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- PDB-6zm3: The structure of an E2 ubiquitin-conjugating complex (UBC2-UEV1) ... -

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Basic information

Entry
Database: PDB / ID: 6zm3
TitleThe structure of an E2 ubiquitin-conjugating complex (UBC2-UEV1) essential for Leishmania amastigote differentiation
Components
  • Putative ubiquitin-conjugating enzyme e2
  • Ubiquitin-conjugating enzyme-like protein
KeywordsSIGNALING PROTEIN / Leishmaniasis / Differentiation / Ubiquitin / Conjugation / UBC2-UEV1 complex
Function / homology
Function and homology information


ubiquitin-protein ligase / ligase activity / transferase activity / ATP binding
Similarity search - Function
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/RWD-like
Similarity search - Domain/homology
Putative ubiquitin-conjugating enzyme e2 / Ubiquitin-conjugating enzyme-like protein
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBurge, R.J. / Dodson, E.J. / Wilkinson, A.J. / Mottram, J.C.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N018230/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/K019384/1 United Kingdom
Wellcome Trust200807/Z/16/Z United Kingdom
Wellcome Trust101528/Z/13/Z United Kingdom
CitationJournal: Plos Pathog. / Year: 2020
Title: Leishmania differentiation requires ubiquitin conjugation mediated by a UBC2-UEV1 E2 complex.
Authors: Burge, R.J. / Damianou, A. / Wilkinson, A.J. / Rodenko, B. / Mottram, J.C.
History
DepositionJul 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Putative ubiquitin-conjugating enzyme e2
BBB: Ubiquitin-conjugating enzyme-like protein
CCC: Putative ubiquitin-conjugating enzyme e2
DDD: Ubiquitin-conjugating enzyme-like protein


Theoretical massNumber of molelcules
Total (without water)67,1554
Polymers67,1554
Non-polymers00
Water4,810267
1
AAA: Putative ubiquitin-conjugating enzyme e2

BBB: Ubiquitin-conjugating enzyme-like protein


  • defined by author&software
  • Evidence: light scattering, SEC-MALLS showed clearly that each protein was monomeric with a heterodimer formed after their mixing., gel filtration, SEC-MALLS showed clearly that each protein was ...Evidence: light scattering, SEC-MALLS showed clearly that each protein was monomeric with a heterodimer formed after their mixing., gel filtration, SEC-MALLS showed clearly that each protein was monomeric with a heterodimer formed after their mixing.
  • 33.6 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)33,5782
Polymers33,5782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area1240 Å2
ΔGint-8 kcal/mol
Surface area15580 Å2
MethodPISA
2
CCC: Putative ubiquitin-conjugating enzyme e2

DDD: Ubiquitin-conjugating enzyme-like protein


Theoretical massNumber of molelcules
Total (without water)33,5782
Polymers33,5782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area1130 Å2
ΔGint-8 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.523, 72.568, 120.094
Angle α, β, γ (deg.)90.000, 91.839, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative ubiquitin-conjugating enzyme e2


Mass: 17298.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (strain MHOM/GT/2001/U1103) (eukaryote)
Strain: MHOM/GT/2001/U1103 / Gene: LMXM_04_0680 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: E9AK51, ubiquitin-protein ligase
#2: Protein Ubiquitin-conjugating enzyme-like protein


Mass: 16279.417 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (strain MHOM/GT/2001/U1103) (eukaryote)
Strain: MHOM/GT/2001/U1103 / Gene: LMXM_13_1580 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: E9API2, ubiquitin-protein ligase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.16 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: UBC2 and UEV1 were mixed in a 1:1 molar ratio to a final concentration of 6.6 mg mL-1 and incubated on ice for 30 min. Crystals were grown using a sitting drop method with a 1:1 ratio of ...Details: UBC2 and UEV1 were mixed in a 1:1 molar ratio to a final concentration of 6.6 mg mL-1 and incubated on ice for 30 min. Crystals were grown using a sitting drop method with a 1:1 ratio of protein to reservoir solution (0.1 M Bis-Tris propane, pH 7.5, 0.2 M sodium formate and 20% PEG) in the drop. Crystals took 2 days to appear.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.65→47.25 Å / Num. obs: 67149 / % possible obs: 100 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.075 / Rrim(I) all: 0.12 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.2 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.04-46.250.0474460.9970.0380.061
1.7-1.731.44932670.3680.7471.635

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
Aimless0.7.4data reduction
Aimless0.7.4data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 1J7D

1j7d


Resolution: 1.7→46.25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.71 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.131
RfactorNum. reflection% reflection
Rfree0.2603 3018 4.912 %
Rwork0.2228 58422 -
all0.225 --
obs-61440 99.964 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.043 Å2
Baniso -1Baniso -2Baniso -3
1-1.251 Å20 Å2-1.504 Å2
2--0.342 Å20 Å2
3----1.494 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 0 267 4889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124778
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.6586499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8875572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49621.969259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90915844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9231536
X-RAY DIFFRACTIONr_chiral_restr0.1150.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023714
X-RAY DIFFRACTIONr_nbd_refined0.2070.22102
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23225
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2273
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2830.216
X-RAY DIFFRACTIONr_mcbond_it2.6442.8742282
X-RAY DIFFRACTIONr_mcangle_it3.6584.2962850
X-RAY DIFFRACTIONr_scbond_it3.4583.222496
X-RAY DIFFRACTIONr_scangle_it4.9814.6793647
X-RAY DIFFRACTIONr_lrange_it6.37339.1627157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3542140.3444286X-RAY DIFFRACTION99.9556
1.744-1.7920.3152030.3154219X-RAY DIFFRACTION99.9774
1.792-1.8440.3232020.2974087X-RAY DIFFRACTION100
1.844-1.9010.3352320.2773957X-RAY DIFFRACTION99.9523
1.901-1.9630.3192030.2883808X-RAY DIFFRACTION100
1.963-2.0320.291850.2533771X-RAY DIFFRACTION99.9747
2.032-2.1080.2741760.2333517X-RAY DIFFRACTION99.9729
2.108-2.1940.3191700.233494X-RAY DIFFRACTION99.7821
2.194-2.2920.3381770.2843287X-RAY DIFFRACTION100
2.292-2.4040.2561830.2383146X-RAY DIFFRACTION100
2.404-2.5340.3041740.2283018X-RAY DIFFRACTION100
2.534-2.6870.3171440.2372872X-RAY DIFFRACTION100
2.687-2.8730.303940.2332709X-RAY DIFFRACTION99.9643
2.873-3.1030.2421330.222495X-RAY DIFFRACTION100
3.103-3.3990.2451000.2232338X-RAY DIFFRACTION100
3.399-3.7990.2321240.1922078X-RAY DIFFRACTION99.9546
3.799-4.3860.208920.1681852X-RAY DIFFRACTION100
4.386-5.3690.2191000.1661568X-RAY DIFFRACTION100
5.369-7.5820.226750.1991199X-RAY DIFFRACTION99.8433
7.582-46.2910.164350.166701X-RAY DIFFRACTION99.729

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