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- PDB-5dka: A C2HC zinc finger is essential for the activity of the RING ubiq... -

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Basic information

Entry
Database: PDB / ID: 5dka
TitleA C2HC zinc finger is essential for the activity of the RING ubiquitin ligase RNF125
ComponentsE3 ubiquitin-protein ligase RNF125
KeywordsLIGASE / RING ubiquitin ligase
Function / homology
Function and homology information


negative regulation of RIG-I signaling pathway / VCP-NPL4-UFD1 AAA ATPase complex / ubiquitin conjugating enzyme binding / negative regulation of type I interferon production / cellular response to leukemia inhibitory factor / Negative regulators of DDX58/IFIH1 signaling / RING-type E3 ubiquitin transferase / protein polyubiquitination / p53 binding / ubiquitin protein ligase activity ...negative regulation of RIG-I signaling pathway / VCP-NPL4-UFD1 AAA ATPase complex / ubiquitin conjugating enzyme binding / negative regulation of type I interferon production / cellular response to leukemia inhibitory factor / Negative regulators of DDX58/IFIH1 signaling / RING-type E3 ubiquitin transferase / protein polyubiquitination / p53 binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / adaptive immune response / Golgi membrane / intracellular membrane-bounded organelle / zinc ion binding
Similarity search - Function
Zinc finger C2HC RNF-type / : / C2HC Zing finger domain / Zinc finger C2HC RNF-type profile. / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site ...Zinc finger C2HC RNF-type / : / C2HC Zing finger domain / Zinc finger C2HC RNF-type profile. / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF125
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBoer, D.R. / Coll, M. / Bijlmakers, M.J.
CitationJournal: Sci Rep / Year: 2016
Title: A C2HC zinc finger is essential for the RING-E2 interaction of the ubiquitin ligase RNF125.
Authors: Bijlmakers, M.J. / Teixeira, J.M. / Boer, R. / Mayzel, M. / Puig-Sarries, P. / Karlsson, G. / Coll, M. / Pons, M. / Crosas, B.
History
DepositionSep 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF125
B: E3 ubiquitin-protein ligase RNF125
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,54313
Polymers52,9852
Non-polymers55911
Water2,378132
1
A: E3 ubiquitin-protein ligase RNF125
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7245
Polymers26,4921
Non-polymers2324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase RNF125
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8198
Polymers26,4921
Non-polymers3277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.670, 52.320, 73.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase RNF125 / RING finger protein 125 / T-cell RING activation protein 1 / TRAC-1


Mass: 26492.350 Da / Num. of mol.: 2 / Mutation: 129 stop mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF125 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q96EQ8, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 273 K / Method: evaporation / Details: 0.1 M HEPES, 10% PEG 8K / PH range: 5.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2015
RadiationMonochromator: SI(111) CHANNEL-CUT CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 28019 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.2
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.3 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSNovember 3, 2014data reduction
XSCALENovember 3, 2014data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HCS

3hcs


Resolution: 1.55→42.71 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.435 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 1401 5 %RANDOM
Rwork0.20983 ---
obs0.2113 26618 94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.216 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.34 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.55→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 11 132 1655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191568
X-RAY DIFFRACTIONr_bond_other_d0.0010.021470
X-RAY DIFFRACTIONr_angle_refined_deg2.1421.9712108
X-RAY DIFFRACTIONr_angle_other_deg1.0573.0123372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76722.18864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0915272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3571514
X-RAY DIFFRACTIONr_chiral_restr0.1360.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02352
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6541.413766
X-RAY DIFFRACTIONr_mcbond_other1.6491.411765
X-RAY DIFFRACTIONr_mcangle_it2.4922.11954
X-RAY DIFFRACTIONr_mcangle_other2.4932.111955
X-RAY DIFFRACTIONr_scbond_it2.9391.713802
X-RAY DIFFRACTIONr_scbond_other2.9381.713802
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6842.4711154
X-RAY DIFFRACTIONr_long_range_B_refined7.78613.0791841
X-RAY DIFFRACTIONr_long_range_B_other7.68712.7131807
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 103 -
Rwork0.313 1970 -
obs--94.66 %
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)
16.8628-2.47484.44383.8773-0.83673.2453-0.16050.64290.3282-0.17230.0242-0.1364-0.1250.28490.13620.1758-0.080.0050.31870.07980.15213.6077-7.8678-15.5248
22.65141.31770.7972.48210.64120.3556-0.01790.00540.0310.0238-0.0112-0.07350.0016-0.07550.02910.1233-0.02150.00450.0743-0.00850.129821.0767-2.3119-6.9699
36.39722.28262.0212.09150.01261.03160.1487-0.12840.38180.0345-0.08870.46460.0553-0.0146-0.05990.0298-0.02960.01810.0325-0.03370.11464.8579-5.0057-8.2713
41.5408-0.14290.12781.21610.77111.7832-0.00160.10740.07940.0173-0.06970.01260.03580.0210.07130.1576-0.0204-0.02310.1124-0.00340.18666.2753-18.3905-15.248
59.811.84310.13831.7127-1.81852.55060.07540.3658-0.20170.0089-0.0737-0.00080.0660.1798-0.00170.10380.00040.01910.0376-0.03540.069514.5652-24.8662-19.4141
61.9955-0.61850.14132.565-0.77682.58630.088-0.1673-0.0230.14580.03440.04430.0737-0.0062-0.12240.1835-0.01720.0120.1147-0.02050.171130.2893-25.6905-5.4368
71.80872.16610.12873.32610.05850.03170.05030.11860.04760.0236-0.00490.09420.02470.0337-0.04540.13810.0060.00850.0814-0.03050.157434.9645-18.0172-11.4561
82.54952.70210.313.20890.00161.371-0.01460.07250.1860.10310.0720.0607-0.0530.2099-0.05740.07150.0098-0.0350.0509-0.02390.140138.8679-17.5775-11.5265
92.808-1.0217-1.75092.52280.03361.2614-0.0324-0.0624-0.02210.03670.005-0.0690.01420.03930.02740.19020.0062-0.03640.1002-0.00140.195525.25-35.3059-4.8173
101.5625-1.8231-0.81713.11760.53652.773-0.22360.066-0.07880.22860.10920.04480.10130.24830.11440.1119-0.0014-0.00010.10290.00130.121214.407-26.4795-3.5097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 43
2X-RAY DIFFRACTION2A44 - 81
3X-RAY DIFFRACTION3A82 - 98
4X-RAY DIFFRACTION4A99 - 119
5X-RAY DIFFRACTION5A120 - 128
6X-RAY DIFFRACTION6B33 - 47
7X-RAY DIFFRACTION7B48 - 67
8X-RAY DIFFRACTION8B68 - 91
9X-RAY DIFFRACTION9B92 - 113
10X-RAY DIFFRACTION10B114 - 128

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