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- PDB-3txm: Crystal structure of Rpn6 from Drosophila melanogaster, Gd(3+) complex -

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Basic information

Entry
Database: PDB / ID: 3txm
TitleCrystal structure of Rpn6 from Drosophila melanogaster, Gd(3+) complex
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


Cross-presentation of soluble exogenous antigens (endosomes) / Degradation of NF-kappa-B inhibitor, CACT / Regulation of ornithine decarboxylase (ODC) / Regulation of RAS by GAPs / Circadian Clock pathway / Activation of NF-kappaB in B cells / 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 ...Cross-presentation of soluble exogenous antigens (endosomes) / Degradation of NF-kappa-B inhibitor, CACT / Regulation of ornithine decarboxylase (ODC) / Regulation of RAS by GAPs / Circadian Clock pathway / Activation of NF-kappaB in B cells / 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 / Downstream TCR signaling / Ubiquitination and degradation of phosphorylated ARM / Separation of Sister Chromatids / FCERI mediated NF-kB activation / Degradation of AXIN / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / 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 / Hedgehog ligand biogenesis / Degradation of PER / Asymmetric localization of PCP proteins / Degradation of CRY / Antigen processing: Ubiquitination & Proteasome degradation / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / Regulation of PTEN stability and activity / Assembly of the pre-replicative complex / Degradation of TIM / UCH proteinases / Orc1 removal from chromatin / Ub-specific processing proteases / 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
GADOLINIUM ION / 26S proteasome non-ATPase regulatory subunit 11
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)45,0387
Polymers44,2171
Non-polymers8216
Water0
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


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-GD3 / GADOLINIUM ION / Gadolinium


Mass: 157.250 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Gd
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: ID23-1 / Wavelength: 1.0332, 1.71024, 1.71072
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
21.710241
31.710721
ReflectionResolution: 3→140.218 Å / Num. all: 12435 / Num. obs: 12435 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.163.70.4891.6653217870.48996.6
3.16-3.363.70.2912.6638417180.29199.8
3.36-3.593.70.1525586415940.15297.9
3.59-3.883.60.0878.4540514900.08798.1
3.88-4.253.60.05812.9501713930.05898.4
4.25-4.753.50.03419.8436412490.03498.4
4.75-5.483.40.03318.9379511080.03398.2
5.48-6.713.60.0292434509620.02998.3
6.71-9.493.50.02125.825617320.02197.3
9.49-38.893.10.01835.412604020.01890.6

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Phasing

PhasingMethod: MAD
Phasing dmFOM : 0.53 / FOM acentric: 0.51 / FOM centric: 0.65 / Reflection: 12536 / Reflection acentric: 11229 / Reflection centric: 1307
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.5-40.3130.980.990.95591439152
5.3-8.50.90.910.8217541500254
4.3-5.30.790.790.821701939231
3.7-4.30.60.590.7221591959200
3.2-3.70.320.310.4538043497307
3-3.20.130.120.220581895163

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
SHELXphasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2759 / WRfactor Rwork: 0.2566 / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.8015 / SU B: 43.853 / SU ML: 0.34 / SU R Cruickshank DPI: 1.397 / SU Rfree: 0.4129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 638 5.1 %RANDOM
Rwork0.2053 ---
obs0.2076 11819 100 %-
all-11819 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 213.44 Å2 / Biso mean: 114.4132 Å2 / Biso min: 67.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å2-0.92 Å20 Å2
2---1.84 Å20 Å2
3---2.76 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 14 0 2731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222761
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9893730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.555352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36125.086116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.0615508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6941514
X-RAY DIFFRACTIONr_chiral_restr0.10.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022011
X-RAY DIFFRACTIONr_nbd_refined0.2360.21346
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.24
X-RAY DIFFRACTIONr_mcbond_it0.4981.51794
X-RAY DIFFRACTIONr_mcangle_it0.93622797
X-RAY DIFFRACTIONr_scbond_it1.19331068
X-RAY DIFFRACTIONr_scangle_it2.1164.5933
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 42 -
Rwork0.375 656 -
all-698 -
obs--100 %
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)
19.09190.06992.16992.3896-0.39761.5379-0.27340.45870.6259-0.06190.0656-0.3013-0.30490.43140.2077-0.3072-0.0655-0.00050.43270.0244-0.3641-11.9299148.649716.585
219.83112.164-2.74933.2733-0.95952.362-0.2069-0.4488-0.09340.106-0.03090.27390.18380.96740.2378-0.42750.0506-0.0366-0.15690.0032-0.5088-49.7986137.56522.6441
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 280
2X-RAY DIFFRACTION1A1 - 2
3X-RAY DIFFRACTION1A423
4X-RAY DIFFRACTION2A281 - 390
5X-RAY DIFFRACTION2A3 - 4
6X-RAY DIFFRACTION2A424

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