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- PDB-5lbn: High-resolution crystal structure of the UBC core domain of UBE2E... -

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Basic information

Entry
Database: PDB / ID: 5lbn
TitleHigh-resolution crystal structure of the UBC core domain of UBE2E1/UbcH6
ComponentsUbiquitin-conjugating enzyme E2 E1
KeywordsTRANSFERASE / UBC core / Ubiquitination / E2 Ubiquitin-conjugating enzyme
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / ubiquitin conjugating enzyme complex / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / E2 ubiquitin-conjugating enzyme ...ISG15 transferase activity / ISG15-protein conjugation / ubiquitin conjugating enzyme complex / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / E2 ubiquitin-conjugating enzyme / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin conjugating enzyme activity / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / ubiquitin ligase complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / CDK-mediated phosphorylation and removal of Cdc6 / ISG15 antiviral mechanism / protein polyubiquitination / ubiquitin-protein transferase activity / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein ubiquitination / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
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 / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsAnandapadamanaban, M. / Moche, M. / Sunnerhagen, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Structure of a TRIM21 - UBE2E1 complex reveals the specificity of E2 and ubiquitin recognition by TRIM E3 RINGs
Authors: Anandapadamanaban, M. / Moche, M. / Sunnerhagen, M.
History
DepositionJun 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ubiquitin-conjugating enzyme E2 E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8033
Polymers17,6191
Non-polymers1842
Water3,477193
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-0 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.301, 40.555, 91.317
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 E1 / (E3-independent) E2 ubiquitin-conjugating enzyme E1 / E2 ubiquitin-conjugating enzyme E1 / UbcH6 / ...(E3-independent) E2 ubiquitin-conjugating enzyme E1 / E2 ubiquitin-conjugating enzyme E1 / UbcH6 / Ubiquitin carrier protein E1 / Ubiquitin-protein ligase E1


Mass: 17619.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2E1, UBCH6 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Ros-2
References: UniProt: P51965, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.1 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium citrate pH 6 and 8% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.282416 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282416 Å / Relative weight: 1
ReflectionResolution: 1.42→37.06 Å / Num. obs: 26209 / % possible obs: 94.8 % / Redundancy: 11.568 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 33.21
Reflection shellResolution: 1.42→1.51 Å / Redundancy: 9.66 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 13.15 / % possible all: 79.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
PDB_EXTRACT3.1data extraction
REFMAC5.8.0151refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→37.06 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.183 1311 5 %RANDOM
Rwork0.1543 ---
obs0.1558 26190 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 62.99 Å2 / Biso mean: 17.7812 Å2 / Biso min: 8.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.42→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 12 193 1417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191337
X-RAY DIFFRACTIONr_bond_other_d00.021265
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.9751828
X-RAY DIFFRACTIONr_angle_other_deg3.64432935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46223.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56315227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5431510
X-RAY DIFFRACTIONr_chiral_restr0.1370.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211527
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02299
X-RAY DIFFRACTIONr_mcbond_it0.960.942660
X-RAY DIFFRACTIONr_mcbond_other0.9250.939659
X-RAY DIFFRACTIONr_mcangle_it1.5291.407839
LS refinement shellResolution: 1.419→1.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 68 -
Rwork0.173 1268 -
all-1336 -
obs--67.14 %
Refinement TLS params.Method: refined / Origin x: 13.786 Å / Origin y: 4.237 Å / Origin z: 9.416 Å
111213212223313233
T0.0138 Å2-0.0011 Å2-0.0076 Å2-0.0414 Å20.0032 Å2--0.0052 Å2
L0.3413 °2-0.4302 °2-0.3878 °2-2.5245 °21.2151 °2--0.88 °2
S0.0094 Å °0.0312 Å °0.0068 Å °-0.0091 Å °-0.0153 Å °-0.039 Å °-0.0512 Å °0.0163 Å °0.0058 Å °

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