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- PDB-8gcb: Structure of RNF125 in complex with a UbcH5b~Ub conjugate -

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Basic information

Entry
Database: PDB / ID: 8gcb
TitleStructure of RNF125 in complex with a UbcH5b~Ub conjugate
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 / VCP-NPL4-UFD1 AAA ATPase complex / ubiquitin conjugating enzyme binding / negative regulation of type I interferon production / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex ...negative regulation of RIG-I signaling pathway / (E3-independent) E2 ubiquitin-conjugating enzyme / VCP-NPL4-UFD1 AAA ATPase complex / ubiquitin conjugating enzyme binding / negative regulation of type I interferon production / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / cellular response to leukemia inhibitory factor / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / p53 binding / 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 / ubiquitin protein ligase binding / protein-containing complex / zinc ion binding / extracellular exosome / 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, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 ...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, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / 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
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: 2.39 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
DepositionMar 1, 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

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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)28,7565
Polymers28,5602
Non-polymers1963
Water00
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)59.325, 59.325, 185.821
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 289 K / Method: microbatch / pH: 9 / Details: 0.1 M BICINE pH 9.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953646 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953646 Å / Relative weight: 1
ReflectionResolution: 2.39→46.5 Å / Num. obs: 13972 / % possible obs: 99.8 % / Redundancy: 25.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.024 / Rrim(I) all: 0.123 / Net I/σ(I): 16.8
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
2.39-2.4824.72.5073507514180.6840.5062.561.598.6
8.94-46.46200.0568713440.9990.0110.05149.699.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→46.5 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.665 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 654 4.7 %RANDOM
Rwork0.2528 ---
obs0.2536 13250 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.87 Å2 / Biso mean: 67.274 Å2 / Biso min: 44.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å2-0 Å2-0 Å2
2--1.52 Å20 Å2
3----3.04 Å2
Refinement stepCycle: final / Resolution: 2.39→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 3 0 1936
Biso mean--63.4 --
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132004
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171873
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.6682718
X-RAY DIFFRACTIONr_angle_other_deg1.1291.5824331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5875241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.78720.874103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33515340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1771516
X-RAY DIFFRACTIONr_chiral_restr0.0520.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
LS refinement shellResolution: 2.39→2.452 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 45 -
Rwork0.341 939 -
all-984 -
obs--97.81 %

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