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- PDB-3txn: Crystal structure of Rpn6 from Drosophila melanogaster, native data -

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Basic information

Entry
Database: PDB / ID: 3txn
TitleCrystal structure of Rpn6 from Drosophila melanogaster, native data
Components26S proteasome regulatory complex subunit p42B
KeywordsHYDROLASE / PROTEIN BINDING / 26 S proteasome / PCI domain / alpha solenoid / regulatory particle / lid
Function / homology
Function and homology information


Activation of NF-kappaB in B cells / Cross-presentation of soluble exogenous antigens (endosomes) / Downstream TCR signaling / Degradation of NF-kappa-B inhibitor, CACT / FCERI mediated NF-kB activation / Regulation of ornithine decarboxylase (ODC) / CLEC7A (Dectin-1) signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Circadian Clock pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha ...Activation of NF-kappaB in B cells / Cross-presentation of soluble exogenous antigens (endosomes) / Downstream TCR signaling / Degradation of NF-kappa-B inhibitor, CACT / FCERI mediated NF-kB activation / Regulation of ornithine decarboxylase (ODC) / CLEC7A (Dectin-1) signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Circadian Clock pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / Ubiquitination and degradation of phosphorylated ARM / Separation of Sister Chromatids / Degradation of AXIN / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Regulation of RAS by GAPs / NIK-->noncanonical NF-kB signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / KEAP1-NFE2L2 pathway / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Nuclear CI is degraded / ABC-family proteins mediated transport / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Ubiquitination and proteolysis of phosphorylated CI / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Interleukin-1 signaling / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Assembly of the pre-replicative complex / Hedgehog ligand biogenesis / Degradation of PER / Asymmetric localization of PCP proteins / Degradation of CRY / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / Regulation of PTEN stability and activity / Degradation of TIM / Antigen processing: Ubiquitination & Proteasome degradation / Orc1 removal from chromatin / Ub-specific processing proteases / UCH proteinases / Neutrophil degranulation / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / proteasome complex / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / structural molecule activity / nucleoplasm / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #570 / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / PCI/PINT associated module / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #570 / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / PCI/PINT associated module / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Winged helix DNA-binding domain superfamily / Mainly Alpha
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 11
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.496 Å
AuthorsPathare, G.R. / Bracher, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together.
Authors: Pathare, G.R. / Nagy, I. / Bohn, S. / Unverdorben, P. / Hubert, A. / Korner, R. / Nickell, S. / Lasker, K. / Sali, A. / Tamura, T. / Nishioka, T. / Forster, F. / Baumeister, W. / Bracher, A.
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 1, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 26S proteasome regulatory complex subunit p42B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5935
Polymers44,2171
Non-polymers3764
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.251, 161.251, 42.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein 26S proteasome regulatory complex subunit p42B / BcDNA.LD18931 / Proteasome p44.5 subunit / isoform B / PSMD11


Mass: 44216.879 Da / Num. of mol.: 1 / Fragment: UNP residues 30-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: BcDNA.LD18931, CG10149, Dmel_CG10149, Rpn6 / Plasmid: pTipRC1 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L-88 / References: UniProt: Q7KLV9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM Tris HCl pH 7.5 200 mM Li2SO4, 12% PEG-3350, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.00686 Å
DetectorType: PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00686 Å / Relative weight: 1
ReflectionResolution: 2.496→140.028 Å / Num. all: 22030 / Num. obs: 22030 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 65.531 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.496-2.633.30.3032.51059931750.30399
2.63-2.793.30.1983.8980030070.19899.5
2.79-2.983.50.1176.3996928660.117100
2.98-3.223.40.0848.6908426520.08499.9
3.22-3.533.20.06211.3785224470.06299.4
3.53-3.953.40.04714.1741922050.04799.5
3.95-4.563.30.03916.2648419650.03999.3
4.56-5.583.10.03518.4505516450.03598.4
5.58-7.893.30.03121.4435813190.03199.3
7.89-52.78230.02920.422787490.02998

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.496→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.29 / WRfactor Rwork: 0.2421 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8273 / SU B: 19.02 / SU ML: 0.189 / SU R Cruickshank DPI: 0.3236 / SU Rfree: 0.2642 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1146 5.2 %RANDOM
Rwork0.2157 ---
obs0.2182 20825 99.21 %-
all-20991 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.59 Å2 / Biso mean: 65.3496 Å2 / Biso min: 28.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å2-0.39 Å20 Å2
2---0.78 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.496→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 22 49 2788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222771
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9923740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0435352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8825.086116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.5515508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2441514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022011
X-RAY DIFFRACTIONr_nbd_refined0.220.21246
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.24
X-RAY DIFFRACTIONr_mcbond_it0.6051.51812
X-RAY DIFFRACTIONr_mcangle_it1.03922797
X-RAY DIFFRACTIONr_scbond_it1.72331073
X-RAY DIFFRACTIONr_scangle_it2.794.5943
LS refinement shellResolution: 2.496→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 77 -
Rwork0.358 1502 -
all-1579 -
obs--98.5 %
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)
12.15242.20330.63515.06161.25891.1917-0.15640.05010.3314-0.2710.04380.4077-0.34380.04630.11250.2185-0.2088-0.0354-0.08460.0525-0.124326.751163.9084-0.665
24.05074.3125-0.62258.4206-1.85712.0640.026-0.108-0.12430.2938-0.1455-0.0279-0.49320.37470.1194-0.1432-0.09810.0397-0.2222-0.0282-0.173217.552425.53015.2882
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 280
2X-RAY DIFFRACTION1A502
3X-RAY DIFFRACTION1A600 - 621
4X-RAY DIFFRACTION2A281 - 390
5X-RAY DIFFRACTION2A500 - 501
6X-RAY DIFFRACTION2A503
7X-RAY DIFFRACTION2A622 - 648

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