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- PDB-3l1z: Crystal structure of the U-BOX domain of human E4B ubiquitin liga... -

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Basic information

Entry
Database: PDB / ID: 3l1z
TitleCrystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme
Components
  • Ubiquitin conjugation factor E4 B
  • Ubiquitin-conjugating enzyme E2 D3
KeywordsLIGASE / E4B / UFD2A / UBCH5C / U-BOX UBIQUITIN LIGASE / E2 UBIQUITIN CONJUGATING ENZYME / UBL CONJUGATION PATHWAY
Function / homology
Function and homology information


granzyme-mediated apoptotic signaling pathway / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / protein K11-linked ubiquitination / ubiquitin-ubiquitin ligase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity ...granzyme-mediated apoptotic signaling pathway / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / protein K11-linked ubiquitination / ubiquitin-ubiquitin ligase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / negative regulation of BMP signaling pathway / protein autoubiquitination / protein K48-linked ubiquitination / response to UV / ubiquitin ligase complex / ERAD pathway / 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 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / protein modification process / RING-type E3 ubiquitin transferase / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ubiquitin conjugation factor E4, core / Ubiquitin conjugation factor E4 / Ubiquitin elongating factor core / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site ...Ubiquitin conjugation factor E4, core / Ubiquitin conjugation factor E4 / Ubiquitin elongating factor core / U-box domain / U-box domain profile. / Modified RING finger domain / U-box 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 / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin conjugation factor E4 B / Ubiquitin-conjugating enzyme E2 D3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 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 1.2Dec 28, 2011Group: Derived calculations
Revision 1.3Sep 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 D3
B: Ubiquitin conjugation factor E4 B


Theoretical massNumber of molelcules
Total (without water)29,5482
Polymers29,5482
Non-polymers00
Water27015
1
A: Ubiquitin-conjugating enzyme E2 D3

B: Ubiquitin conjugation factor E4 B


Theoretical massNumber of molelcules
Total (without water)29,5482
Polymers29,5482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area1320 Å2
ΔGint-7 kcal/mol
Surface area12500 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-7 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.708, 142.708, 83.133
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D3 / Ubiquitin-protein ligase D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2-17 kDa ...Ubiquitin-protein ligase D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / E2(17)KB 3


Mass: 17998.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D3, UBCH5C / Plasmid: pT7.7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61077, ubiquitin-protein ligase
#2: Protein Ubiquitin conjugation factor E4 B / Ubiquitin fusion degradation protein 2 / Homozygously deleted in neuroblastoma 1


Mass: 11548.991 Da / Num. of mol.: 1 / Fragment: U box domain, residues 1208-1302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE4B, HDNB1, KIAA0684, UFD2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O95155
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 4M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.17→32.78 Å / Num. obs: 8196 / % possible obs: 92.17 % / Redundancy: 58.8 % / Rmerge(I) obs: 0.192 / Net I/σ(I): 18.06
Reflection shellResolution: 3.17→3.23 Å / Redundancy: 57.6 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 6.18 / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1L1X AND 3L1Y

1l1x
PDB Unreleased entry

3l1y


Resolution: 3.17→32.78 Å / SU ML: 0.45 / Isotropic thermal model: Isotropic and TLS / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 808 9.86 %RANDOM
Rwork0.2315 ---
obs0.2364 8196 92.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.003 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 451.55 Å2 / Biso mean: 93.63 Å2 / Biso min: 35.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.959 Å2-0 Å2-0 Å2
2---1.959 Å2-0 Å2
3----8.964 Å2
Refinement stepCycle: LAST / Resolution: 3.17→32.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 0 15 1865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031900
X-RAY DIFFRACTIONf_angle_d0.6892587
X-RAY DIFFRACTIONf_dihedral_angle_d16.487723
X-RAY DIFFRACTIONf_chiral_restr0.043282
X-RAY DIFFRACTIONf_plane_restr0.004340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.3690.45121490.35191221X-RAY DIFFRACTION96
3.369-3.62890.42031300.30871146X-RAY DIFFRACTION88
3.6289-3.99350.29471170.2491209X-RAY DIFFRACTION91
3.9935-4.570.2631040.21321204X-RAY DIFFRACTION89
4.57-5.75270.23711560.18851187X-RAY DIFFRACTION90
5.7527-32.78710.23011520.20061421X-RAY DIFFRACTION98
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)
14.1859-4.48991.78942.1187-2.30421.41850.33540.2043-1.5728-0.09090.09661.6524-0.29310.158-0.41720.6701-0.23940.0140.9508-0.07321.3354-69.924333.004914.5012
22.8471-2.04162.20711.94089.62972.04171.21410.24121.70651.4715-1.4446-0.16611.9651-1.00760.38240.6709-0.12710.14690.6446-0.04690.5476-62.813430.882719.8036
34.62790.9785-1.62582.2815-2.59383.1001-0.3169-0.5614-0.96540.90110.0501-0.3247-0.39020.22480.13160.959-0.00280.09240.75560.16330.8853-51.167733.563726.6666
41.9576-7.0299-3.19888.0917.07719.49080.7049-0.6979-0.9127-0.7347-0.25810.4092-0.9659-1.3217-0.4960.8233-0.0301-0.03080.96810.2460.9865-60.423242.435921.4509
5-1.35090.3439-5.8047-0.46123.42059.15360.1334-1.05920.09160.02880.5009-0.2048-1.08051.77440.42660.62820.0404-0.22170.31940.1064-1.0274-48.343841.275622.787
6-3.21891.99426.63934.43032.31671.3524-0.1474-1.3429-3.2349-0.06230.59730.2217-0.45080.7224-0.1830.8352-0.1253-0.0931.2750.51411.5694-32.423637.725422.9664
74.10351.18251.66082.82511.95712.3501-0.2397-0.5234-0.2785-0.27780.0190.3318-0.2285-0.36690.19790.4984-0.0293-0.08620.49290.12330.816-45.533641.594414.0418
82.2027-1.0019-0.72822.81078.39959.6982-0.18120.4518-1.4019-0.7692-0.555-0.1198-0.86470.44960.58710.61110.04580.09280.52410.18540.6374-48.000230.852512.0588
91.15091.9257-1.10218.6856-0.10454.9978-0.0523-0.0792-1.3952-0.1570.4442-2.08180.32970.5602-0.29010.3931-0.0794-0.05290.45620.04481.027-30.480939.56527.7085
108.77811.9747-1.16167.0792-0.57060.6981-0.2472-1.5877-1.2686-0.44141.05991.4925-0.38930.3414-0.73440.5218-0.043-0.30730.8130.09280.9653-29.763349.413117.9626
11-0.4602-2.54283.9028.0078-0.72496.1148-0.5063-0.621-0.50451.52560.74150.6223-3.80411.4419-0.47651.959-0.54360.33141.70840.06420.6307-54.530448.874230.7253
126.78741.6373-3.0387-0.7306-0.04111.7749-0.29330.35220.09650.06340.02730.3744-0.1898-0.3450.18250.88620.3589-0.41981.1821-0.2880.9809-52.862260.353226.0537
137.26357.8135.60862.7506-1.9741-2.30510.1790.8276-3.6037-0.6069-0.7746-3.124-0.0057-0.40960.48840.18790.14870.0450.4842-0.07691.0492-59.515758.796619.1372
143.9493-2.69351.03414.9895-5.66199.4772-0.60540.79521.2077-0.5575-0.17840.22130.3383-0.56520.58040.6114-0.102-0.14910.7930.11970.883-51.397662.29514.2526
158.9854-4.3061.9931.3209-3.07435.96720.62040.349-1.4445-0.7056-0.19220.2186-0.09840.6573-0.48080.6025-0.05010.18880.4554-0.141.082-58.337357.14737.6476
167.9948-4.1182-5.97795.66484.47515.34310.02010.97731.33650.6608-0.1418-0.29320.5001-0.39340.15470.6687-0.0329-0.08070.70980.1270.6663-57.913566.52844.8721
17-0.63563.1969-7.33762.0818-2.57428.44520.34-0.23261.39830.0606-1.05-0.1074-0.27761.84380.62890.45880.1070.24150.79810.19061.4895-44.04560.888714.8262
185.6226-4.5554-6.0267.35766.02490.3959-1.4904-0.642-0.11871.1610.09550.22320.26810.69630.97860.79030.0104-0.1480.9917-0.04330.5619-44.080352.057928.8023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:3)A-1 - 3
2X-RAY DIFFRACTION2(chain A and resid 4:9)A4 - 9
3X-RAY DIFFRACTION3(chain A and resid 10:30)A10 - 30
4X-RAY DIFFRACTION4(chain A and resid 31:35)A31 - 35
5X-RAY DIFFRACTION5(chain A and resid 36:40)A36 - 40
6X-RAY DIFFRACTION6(chain A and resid 41:46)A41 - 46
7X-RAY DIFFRACTION7(chain A and resid 47:87)A47 - 87
8X-RAY DIFFRACTION8(chain A and resid 88:108)A88 - 108
9X-RAY DIFFRACTION9(chain A and resid 109:137)A109 - 137
10X-RAY DIFFRACTION10(chain A and resid 138:150)A138 - 150
11X-RAY DIFFRACTION11(chain B and resid 1223:1227)B1223 - 1227
12X-RAY DIFFRACTION12(chain B and resid 1228:1233)B1228 - 1233
13X-RAY DIFFRACTION13(chain B and resid 1234:1239)B1234 - 1239
14X-RAY DIFFRACTION14(chain B and resid 1240:1253)B1240 - 1253
15X-RAY DIFFRACTION15(chain B and resid 1254:1265)B1254 - 1265
16X-RAY DIFFRACTION16(chain B and resid 1266:1279)B1266 - 1279
17X-RAY DIFFRACTION17(chain B and resid 1280:1288)B1280 - 1288
18X-RAY DIFFRACTION18(chain B and resid 1289:1300)B1289 - 1300

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