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- PDB-5irs: crystal structure of the proteasomal Rpn13 PRU-domain -

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Basic information

Entry
Database: PDB / ID: 5irs
Titlecrystal structure of the proteasomal Rpn13 PRU-domain
ComponentsProteasomal ubiquitin receptor ADRM1
KeywordsPROTEIN BINDING / Ubiquitin
Function / homology
Function and homology information


proteasome regulatory particle, lid subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / molecular function inhibitor activity / proteasome binding / endopeptidase activator activity / proteasome assembly / Regulation of activated PAK-2p34 by proteasome mediated degradation ...proteasome regulatory particle, lid subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / molecular function inhibitor activity / proteasome binding / endopeptidase activator activity / proteasome assembly / 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 / proteasome complex / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / 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 / 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 / transcription elongation by RNA polymerase II / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / 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 / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Proteasomal ubiquitin receptor Rpn13/ADRM1 / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain ...Proteasomal ubiquitin receptor Rpn13/ADRM1 / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / 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. / PH-domain like / Roll / Mainly Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Proteasomal ubiquitin receptor ADRM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.796 Å
AuthorsChen, X. / Shi, K. / Walters, K. / Aihara, H.
CitationJournal: Structure / Year: 2016
Title: Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome.
Authors: Chen, X. / Randles, L. / Shi, K. / Tarasov, S.G. / Aihara, H. / Walters, K.J.
History
DepositionMar 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Data collection
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 16, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasomal ubiquitin receptor ADRM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9193
Polymers16,6111
Non-polymers3092
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.555, 56.476, 64.089
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 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: 16610.850 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
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.796→50 Å / Num. obs: 14838 / % possible obs: 99.06 % / Redundancy: 6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.72
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.82 / % possible all: 96.35

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Processing

Software
NameVersionClassification
PHENIXdev_1218refinement
HKL-2000HKL-2000data reduction
HKL-2000HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2R2Y

2r2y


Resolution: 1.796→35.451 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 1433 9.97 %Random selection
Rwork0.167 ---
obs0.1713 14367 95.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.796→35.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms911 0 16 67 994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019972
X-RAY DIFFRACTIONf_angle_d1.5011307
X-RAY DIFFRACTIONf_dihedral_angle_d13.881375
X-RAY DIFFRACTIONf_chiral_restr0.1137
X-RAY DIFFRACTIONf_plane_restr0.006170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7956-1.85980.26991310.23951191X-RAY DIFFRACTION89
1.8598-1.93420.25281370.23041237X-RAY DIFFRACTION94
1.9342-2.02220.24331360.18811275X-RAY DIFFRACTION95
2.0222-2.12880.20151360.17511257X-RAY DIFFRACTION95
2.1288-2.26220.22721430.17351273X-RAY DIFFRACTION97
2.2622-2.43680.25411460.18261294X-RAY DIFFRACTION97
2.4368-2.6820.2071470.17051301X-RAY DIFFRACTION96
2.682-3.06990.2211470.17751318X-RAY DIFFRACTION98
3.0699-3.8670.19051510.15031360X-RAY DIFFRACTION99
3.867-35.45840.19831590.15771428X-RAY DIFFRACTION99
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)
11.1001-0.0779-0.95090.79481.32192.874-0.64980.64540.3509-0.62130.57990.7731-1.3008-1.7865-0.09720.42850.0536-0.09480.44610.08690.285414.746352.09461.0626
22.42772.1358-0.45657.67940.08430.1311-0.04391.0642-0.1867-1.3731-0.1440.2955-0.6958-1.2266-0.38080.27450.0473-0.05070.3785-0.05010.148413.605641.65663.1515
30.5576-0.01710.57613.2278-0.49550.6640.0426-0.9123-0.17880.97760.04131.18220.19-0.15750.00340.37220.017-0.02530.39560.02910.362313.563138.146216.6615
40.60330.41950.47510.4320.1351.3556-0.1071-0.4766-0.19790.18670.0541-0.02280.49470.77460.20841.14280.51750.22720.6532-0.1732-0.00414.872836.115627.0272
52.5520.11252.82750.83470.73347.31670.2032-1.2846-0.58710.82020.2510.08491.0274-1.54320.01030.38280.0240.02330.35360.04030.306212.298833.696219.2824
61.0821-1.07320.29571.0082-0.32470.68640.01050.1031-0.1410.01520.07180.088-0.1986-0.65940.01180.2022-0.0209-0.01320.2343-0.01040.244810.842343.62718.0941
71.52430.727-0.60631.22820.94951.9952-0.68210.6731.1646-0.1782-0.22321.6048-1.4454-0.6976-0.1150.5895-0.0261-0.14170.26780.00390.461817.082860.25847.4434
80.37590.50450.26390.75590.77281.4606-0.1541-0.06550.2173-0.5046-0.07870.5532-0.827-0.18330.00020.2208-0.0119-0.01720.2042-0.01360.253713.14448.424310.7049
90.3597-0.13661.2035.82911.19645.04140.5907-0.53160.04520.4593-0.35611.20420.4246-1.58080.53060.10160.01550.04040.4212-0.0770.41174.313244.673410.796
100.29660.10560.05650.57280.28830.21210.2941-0.75410.29610.1771-0.29910.1986-0.2008-0.07330.00310.244-0.0262-0.02260.2109-0.04780.265419.608953.639914.1195
110.88970.8565-0.26911.58620.98322.0568-0.1105-0.33670.39340.63870.7727-1.2944-0.1151.27590.18360.3015-0.0697-0.01840.3941-0.0220.487927.527646.713512.5128
121.8513-1.39921.15413.1075-0.13811.01040.12070.0002-2.0507-1.5078-0.4491-1.42421.45541.145-0.02740.4630.09930.12840.36540.080.582827.160331.491111.5607
130.10130.0245-0.06570.188-0.16580.14770.63090.1032-0.4685-1.69280.019-1.1812-0.0733-0.05430.00720.81180.1487-0.12730.4498-0.07390.552322.160527.952911.0411
140.4497-0.083-0.23790.3929-0.26390.5433-0.10440.1367-0.333-0.6132-0.2048-0.03860.24140.4883-0.00270.2480.0188-0.03780.2005-0.04260.292921.395735.48379.4801
151.7003-0.30070.44650.32530.42051.08980.406-0.5333-0.64230.9394-0.1808-1.236-0.22261.0557-0.04250.2735-0.151-0.08980.3432-0.01140.448527.035746.573517.4046
160.1857-0.6692-0.8092.87773.2623.7407-0.4039-0.70010.01722.28550.084-0.3777-0.0389-0.4995-0.36340.5622-0.0223-0.19660.35360.0310.335223.791543.732220.975
172.0712-0.5305-0.81121.6291-0.68480.8193-0.04240.9904-0.692-0.17330.34830.2140.16330.51230.020.2428-0.0145-0.04770.3077-0.09430.325615.551335.66936.9825
181.4732-0.2596-1.2726.69680.8031.1835-0.18440.4726-0.6768-1.8972-0.0958-0.09580.5941-0.3411-0.04620.4694-0.00160.10770.3588-0.05380.369422.555737.2328-0.1901
190.72160.3254-0.36840.51960.26320.5526-0.13220.23910.0747-0.84780.1647-0.8285-0.40210.23750.00190.3271-0.06840.02960.34190.01040.270525.261946.63832.8318
203.9713-0.039-3.48251.6016-3.7681.998-0.23770.62230.6961-0.52050.4055-1.536-0.55852.54920.25390.3447-0.16520.11280.4374-0.04420.4527.762752.38326.7676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 21:24)
2X-RAY DIFFRACTION2(chain A and resid 25:28)
3X-RAY DIFFRACTION3(chain A and resid 29:32)
4X-RAY DIFFRACTION4(chain A and resid 33:36)
5X-RAY DIFFRACTION5(chain A and resid 37:42)
6X-RAY DIFFRACTION6(chain A and resid 43:49)
7X-RAY DIFFRACTION7(chain A and resid 50:57)
8X-RAY DIFFRACTION8(chain A and resid 58:62)
9X-RAY DIFFRACTION9(chain A and resid 63:70)
10X-RAY DIFFRACTION10(chain A and resid 71:77)
11X-RAY DIFFRACTION11(chain A and resid 78:83)
12X-RAY DIFFRACTION12(chain A and resid 84:87)
13X-RAY DIFFRACTION13(chain A and resid 88:91)
14X-RAY DIFFRACTION14(chain A and resid 92:95)
15X-RAY DIFFRACTION15(chain A and resid 96:100)
16X-RAY DIFFRACTION16(chain A and resid 101:105)
17X-RAY DIFFRACTION17(chain A and resid 106:113)
18X-RAY DIFFRACTION18(chain A and resid 114:120)
19X-RAY DIFFRACTION19(chain A and resid 121:127)
20X-RAY DIFFRACTION20(chain A and resid 128:131)

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