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- PDB-8gbq: Structure of RNF125 in complex with UbcH5b -

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Basic information

Entry
Database: PDB / ID: 8gbq
TitleStructure of RNF125 in complex with UbcH5b
Components
  • E3 ubiquitin-protein ligase RNF125
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / ubiquitin RING E3 ligase Ubiquitin conjugating enzyme Complex
Function / homology
Function and homology information


negative regulation of RIG-I signaling pathway / (E3-independent) E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme binding / VCP-NPL4-UFD1 AAA ATPase complex / negative regulation of type I interferon production / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / cellular response to leukemia inhibitory factor ...negative regulation of RIG-I signaling pathway / (E3-independent) E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme binding / VCP-NPL4-UFD1 AAA ATPase complex / negative regulation of type I interferon production / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / cellular response to leukemia inhibitory factor / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / RING-type E3 ubiquitin transferase / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / p53 binding / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / adaptive immune response / protein ubiquitination / Golgi membrane / intracellular membrane-bounded organelle / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol
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) / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active 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) / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase RNF125
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsMiddleton, A.J. / Day, C.L. / Fokkens, T.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
CitationJournal: Structure / Year: 2023
Title: Zinc finger 1 of the RING E3 ligase, RNF125, interacts with the E2 to enhance ubiquitylation.
Authors: Middleton, A.J. / Barzak, F.M. / Fokkens, T.J. / Nguyen, K. / Day, C.L.
History
DepositionFeb 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2
B: E3 ubiquitin-protein ligase RNF125
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8486
Polymers28,5602
Non-polymers2884
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.181, 56.181, 164.347
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-341-

HOH

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 17214.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Protein E3 ubiquitin-protein ligase RNF125 / RING finger protein 125 / T-cell RING activation protein 1 / TRAC-1


Mass: 11345.220 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF125 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96EQ8, RING-type E3 ubiquitin transferase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES 9.5 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.74→48.65 Å / Num. obs: 59049 / % possible obs: 99.4 % / Redundancy: 14.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.017 / Rrim(I) all: 0.064 / Net I/σ(I): 21.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.74-1.7713.21.2632036515370.6870.3421.31289
9.04-48.6511.10.04232142890.9980.0120.04450.698.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→41.87 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.19 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 2920 4.95 %
Rwork0.1839 56129 -
obs0.1848 59049 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.34 Å2 / Biso mean: 45.1628 Å2 / Biso min: 23.68 Å2
Refinement stepCycle: final / Resolution: 1.74→41.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 9 152 2084
Biso mean--43.66 46.22 -
Num. residues----240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.770.29151260.30332325245184
1.77-1.80.29651520.249426302782100
1.8-1.830.29441360.252227082844100
1.83-1.870.26681560.246127182874100
1.87-1.910.28491140.23126712785100
1.91-1.950.25041500.221727132863100
1.95-1.990.24581740.201726252799100
1.99-2.040.21451340.203326802814100
2.04-2.10.22731140.19827392853100
2.1-2.160.18971080.183127522860100
2.16-2.230.22191520.19226482800100
2.23-2.310.24141340.192527172851100
2.31-2.40.19961080.192226922800100
2.4-2.510.21241400.196327022842100
2.51-2.640.23371570.217226772834100
2.64-2.810.24611280.208927662894100
2.81-3.020.24571640.206326282792100
3.03-3.330.17631220.196327002822100
3.33-3.810.18911620.176826702832100
3.81-4.80.1651460.14826912837100
4.8-41.870.1691430.1552677282099
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)
12.1736-0.8197-1.34067.23122.22595.38050.05440.97180.4042-0.8665-0.20531.227-0.3433-0.41260.30050.3432-0.0331-0.08590.70060.06940.4528-2.8225-14.1767-23.4329
22.23563.33825.25164.89932.94866.517-0.22180.4181.0252-1.1405-0.38291.3677-1.1692-0.66050.65420.6332-0.034-0.14510.70290.19620.83714.1878-4.9102-22.3988
36.13122.82353.55729.6539.03528.8469-0.43520.56680.3503-1.006-0.0233-0.1169-1.15310.21190.50210.3878-0.0065-0.05520.45710.14290.31578.8399-10.356-23.4611
44.7133.65621.96415.83570.77223.3416-0.4930.48510.5827-0.20790.15310.2045-0.5252-0.09740.30160.24790.0401-0.06010.33550.07120.314210.4586-10.0398-15.332
56.78347.02367.31969.53148.5762.2405-0.17480.7423-0.2245-0.43220.2589-0.6986-0.14520.690.07210.3424-0.059-0.01010.43570.08890.373419.443-8.5357-14.5387
66.45956.28581.9325.97261.14942.1799-0.0405-0.1344-0.19710.0584-0.0644-0.25020.0201-0.03110.06720.16920.0468-0.00060.21030.02140.228712.5315-15.8713-9.0047
710.03426.61017.05889.03785.87588.5106-0.4614-0.13030.9882-0.076-0.03520.9552-0.5117-0.67170.43650.2150.04620.00480.27220.04950.3567.4434-7.7923-9.8209
82.06061.05682.4442.08024.56582.08790.1733-0.2423-0.4920.631-0.12230.3840.2306-0.7081-0.05980.40890.00660.00040.39630.05030.432318.2768-11.0786-0.3359
96.07494.98654.70222.08894.72058.4051-0.0293-0.0444-0.24790.19390.1077-0.12530.22490.3024-0.12770.2172-0.0093-0.03510.18940.03540.320725.6636-6.12462.4803
104.85290.54471.76767.6139-2.47537.653-0.44480.45981.0629-0.78270.2355-0.0715-0.75660.08080.24450.3954-0.0764-0.06050.26480.10570.577623.82912.7259-7.535
116.70012.37151.25896.0906-5.12858.6659-0.28280.24090.4954-0.242-0.11550.2805-0.126-0.30470.43920.22630.0694-0.04330.3569-0.07690.2505-12.3208-20.6158-16.7749
122.5103-1.27610.51116.9626-1.09547.7943-0.0638-0.2087-0.0786-0.0068-0.1508-0.41080.20110.31840.2480.17490.04270.01980.2986-0.01690.2508-6.6285-27.4442-7.9501
132.02450.87052.05643.55941.18339.66190.00020.8893-1.1312-0.07120.0048-0.18920.71190.8595-0.10850.3004-0.01090.04830.2885-0.00430.4034-10.3963-31.8005-4.4324
142.0662-1.16540.40798.4907-6.31912.05960.0466-0.63940.58840.3562-0.24761.3073-0.5218-1.37050.06880.2980.07760.00130.6376-0.15910.4748-24.4334-22.4712-13.3134
154.45031.0537-3.8198.6353.77098.6557-0.19380.43330.4991-0.49150.19990.2841-0.9395-0.29640.050.38960.048-0.13970.5768-0.01370.4084-18.5047-17.8891-26.6953
162.03620.01753.37629.6434-2.3836.9517-0.4151.08190.7025-1.152-0.8868-2.5525-1.26343.39761.34850.6858-0.25230.06221.09630.20610.7346-9.0917-18.8364-34.8872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )A1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 28 )A16 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 38 )A29 - 38
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 65 )A39 - 65
5X-RAY DIFFRACTION5chain 'A' and (resid 66 through 74 )A66 - 74
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 98 )A75 - 98
7X-RAY DIFFRACTION7chain 'A' and (resid 99 through 111 )A99 - 111
8X-RAY DIFFRACTION8chain 'A' and (resid 112 through 120 )A112 - 120
9X-RAY DIFFRACTION9chain 'A' and (resid 121 through 130 )A121 - 130
10X-RAY DIFFRACTION10chain 'A' and (resid 131 through 147 )A131 - 147
11X-RAY DIFFRACTION11chain 'B' and (resid 34 through 46 )B34 - 46
12X-RAY DIFFRACTION12chain 'B' and (resid 47 through 77 )B47 - 77
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 86 )B78 - 86
14X-RAY DIFFRACTION14chain 'B' and (resid 87 through 95 )B87 - 95
15X-RAY DIFFRACTION15chain 'B' and (resid 96 through 118 )B96 - 118
16X-RAY DIFFRACTION16chain 'B' and (resid 119 through 126 )B119 - 126

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