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- PDB-4qft: Structure of COP9 signalosome complex subunit 6 -

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Basic information

Entry
Database: PDB / ID: 4qft
TitleStructure of COP9 signalosome complex subunit 6
ComponentsCOP9 signalosome complex subunit 6
KeywordsSIGNALING PROTEIN / subunit of the Cop9 signalosome
Function / homology
Function and homology information


protein deneddylation / regulation of protein neddylation / COP9 signalosome / protein neddylation / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Cargo recognition for clathrin-mediated endocytosis / Neddylation / perinuclear region of cytoplasm / nucleoplasm ...protein deneddylation / regulation of protein neddylation / COP9 signalosome / protein neddylation / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Cargo recognition for clathrin-mediated endocytosis / Neddylation / perinuclear region of cytoplasm / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
COP9 signalosome subunit 6 / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. ...COP9 signalosome subunit 6 / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COP9 signalosome complex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsBirol, M. / Hoh, F. / Dumas, C. / Echalier, A.
CitationJournal: PLoS ONE / Year: 2014
Title: Structural and biochemical characterization of the Cop9 signalosome CSN5/CSN6 heterodimer.
Authors: Birol, M. / Enchev, R.I. / Padilla, A. / Stengel, F. / Aebersold, R. / Betzi, S. / Yang, Y. / Hoh, F. / Peter, M. / Dumas, C. / Echalier, A.
History
DepositionMay 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: COP9 signalosome complex subunit 6


Theoretical massNumber of molelcules
Total (without water)20,7801
Polymers20,7801
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: COP9 signalosome complex subunit 6

A: COP9 signalosome complex subunit 6


Theoretical massNumber of molelcules
Total (without water)41,5602
Polymers41,5602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_674x-y+1,-y+2,-z-1/31
Buried area4960 Å2
ΔGint-26 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.838, 96.838, 48.333
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21A-428-

HOH

31A-470-

HOH

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Components

#1: Protein COP9 signalosome complex subunit 6 / SGN6 / Signalosome subunit 6 / JAB1-containing signalosome subunit 6 / MOV34 homolog / Vpr- ...SGN6 / Signalosome subunit 6 / JAB1-containing signalosome subunit 6 / MOV34 homolog / Vpr-interacting protein / hVIP


Mass: 20779.758 Da / Num. of mol.: 1 / Fragment: unp residues 31-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS6, CSN6, HVIP / Production host: Escherichia coli (E. coli) / References: UniProt: Q7L5N1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Tri-Sodium citrate, 0.1 M Bis-Tris propane, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.76→48 Å / Num. all: 26172 / Num. obs: 26172 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.76→1.86 Å / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→48 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.709 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.112 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20604 1330 5.1 %RANDOM
Rwork0.15274 ---
obs0.1554 24826 99.99 %-
all-263696 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.68 Å20 Å2
2--0.68 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 1.76→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 0 175 1546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191517
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9582074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0065192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32724.63869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66615272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.017157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211159
X-RAY DIFFRACTIONr_rigid_bond_restr2.34731517
X-RAY DIFFRACTIONr_sphericity_free34.822544
X-RAY DIFFRACTIONr_sphericity_bonded17.35851611
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 85 -
Rwork0.183 1827 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -13.396 Å / Origin y: 74.93 Å / Origin z: -0.417 Å
111213212223313233
T0.0349 Å20.0009 Å2-0.0035 Å2-0.0446 Å2-0.0088 Å2--0.0209 Å2
L0.3902 °2-0.0308 °20.0402 °2-0.4782 °2-0.1852 °2--0.4161 °2
S0.0389 Å °0.0198 Å °-0.0523 Å °-0.0235 Å °-0.0532 Å °0.0474 Å °0.0739 Å °0.0145 Å °0.0142 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 125
2X-RAY DIFFRACTION1A155 - 172

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