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- PDB-3q5x: Structure of proteasome tether -

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Basic information

Entry
Database: PDB / ID: 3q5x
TitleStructure of proteasome tether
ComponentsProtein cut8
KeywordsCELL CYCLE / nuclear proteasome tether / 26S / novel fold / dimer
Function / homology
Function and homology information


proteasome localization / sterol binding / nuclear protein quality control by the ubiquitin-proteasome system / proteasome binding / nuclear periphery / nuclear envelope / chromatin / identical protein binding / nucleus
Similarity search - Function
Tethering factor for nuclear proteasome Cut8/Sts1 / Tethering factor for nuclear proteasome Cut8/Sts1 / Cut8/Sts1 superfamily / Cut8, nuclear proteasome tether protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Tethering factor for nuclear proteasome cut8
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsSchumacher, M.A.
CitationJournal: To be Published
Title: Structure of Proteasome Tether
Authors: Schumacher, M.A. / Glover, T. / Weijun, X.
History
DepositionDec 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Protein cut8


Theoretical massNumber of molelcules
Total (without water)28,4631
Polymers28,4631
Non-polymers00
Water181
1
A: Protein cut8

A: Protein cut8


Theoretical massNumber of molelcules
Total (without water)56,9272
Polymers56,9272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5710 Å2
ΔGint-43 kcal/mol
Surface area21120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.440, 36.200, 53.990
Angle α, β, γ (deg.)90.00, 108.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein cut8 / Cell untimely torn protein 8


Mass: 28463.439 Da / Num. of mol.: 1 / Fragment: UNP residues 1-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: cut8, SPAC17C9.13c / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38937
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 45.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2 M AMMONIUM SULFATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 / Wavelength: 0.98 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 12, 2007 / Details: MIRRORS
RadiationMonochromator: GRAPOHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.981
ReflectionResolution: 2.98→49 Å / Num. obs: 5346 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 1.2 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.06 / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KRH

3krh
PDB Unreleased entry


Resolution: 2.98→34.99 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 783903.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED. THE AUTHORS USED A SIGMA CUTOFF FOR REFINEMENT OF (3 TIMES RES RANGE 40-2.98), WHICH AIDED IN DIMINISHING AFFECTS FROM ANISTOTROPY. THE DATA WERE QUITE WEAK ...Details: BULK SOLVENT MODEL USED. THE AUTHORS USED A SIGMA CUTOFF FOR REFINEMENT OF (3 TIMES RES RANGE 40-2.98), WHICH AIDED IN DIMINISHING AFFECTS FROM ANISTOTROPY. THE DATA WERE QUITE WEAK (COLLECTED IN HOUSE) BUT THE REFLECTIONS AT THIS SIGMA WERE QUITE STRONG.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 742 13.9 %RANDOM
Rwork0.262 ---
obs0.262 5346 95.7 %-
all-5586 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2785 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 74 Å2
Baniso -1Baniso -2Baniso -3
1--25.73 Å20 Å23.6 Å2
2--36.74 Å20 Å2
3----11.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.68 Å0.59 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.98→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 0 1 1570
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.98→3.17 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 109 12.4 %
Rwork0.377 770 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top

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