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- PDB-5jog: CRYSTAL STRUCTURE OF CSN5(2-257) IN COMPLEX WITH CNS5i-3 -

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Basic information

Entry
Database: PDB / ID: 5jog
TitleCRYSTAL STRUCTURE OF CSN5(2-257) IN COMPLEX WITH CNS5i-3
ComponentsCOP9 signalosome complex subunit 5
KeywordsHYDROXYLASE / COP9 signalosome / metal protease / inhibitor
Function / homology
Function and homology information


macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex / protein deneddylation / COP9 signalosome / protein neddylation / metal-dependent deubiquitinase activity ...macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex / protein deneddylation / COP9 signalosome / protein neddylation / metal-dependent deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases) / protein deubiquitination / regulation of JNK cascade / translation initiation factor activity / post-translational protein modification / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / positive regulation of DNA-binding transcription factor activity / metallopeptidase activity / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / Neddylation / transcription coactivator activity / regulation of cell cycle / translation / chromatin / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / positive regulation of transcription by RNA polymerase II / proteolysis / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Cop9 signalosome subunit 5 C-terminal domain / Cop9 signalosome subunit 5 C-terminal domain / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile.
Similarity search - Domain/homology
Chem-6LT / COP9 signalosome complex subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsRenatus, M. / Wiesmann, C.
CitationJournal: Nat Commun / Year: 2016
Title: Targeted inhibition of the COP9 signalosome for treatment of cancer.
Authors: Schlierf, A. / Altmann, E. / Quancard, J. / Jefferson, A.B. / Assenberg, R. / Renatus, M. / Jones, M. / Hassiepen, U. / Schaefer, M. / Kiffe, M. / Weiss, A. / Wiesmann, C. / Sedrani, R. / ...Authors: Schlierf, A. / Altmann, E. / Quancard, J. / Jefferson, A.B. / Assenberg, R. / Renatus, M. / Jones, M. / Hassiepen, U. / Schaefer, M. / Kiffe, M. / Weiss, A. / Wiesmann, C. / Sedrani, R. / Eder, J. / Martoglio, B.
History
DepositionMay 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COP9 signalosome complex subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5223
Polymers28,9511
Non-polymers5712
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.363, 101.363, 68.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein COP9 signalosome complex subunit 5 / Signalosome subunit 5 / Jun activation domain-binding protein 1


Mass: 28950.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS5, CSN5, JAB1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92905, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-6LT / 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide


Mass: 505.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H29F2N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Protein solution: 18.9 mg/ml protein in 50mM NaCl, 50mM Mes/NaOH pH 6.0, 10uM ZnCl2, 0.5 mM TCEP with 1mM compound Crystallization solution: 35% MPD, 0.1M MES/NaOH pH 6.0, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.459→56.813 Å / Num. obs: 12742 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 68.94 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 26.5
Reflection shellResolution: 2.459→2.468 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JOH

5joh


Resolution: 2.46→56.81 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.877 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.283 / SU Rfree Blow DPI: 0.219 / SU Rfree Cruickshank DPI: 0.226
RfactorNum. reflection% reflectionSelection details
Rfree0.243 654 5.14 %RANDOM
Rwork0.208 ---
obs0.21 12730 99.9 %-
Displacement parametersBiso mean: 82.25 Å2
Baniso -1Baniso -2Baniso -3
1--15.7458 Å20 Å20 Å2
2---15.7458 Å20 Å2
3---31.4917 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.46→56.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 38 27 1827
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011846HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.152495HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d629SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes260HARMONIC5
X-RAY DIFFRACTIONt_it1846HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion20.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion226SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2041SEMIHARMONIC4
LS refinement shellResolution: 2.46→2.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 163 5.41 %
Rwork0.232 2852 -
all0.235 3015 -
obs--99.83 %

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