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- PDB-6a73: Complex structure of CSN2 with IP6 -

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Basic information

Entry
Database: PDB / ID: 6a73
TitleComplex structure of CSN2 with IP6
ComponentsCOP9 signalosome complex subunit 2,Endolysin
KeywordsSIGNALING PROTEIN / subunit2 of COP9 Signalosome (CSN).
Function / homology
Function and homology information


trophectodermal cell proliferation / protein deneddylation / regulation of protein neddylation / COP9 signalosome / protein neddylation / RHOBTB1 GTPase cycle / inner cell mass cell proliferation / skeletal muscle cell differentiation / viral release from host cell by cytolysis / peptidoglycan catabolic process ...trophectodermal cell proliferation / protein deneddylation / regulation of protein neddylation / COP9 signalosome / protein neddylation / RHOBTB1 GTPase cycle / inner cell mass cell proliferation / skeletal muscle cell differentiation / viral release from host cell by cytolysis / peptidoglycan catabolic process / DNA Damage Recognition in GG-NER / neuron differentiation / Formation of TC-NER Pre-Incision Complex / transcription corepressor activity / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / lysozyme activity / Neddylation / host cell cytoplasm / transcription by RNA polymerase II / defense response to bacterium / protein phosphorylation / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / PCI/PINT associated module / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 ...: / PCI/PINT associated module / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily / Tetratricopeptide-like helical domain superfamily / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Endolysin / COP9 signalosome complex subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage RB59 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.447 Å
AuthorsLiu, L. / Li, D. / Rao, F. / Wang, T.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2018YFA0507103 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Basis for metabolite-dependent Cullin-RING ligase deneddylation by the COP9 signalosome.
Authors: Lin, H. / Zhang, X. / Liu, L. / Fu, Q. / Zang, C. / Ding, Y. / Su, Y. / Xu, Z. / He, S. / Yang, X. / Wei, X. / Mao, H. / Cui, Y. / Wei, Y. / Zhou, C. / Du, L. / Huang, N. / Zheng, N. / Wang, T. / Rao, F.
History
DepositionJul 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 26, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.5Nov 22, 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
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 2,Endolysin
B: COP9 signalosome complex subunit 2,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1436
Polymers70,6312
Non-polymers1,5124
Water3,081171
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A: COP9 signalosome complex subunit 2,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0713
Polymers35,3151
Non-polymers7562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-19 kcal/mol
Surface area15860 Å2
MethodPISA
2
B: COP9 signalosome complex subunit 2,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0713
Polymers35,3151
Non-polymers7562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-6 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.804, 70.164, 81.350
Angle α, β, γ (deg.)107.03, 103.94, 90.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein COP9 signalosome complex subunit 2,Endolysin / Signalosome subunit 2 / Alien homolog / JAB1-containing signalosome subunit 2 / Thyroid receptor- ...Signalosome subunit 2 / Alien homolog / JAB1-containing signalosome subunit 2 / Thyroid receptor-interacting protein 15 / TRIP-15 / Lysis protein / Lysozyme / Muramidase


Mass: 35315.383 Da / Num. of mol.: 2 / Mutation: C54T, C97A
Source method: isolated from a genetically manipulated source
Details: human CSN2 hybrid with lysozyme,human CSN2 hybrid with lysozyme,human CSN2 hybrid with lysozyme,human CSN2 hybrid with lysozyme
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage RB59 (virus)
Gene: COPS2, CSN2, TRIP15, e, RB59_126 / Production host: Escherichia coli (E. coli) / References: UniProt: P61201, UniProt: A0A097J809, lysozyme
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate ,100mM Bis-Tris pH 5.5, 25%PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.447→20.003 Å / Num. obs: 27516 / % possible obs: 91.8 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 26.1
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.189 / Num. unique obs: 1305 / % possible all: 87.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L17 and 4ZWJ

1l17

4zwj


Resolution: 2.447→20.003 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.82 / Phase error: 34.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2879 1379 5.01 %Random Selection
Rwork0.2473 ---
obs0.2503 27504 91.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.447→20.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 82 171 4973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054881
X-RAY DIFFRACTIONf_angle_d0.9256588
X-RAY DIFFRACTIONf_dihedral_angle_d18.1252946
X-RAY DIFFRACTIONf_chiral_restr0.046720
X-RAY DIFFRACTIONf_plane_restr0.005820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4471-2.53440.42541120.30542059X-RAY DIFFRACTION72
2.5344-2.63570.31861340.27592435X-RAY DIFFRACTION86
2.6357-2.75540.3431380.28592566X-RAY DIFFRACTION90
2.7554-2.90020.35951410.30212626X-RAY DIFFRACTION92
2.9002-3.08130.38621350.30362677X-RAY DIFFRACTION94
3.0813-3.31820.30111430.26542734X-RAY DIFFRACTION96
3.3182-3.65030.30461390.24042749X-RAY DIFFRACTION96
3.6503-4.17440.3041430.21932715X-RAY DIFFRACTION97
4.1744-5.24350.27261490.21372772X-RAY DIFFRACTION97
5.2435-20.00380.25771450.22862792X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -9.3689 Å / Origin y: 7.5026 Å / Origin z: -57.8356 Å
111213212223313233
T0.2327 Å20.0054 Å20 Å2-0.2848 Å20.0012 Å2--0.4472 Å2
L0.5641 °20.0318 °2-0.0254 °2--0.3198 °2-1.1332 °2--4.6581 °2
S-0.1767 Å °0.0081 Å °-0.0041 Å °-0.0046 Å °-0.2214 Å °-0.2043 Å °0.0212 Å °0.5886 Å °0.2621 Å °
Refinement TLS groupSelection details: all

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