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- PDB-4r14: Crystal structure of human CSN6 MPN domain -

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Basic information

Entry
Database: PDB / ID: 4r14
TitleCrystal structure of human CSN6 MPN domain
ComponentsCOP9 signalosome complex subunit 6
KeywordsPROTEIN BINDING / MPN domain / protein-protein interaction
Function / homology
Function and homology information


regulation of protein neddylation / protein deneddylation / 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 ...regulation of protein neddylation / protein deneddylation / 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 / cytoplasm / cytosol
Similarity search - Function
COP9 signalosome subunit 6 / 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.
Similarity search - Domain/homology
: / COP9 signalosome complex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.601 Å
AuthorsJiang, T. / Xu, M. / Ma, X.L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure of the human CSN6 MPN domain
Authors: Ma, X.L. / Xu, M. / Jiang, T.
History
DepositionAug 4, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COP9 signalosome complex subunit 6
B: COP9 signalosome complex subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,07010
Polymers41,4652
Non-polymers1,6058
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-188 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.552, 66.552, 86.829
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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: 20732.621 Da / Num. of mol.: 2 / Fragment: MPN domain, UNP residues 38-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS6, CSN6, HVIP / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: Q7L5N1
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Hg

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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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1M Tris pH 7.7, 26% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.0055 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0055 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 13213 / Num. obs: 13213 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.4 % / Biso Wilson estimate: 31.79 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 56.35
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 22.9 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 7 / Num. unique all: 650 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.601→34.677 Å / SU ML: 0.41 / σ(F): 2 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 625 4.89 %RANDOM
Rwork0.2252 ---
all0.2268 13213 --
obs0.2268 12780 96.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→34.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 8 0 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012552
X-RAY DIFFRACTIONf_angle_d1.1353468
X-RAY DIFFRACTIONf_dihedral_angle_d14.773946
X-RAY DIFFRACTIONf_chiral_restr0.047396
X-RAY DIFFRACTIONf_plane_restr0.006440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6015-2.86310.38051480.3117273988
2.8631-3.27720.28041650.27043139100
3.2772-4.12780.23941670.21583150100
4.1278-34.68040.21761450.182312799
Refinement TLS params.Method: refined / Origin x: 33.2768 Å / Origin y: -7.3 Å / Origin z: 8.8921 Å
111213212223313233
T1.0099 Å20.0016 Å2-0.0026 Å2-0.2653 Å2-0.0033 Å2--0.4771 Å2
L2.9527 °2-0.0416 °20.4633 °2--0.3307 °2-0.0336 °2--3.2886 °2
S-0.4587 Å °0.0036 Å °0.3251 Å °-0.007 Å °0.3142 Å °-0.006 Å °-0.5236 Å °0.0107 Å °0.1967 Å °
Refinement TLS groupSelection details: all

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