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- PDB-2r2y: Crystal structure of the proteasomal Rpn13 PRU-domain -

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Basic information

Entry
Database: PDB / ID: 2r2y
TitleCrystal structure of the proteasomal Rpn13 PRU-domain
ComponentsProtein ADRM1
KeywordsPROTEIN BINDING / proteasome / ubiquitin / PH-domain / 19S regulator / receptor / UBIQUITIN-PROTEASOME-DEGRADATION PATHWAY / RECEPTOR DOMAIN FOR UBIQUITIN AND PROTEASOME BINDING
Function / homology
Function and homology information


Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 ...Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Asymmetric localization of PCP proteins / Regulation of RUNX3 expression and activity / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / follicle-stimulating hormone signaling pathway / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / UCH proteinases / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / Hedgehog ligand biogenesis / TNFR2 non-canonical NF-kB pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / Degradation of beta-catenin by the destruction complex / Activation of NF-kappaB in B cells / The role of GTSE1 in G2/M progression after G2 checkpoint / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Downstream TCR signaling / Separation of Sister Chromatids / MAPK6/MAPK4 signaling / Sertoli cell development / GLI3 is processed to GLI3R by the proteasome / ABC-family proteins mediated transport / positive regulation of growth hormone receptor signaling pathway / Neddylation / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / regulation of T cell differentiation in thymus / Antigen processing: Ubiquitination & Proteasome degradation / oogenesis / seminiferous tubule development / spermatid development / adipose tissue development / ovarian follicle development / proteasome complex / thymus development / nucleus / cytoplasm
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
Proteasomal ubiquitin receptor ADRM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsGroll, M. / Walters, K. / Dikic, I. / Finley, D.
CitationJournal: Nature / Year: 2008
Title: Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction.
Authors: Schreiner, P. / Chen, X. / Husnjak, K. / Randles, L. / Zhang, N. / Elsasser, S. / Finley, D. / Dikic, I. / Walters, K.J. / Groll, M.
History
DepositionAug 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ADRM1


Theoretical massNumber of molelcules
Total (without water)16,8551
Polymers16,8551
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.428, 56.223, 63.242
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 Protein ADRM1 / Adhesion-regulating molecule 1 / 110 kDa cell membrane glycoprotein / Gp110 / ARM-1


Mass: 16855.115 Da / Num. of mol.: 1 / Fragment: PRU-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: cDNA Mus Musculus / Gene: Adrm1, Gp110 / Plasmid: PrSet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: Q9JKV1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Description: Experimental Phases were obtained by SAD on a Se-derivative

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMPG/DESY, HAMBURG BW611.05
SYNCHROTRONMPG/DESY, HAMBURG BW620.9793
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDMar 13, 2007
MAR CCD 165 mm2CCDMar 13, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.051
20.97931
ReflectionResolution: 1.67→15 Å / Num. all: 16853 / Num. obs: 16853 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.67→1.7 Å / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→14.95 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.956 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23005 873 5.1 %RANDOM
Rwork0.21371 ---
obs0.21453 16267 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.018 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 0 79 974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022915
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9551231
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2715108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.46123.91346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99915171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.537157
X-RAY DIFFRACTIONr_chiral_restr0.1010.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02692
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2342
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2608
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.220
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1321.5558
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8522883
X-RAY DIFFRACTIONr_scbond_it2.7623404
X-RAY DIFFRACTIONr_scangle_it4.1634.5348
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 60 -
Rwork0.281 1167 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: 17.7466 Å / Origin y: 43.4234 Å / Origin z: 10.1198 Å
111213212223313233
T-0.0579 Å2-0.0104 Å2-0.0188 Å2--0.0578 Å2-0.0183 Å2---0.092 Å2
L1.8165 °2-0.0291 °20.1886 °2-3.359 °20.2831 °2--1.0313 °2
S0.007 Å °-0.0234 Å °-0.0269 Å °0.0858 Å °-0.0095 Å °-0.0533 Å °-0.0091 Å °0.0069 Å °0.0025 Å °

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