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- PDB-8vwo: Crystal structure of hRpn13 Pru bound with U-shaped peptide -

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Basic information

Entry
Database: PDB / ID: 8vwo
TitleCrystal structure of hRpn13 Pru bound with U-shaped peptide
Components
  • GLY-PRO-GLY-SER-MET-THR-THR
  • Proteasomal ubiquitin receptor ADRM1
KeywordsPROTEIN BINDING / Peptide binding / Complex / Proteasome / hRpn13 Pru
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 / proteasome complex ...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 / proteasome complex / 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 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / 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 / 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 / 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 / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
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.
Similarity search - Domain/homology
ACETATE ION / Proteasomal ubiquitin receptor ADRM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChandravanshi, M. / Walters, K.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 ZIABC011490 and FLEX award United States
CitationJournal: Nat Commun / Year: 2025
Title: An adaptive peptide-binding site in ubiquitin receptor hRpn13 revealed by structural studies
Authors: Hassan, B. / Chandravanshi, M. / Ng, M.Y. / Negi, H. / Wilson, B.A.P. / Walters, K.J.
History
DepositionFeb 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasomal ubiquitin receptor ADRM1
B: GLY-PRO-GLY-SER-MET-THR-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5134
Polymers17,3922
Non-polymers1212
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-4 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.262, 56.974, 77.793
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 16742.045 Da / Num. of mol.: 1 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1, GP110 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q16186
#2: Protein/peptide GLY-PRO-GLY-SER-MET-THR-THR


Mass: 649.715 Da / Num. of mol.: 1 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1 / Details (production host): Plasmid (pRSET) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.96 Å3/Da / Density % sol: 37.32 %
Crystal growTemperature: 277.15 K / Method: microbatch / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6 and 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→38.9 Å / Num. obs: 12367 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 17.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Χ2: 0.86 / Net I/σ(I): 13.9
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.238 / Num. unique obs: 717 / CC1/2: 0.973 / Rpim(I) all: 0.099 / Rrim(I) all: 0.258 / Χ2: 0.85 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
DIALSdata reduction
Cootmodel building
REFMACREFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→38.9 Å / SU ML: 0.1472 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 20.8182
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216 582 4.72 %
Rwork0.1952 11739 -
obs0.1961 12321 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.28 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 8 61 1037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011997
X-RAY DIFFRACTIONf_angle_d1.31021339
X-RAY DIFFRACTIONf_chiral_restr0.0819139
X-RAY DIFFRACTIONf_plane_restr0.0217174
X-RAY DIFFRACTIONf_dihedral_angle_d13.2355382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-2.040.21731410.18072878X-RAY DIFFRACTION99.83
2.04-2.330.21451460.18242902X-RAY DIFFRACTION99.97
2.33-2.940.2261430.20422947X-RAY DIFFRACTION99.9
2.94-38.90.21141520.19933012X-RAY DIFFRACTION97.53

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