31930.54450.0641.768684.029853.2776-8.1393
193.61811.38682.02834.49262.54138.71450.10560.25670.33210.7971.1757-0.1675-1.88420.0845-0.30810.9527-0.0116-0.23761.295-0.09771.877283.9658.9454-3.9007
203.17660.38980.9866.7193-0.02676.3843-0.0631-1.94762.6413-1.1362-1.5925-1.5015-0.44260.36890.2210.8324-0.0686-0.27281.4726-0.17821.989776.818262.0029-7.5143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 163 )
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 213 )
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 255 )
6X-RAY DIFFRACTION6chain 'A' and (resid 256 through 312 )
7X-RAY DIFFRACTION7chain 'C' and (resid 23 through 30 )
8X-RAY DIFFRACTION8chain 'C' and (resid 31 through 44 )
9X-RAY DIFFRACTION9chain 'C' and (resid 45 through 60 )
10X-RAY DIFFRACTION10chain 'C' and (resid 61 through 80 )
11X-RAY DIFFRACTION11chain 'C' and (resid 81 through 87 )
12X-RAY DIFFRACTION12chain 'C' and (resid 88 through 97 )
13X-RAY DIFFRACTION13chain 'C' and (resid 98 through 119 )
14X-RAY DIFFRACTION14chain 'C' and (resid 120 through 136 )
15X-RAY DIFFRACTION15chain 'B' and (resid 287 through 297 )
16X-RAY DIFFRACTION16chain 'B' and (resid 298 through 313 )
17X-RAY DIFFRACTION17chain 'B' and (resid 314 through 347 )
18X-RAY DIFFRACTION18chain 'B' and (resid 348 through 362 )
19X-RAY DIFFRACTION19chain 'B' and (resid 363 through 373 )
20X-RAY DIFFRACTION20chain 'B' and (resid 374 through 384 )

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