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- PDB-5d1m: Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragmen... -

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Basic information

Entry
Database: PDB / ID: 5d1m
TitleCrystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
Components
  • E3 ubiquitin-protein ligase RNF25
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / ubiquitin conjugating enzyme (E2) / ubiquitin ligase (E3) / RING finger / ubiquitination / ubiquitin
Function / homology
Function and homology information


protein-RNA covalent cross-linking repair / protein K6-linked ubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / NF-kappaB binding / protein K48-linked ubiquitination / protein autoubiquitination / cytosolic ribosome / rescue of stalled ribosome ...protein-RNA covalent cross-linking repair / protein K6-linked ubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / NF-kappaB binding / protein K48-linked ubiquitination / protein autoubiquitination / cytosolic ribosome / rescue of stalled ribosome / 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 / positive regulation of NF-kappaB transcription factor activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RNF25 / RWD domain / RWD domain profile. / RWD / RWD domain / Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...E3 ubiquitin-protein ligase RNF25 / RWD domain / RWD domain profile. / RWD / RWD domain / Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
OXALATE ION / DI(HYDROXYETHYL)ETHER / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase RNF25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.581 Å
AuthorsLiang, Y.-H. / Li, S. / Weissman, A.M. / Ji, X.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B.
Authors: Li, S. / Liang, Y.H. / Mariano, J. / Metzger, M.B. / Stringer, D.K. / Hristova, V.A. / Li, J. / Randazzo, P.A. / Tsai, Y.C. / Ji, X. / Weissman, A.M.
History
DepositionAug 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Mar 14, 2018Group: Database references / Derived calculations
Category: citation / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 27, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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 RNF25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7768
Polymers32,3272
Non-polymers4496
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-7 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.696, 47.415, 67.975
Angle α, β, γ (deg.)90.000, 118.320, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-364-

HOH

21A-375-

HOH

31A-400-

HOH

41A-513-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating ...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: 16755.227 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 / Plasmid: pETDUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62837, ubiquitin-protein ligase
#2: Protein E3 ubiquitin-protein ligase RNF25 / RING finger protein 25


Mass: 15571.507 Da / Num. of mol.: 1 / Fragment: UNP residues 126-258 / Mutation: P199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF25 / Plasmid: pETDUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q96BH1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 5 types, 381 molecules

#3: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 10000, 8% Ethylene glycol, 0.1M HEPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 9, 2010 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 39104 / Num. obs: 38987 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 22.22 Å2 / Rmerge(I) obs: 0.033 / Χ2: 1.097 / Net I/σ(I): 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.58-1.644.80.2895.29637971.16196.9
1.64-1.75.60.227.73638661.144100
1.7-1.7860.16310.61838711.082100
1.78-1.876.30.11715.30638901.011100
1.87-1.996.30.0822.97939091.067100
1.99-2.146.40.05632.43738931.049100
2.14-2.366.50.04143.34338871.04100
2.36-2.76.60.03159.43739351.104100
2.7-3.46.60.02371.11239361.007100
3.4-506.50.02775.77940031.31899.7

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5D1K

5d1k


Resolution: 1.581→30.398 Å / Occupancy max: 1 / Occupancy min: 0.09 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.16 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 1000 2.57 %RANDOM
Rwork0.1882 ---
obs0.1891 38983 95.79 %-
all-40696 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.829 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 74.61 Å2 / Biso mean: 27.7522 Å2 / Biso min: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1--4.684 Å20 Å2-0.2176 Å2
2--7.9872 Å20 Å2
3----3.9489 Å2
Refinement stepCycle: LAST / Resolution: 1.581→30.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 23 375 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092331
X-RAY DIFFRACTIONf_angle_d1.1753187
X-RAY DIFFRACTIONf_chiral_restr0.085332
X-RAY DIFFRACTIONf_plane_restr0.006425
X-RAY DIFFRACTIONf_dihedral_angle_d14.09945
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.5811-1.66440.40071040.408539504054405471
1.6644-1.76870.27861480.259562457725772100
1.7687-1.90520.20721480.1845561557635763100
1.9052-2.09690.21371480.1657564157895789100
2.0969-2.40030.22381500.1909568858385838100
2.4003-3.02360.23861490.1864566758165816100
3.0236-30.40350.20161530.174579859515942100

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