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- PDB-4e0q: Crystal structure of MPN domain from COP9 signalosome -

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Basic information

Entry
Database: PDB / ID: 4e0q
TitleCrystal structure of MPN domain from COP9 signalosome
ComponentsCOP9 signalosome complex subunit 6
KeywordsUNKNOWN FUNCTION / MPN (Mpr1p and PAD1p N-terminal) domain
Function / homology
Function and homology information


male germ-line cyst encapsulation / female germ-line stem cell population maintenance / Formation of TC-NER Pre-Incision Complex / Cargo recognition for clathrin-mediated endocytosis / Neddylation / DNA Damage Recognition in GG-NER / protein deneddylation / COP9 signalosome / oogenesis / germ cell development ...male germ-line cyst encapsulation / female germ-line stem cell population maintenance / Formation of TC-NER Pre-Incision Complex / Cargo recognition for clathrin-mediated endocytosis / Neddylation / DNA Damage Recognition in GG-NER / protein deneddylation / COP9 signalosome / oogenesis / germ cell development / protein stabilization / identical protein binding / 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 speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZhang, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Febs Lett. / Year: 2012
Title: The crystal structure of the MPN domain from the COP9 signalosome subunit CSN6
Authors: Zhang, H. / Gao, Z.Q. / Wang, W.J. / Liu, G.F. / Shtykova, E.V. / Xu, J.H. / Li, L.F. / Su, X.D. / Dong, Y.H.
History
DepositionMar 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Nov 21, 2012Group: Refinement description
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
B: COP9 signalosome complex subunit 6


Theoretical massNumber of molelcules
Total (without water)32,8782
Polymers32,8782
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-11 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.062, 109.062, 46.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:15 or resseq 17:21 or resseq 29:55 or resseq 62:92 or resseq 111:124 )A1 - 15
121chain A and (resseq 1:15 or resseq 17:21 or resseq 29:55 or resseq 62:92 or resseq 111:124 )A17 - 21
131chain A and (resseq 1:15 or resseq 17:21 or resseq 29:55 or resseq 62:92 or resseq 111:124 )A29 - 55
141chain A and (resseq 1:15 or resseq 17:21 or resseq 29:55 or resseq 62:92 or resseq 111:124 )A62 - 92
151chain A and (resseq 1:15 or resseq 17:21 or resseq 29:55 or resseq 62:92 or resseq 111:124 )A111 - 124
211chain B and (resseq 1:15 or resseq 17:21 or resseq 29:55 or resseq 62:92 or resseq 111:124 )B1 - 15
221chain B and (resseq 1:15 or resseq 17:21 or resseq 29:55 or resseq 62:92 or resseq 111:124 )B17 - 21
231chain B and (resseq 1:15 or resseq 17:21 or resseq 29:55 or resseq 62:92 or resseq 111:124 )B29 - 55
241chain B and (resseq 1:15 or resseq 17:21 or resseq 29:55 or resseq 62:92 or resseq 111:124 )B62 - 92
251chain B and (resseq 1:15 or resseq 17:21 or resseq 29:55 or resseq 62:92 or resseq 111:124 )B111 - 124

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Components

#1: Protein COP9 signalosome complex subunit 6 / Dch6 / Signalosome subunit 6


Mass: 16439.066 Da / Num. of mol.: 2 / Fragment: MPN domain, UNP residues 51-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CSN6, CG6932 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VCY3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 0.2M sodium malonate, pH4.9, 15%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 10201 / Num. obs: 9806 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.4 % / Biso Wilson estimate: 54.42 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 84.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 27.8 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 11 / Num. unique all: 494 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→33.632 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.64 / σ(F): 1.91 / Phase error: 27.06 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER F_PLUS AND F_MINUS COLUMN.
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 888 4.79 %RANDOM
Rwork0.2304 ---
all0.2319 9306 --
obs0.2319 9260 99.51 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.727 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 162.99 Å2 / Biso mean: 66.246 Å2 / Biso min: 25.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.8644 Å2-0 Å2-0 Å2
2---1.8644 Å2-0 Å2
3---3.7289 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 0 14 1915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091935
X-RAY DIFFRACTIONf_angle_d1.2192604
X-RAY DIFFRACTIONf_dihedral_angle_d15.727730
X-RAY DIFFRACTIONf_chiral_restr0.115289
X-RAY DIFFRACTIONf_plane_restr0.005328
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A759X-RAY DIFFRACTIONPOSITIONAL0.071
12B759X-RAY DIFFRACTIONPOSITIONAL0.071
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4967-2.65310.3771510.3046291398
2.6531-2.85780.33831540.28742939100
2.8578-3.14520.36091550.26152930100
3.1452-3.59990.22651600.21522948100
3.5999-4.53370.24471240.19462959100
4.5337-33.63480.22891440.23292944100
Refinement TLS params.Method: refined / Origin x: 17.3351 Å / Origin y: 36.5388 Å / Origin z: 14.6576 Å
111213212223313233
T0.2607 Å20.0021 Å2-0.0018 Å2-0.3265 Å2-0.029 Å2--0.2653 Å2
L1.0777 °2-0.1205 °2-0.0696 °2-1.3876 °2-0.7171 °2--1.4749 °2
S0.0149 Å °0.1491 Å °-0.0396 Å °0.1006 Å °-0.0485 Å °-0.1196 Å °-0.0917 Å °-0.2017 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA51 - 184
2X-RAY DIFFRACTION1allB51 - 176
3X-RAY DIFFRACTION1allA201 - 210
4X-RAY DIFFRACTION1allB201 - 204

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