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- PDB-3l1y: Crystal structure of human UBC4 E2 conjugating enzyme -

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Basic information

Entry
Database: PDB / ID: 3l1y
TitleCrystal structure of human UBC4 E2 conjugating enzyme
ComponentsUbiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / E2 CONJUGATING ENZYME / UBIQUITIN LIGASE / Ubl conjugation pathway
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / 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 / Negative regulators of DDX58/IFIH1 signaling ...(E3-independent) E2 ubiquitin-conjugating enzyme / 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 / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / protein modification process / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / 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 / ubiquitin protein ligase binding / protein-containing complex / extracellular exosome / 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 D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBenirschke, R. / Thompson, J.R. / Mer, G.
CitationJournal: Structure / Year: 2010
Title: Molecular Basis for the Association of Human E4B U Box Ubiquitin Ligase with E2-Conjugating Enzymes UbcH5c and Ubc4.
Authors: Benirschke, R.C. / Thompson, J.R. / Nomine, Y. / Wasielewski, E. / Juranic, N. / Macura, S. / Hatakeyama, S. / Nakayama, K.I. / Botuyan, M.V. / Mer, G.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2


Theoretical massNumber of molelcules
Total (without water)18,0471
Polymers18,0471
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.230, 59.120, 45.240
Angle α, β, γ (deg.)90.00, 106.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18046.639 Da / Num. of mol.: 1 / Fragment: residues 1-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, UBC4, UBCH5B / Plasmid: pT7.7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62837, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE AT POSITION 128 IS A NATURAL VARIANT AS IN AAC41750

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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 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M sodium formate, 0.1M sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→43.31 Å / Num. obs: 17905 / % possible obs: 99.92 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.14
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 13.15 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0063refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X23

1x23


Resolution: 1.6→43.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.236 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 958 5.1 %RANDOM
Rwork0.187 ---
obs0.18918 17905 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.751 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.21 Å2
2--0.03 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 0 176 1396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221320
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.9561813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2635169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32823.59464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40915217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8791510
X-RAY DIFFRACTIONr_chiral_restr0.1350.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0221050
X-RAY DIFFRACTIONr_mcbond_it0.971.5802
X-RAY DIFFRACTIONr_mcangle_it1.72821321
X-RAY DIFFRACTIONr_scbond_it3.2873518
X-RAY DIFFRACTIONr_scangle_it4.9074.5485
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 61 -
Rwork0.413 1346 -
obs--100 %
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)
10.5594-1.51420.63974.38790.356416.0278-0.07750.0802-0.03210.2467-0.13840.11190.35160.81980.21590.1262-0.00420.00550.26980.03430.06160.8053.94635.467
20.8032-0.4773-0.92763.58773.13815.6672-0.105-0.139-0.1850.12110.00170.03610.25510.04130.10330.18680.0102-0.00860.13310.02060.0616-1.805-3.42318.43
30.17330.1758-0.41760.7938-1.05892.49030.0239-0.02390.0341-0.09790.0510.04120.0379-0.0078-0.07480.1861-0.0105-0.02140.1142-0.00510.04091.6278.7578.163
41.17660.6613-0.65271.379-1.26294.2122-0.0290.14780.14-0.09530.19590.2218-0.0627-0.3079-0.1670.176-0.0025-0.02760.15110.03220.0903-8.1578.7799.641
51.9869-1.480.89622.9662-0.75652.56860.00690.0196-0.0251-0.1111-0.01060.11690.0004-0.15050.00370.1979-0.0278-0.02040.10060.00780.0237-2.53816.162-9.163
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 6
2X-RAY DIFFRACTION2A7 - 21
3X-RAY DIFFRACTION3A22 - 92
4X-RAY DIFFRACTION4A93 - 117
5X-RAY DIFFRACTION5A118 - 151

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