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- PDB-4d0p: Crystal structure of human CSN4 -

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Basic information

Entry
Database: PDB / ID: 4d0p
TitleCrystal structure of human CSN4
ComponentsCOP9 SIGNALOSOME COMPLEX SUBUNIT 4
KeywordsSIGNALING PROTEIN / PCI
Function / homology
Function and homology information


deNEDDylase activity / protein deneddylation / regulation of protein neddylation / COP9 signalosome / protein neddylation / RHOBTB1 GTPase cycle / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / cell junction / synaptic vesicle ...deNEDDylase activity / protein deneddylation / regulation of protein neddylation / COP9 signalosome / protein neddylation / RHOBTB1 GTPase cycle / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / cell junction / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / Neddylation / nuclear speck / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
COP9 signalosome complex subunit 4, helix turn helix domain / CSN4/RPN5/eIF3a helix turn helix domain / : / PSMD12/CSN4, N-terminal / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...COP9 signalosome complex subunit 4, helix turn helix domain / CSN4/RPN5/eIF3a helix turn helix domain / : / PSMD12/CSN4, N-terminal / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COP9 signalosome complex subunit 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsBunker, R.D. / Lingaraju, G.M. / Thoma, N.H.
CitationJournal: Nature / Year: 2014
Title: Crystal Structure of the Cop9 Signalosome
Authors: Lingaraju, G.M. / Bunker, R.D. / Cavadini, S. / Hess, D. / Hassiepen, U. / Renatus, M. / Fischer, E.S. / Thoma, N.H.
History
DepositionApr 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,57912
Polymers44,1871
Non-polymers39211
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.660, 63.530, 75.800
Angle α, β, γ (deg.)90.00, 101.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein COP9 SIGNALOSOME COMPLEX SUBUNIT 4 / SGN4 / SIGNALOSOME SUBUNIT 4 / JAB1-CONTAINING SIGNALOSOME SUBUNIT 4


Mass: 44187.148 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9BT78
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTALLIZED WITH AN N-TERMINAL STREP(II) FUSION TAG

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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: 3.03 Å3/Da / Density % sol: 0.59 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 7.5
Details: 16 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM DTT WAS MIXED EQUALLY WITH 100 MM HEPES PH 7.5, 4.3 M NACL. CRYSTALS WERE GROWN BY VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 25, 2013 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→32 Å / Num. obs: 69613 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 30.58 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.3
Reflection shellResolution: 1.6→1.61 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XDSAIMLESSdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.6→31.76 Å / Cor.coef. Fo:Fc: 0.9601 / Cor.coef. Fo:Fc free: 0.9583 / SU R Cruickshank DPI: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.069 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.067
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=6343. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=6343. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=13. RESIDUES -24 TO -9 OF THE FUSION TAG AND RESIDUE 363 THE C-TERMINUS ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.1929 3564 5.12 %RANDOM
Rwork0.1789 ---
obs0.1796 69593 99.98 %-
Displacement parametersBiso mean: 40.76 Å2
Baniso -1Baniso -2Baniso -3
1--3.7237 Å20 Å21.488 Å2
2---0.7194 Å20 Å2
3---4.4431 Å2
Refine analyzeLuzzati coordinate error obs: 0.237 Å
Refinement stepCycle: LAST / Resolution: 1.6→31.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 14 336 3299
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016061HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9810962HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1391SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes915HARMONIC5
X-RAY DIFFRACTIONt_it6061HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion13.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion404SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies8HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6677SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2192 218 4.24 %
Rwork0.2143 4920 -
all0.2145 5138 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.14992.1574-3.12440.5517-1.692-1.7275-0.36960.6210.0978-0.0070.506-0.15890.15070.308-0.1364-0.2772-0.1327-0.05230.4966-0.3254-0.1892-19.92056.423455.5244
27.8993-0.7512-1.03462.0820.94225.7616-0.24411.208-0.0727-0.1704-0.35410.22950.0893-1.36560.5981-0.3057-0.0474-0.05850.2819-0.2091-0.1775-10.216811.280857.2824
32.7754-1.2874-1.81681.53312.51456.7653-0.17170.2992-0.1017-0.0606-0.25170.2075-0.1157-0.6950.4233-0.1225-0.0047-0.01570.0156-0.061-0.0705-6.035414.296269.1575
44.8186-1.3322-1.13152.86573.38766.9981-0.03370.0542-0.21720.0033-0.05380.12560.2389-0.10830.0875-0.04350.034-0.0052-0.0652-0.0264-0.0866-0.390716.32381.1286
51.35080.2096-0.05182.21450.97373.35010.01640.093-0.125-0.08460.0556-0.1368-0.13550.1727-0.072-0.01540.0006-0.0038-0.0249-0.0323-0.04075.621821.953887.4059
62.45311.7227-1.46342.1249-1.04692.5632-0.11030.2045-0.1444-0.13980.0612-0.13710.24480.02170.0491-0.01930.00810.0103-0.0748-0.007-0.05599.962632.687493.8427
71.63440.0823-0.89131.05660.6444.75540.1409-0.07390.1772-0.0118-0.0001-0.0233-0.39080.2084-0.14080.013-0.01940.0119-0.0659-0.0012-0.03579.987343.8118103.8637
81.37480.78660.92751.88221.09985.50470.1845-0.16140.19040.3097-0.15610.25660.0143-0.4681-0.0285-0.06610.00840.0562-0.0726-0.0192-0.0485-0.656440.9426112.3003
94.00161.2940.72510.64550.1962.2320.1003-0.10420.22410.6169-0.21380.1770.6493-0.36490.11360.0987-0.09280.0592-0.0632-0.0533-0.04040.103436.5604126.8592
102.8970.83542.70736.87273.56622.28410.166-0.5213-0.2480.82640.0053-0.28230.31640.0152-0.17130.2597-0.0404-0.0046-0.09890.0157-0.0696.078631.717130.1022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-8 - 18}
2X-RAY DIFFRACTION2{A|19 - 58}
3X-RAY DIFFRACTION3{A|59 - 116}
4X-RAY DIFFRACTION4{A|117 - 140}
5X-RAY DIFFRACTION5{A|141 - 180}
6X-RAY DIFFRACTION6{A|181 - 218}
7X-RAY DIFFRACTION7{A|219 - 268}
8X-RAY DIFFRACTION8{A|269 - 315}
9X-RAY DIFFRACTION9{A|316 - 344}
10X-RAY DIFFRACTION10{A|345 - 362}

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