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- PDB-3bzh: Crystal structure of human ubiquitin-conjugating enzyme E2 E1 -

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Basic information

Entry
Database: PDB / ID: 3bzh
TitleCrystal structure of human ubiquitin-conjugating enzyme E2 E1
ComponentsUbiquitin-conjugating enzyme E2 E1
KeywordsLIGASE / STRUCTURAL GENOMICS CONSORTIUM / UBIQUITIN / UBIQUITIN-CONJUGATING ENZYME / SGC / Ubl conjugation pathway
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / 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 / Phosphorylation of the APC/C / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity ...ISG15 transferase activity / ISG15-protein conjugation / 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 / Phosphorylation of the APC/C / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / protein monoubiquitination / ubiquitin ligase complex / protein K48-linked ubiquitination / 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: 1.6 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Li, Y. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Mol Cell Proteomics / Year: 2012
Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.
Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S.
History
DepositionJan 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5792
Polymers21,4871
Non-polymers921
Water1,20767
1
A: Ubiquitin-conjugating enzyme E2 E1
hetero molecules

A: Ubiquitin-conjugating enzyme E2 E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1594
Polymers42,9742
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.630, 51.630, 109.437
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 E1 / Ubiquitin-protein ligase E1 / Ubiquitin carrier protein E1 / UbcH6


Mass: 21487.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2E1, UBCH6 / Plasmid: pET28-MHL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51965, ubiquitin-protein ligase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.96 Å3/Da / Density % sol: 37.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.2M (NH4)2SO4, 0.1M Bis-Tris-Propane pH 9.0, 0.001M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97942 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 15, 2007 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 22998 / Num. obs: 22998 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Rsym value: 0.037 / Net I/σ(I): 64.3816
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 2.42 / Num. unique all: 2245 / Rsym value: 0.835 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y6L

1y6l


Resolution: 1.6→35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.713 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.22571 1178 5.1 %RANDOM
Rwork0.20536 ---
all0.20639 21768 --
obs0.20639 21768 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.253 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 6 67 1309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221342
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.971843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5995175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61623.84652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4715214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.945158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021033
X-RAY DIFFRACTIONr_nbd_refined0.2020.2631
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2973
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.213
X-RAY DIFFRACTIONr_mcbond_it1.5333870
X-RAY DIFFRACTIONr_mcangle_it2.3641408
X-RAY DIFFRACTIONr_scbond_it3.1975530
X-RAY DIFFRACTIONr_scangle_it4.7617435
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 80 -
Rwork0.237 1555 -
obs--99.15 %
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)
118.582-2.37485.49036.17391.811425.2736-0.14931.3198-0.1541-0.5713-0.07290.0086-0.42920.09040.22220.1048-0.0354-0.03970.0887-0.02350.14414.615-16.3841-23.4923
211.6687-4.8111-0.31413.19842.863415.5494-0.1840.3003-0.6342-0.40210.01610.28180.94791.52160.16780.10310.12220.17510.26140.11010.057-0.852410.6678-3.005
31.7696-0.56131.47810.459.337431.1076-0.14360.3760.3042-0.0922-0.4874-0.5506-0.57780.46330.6310.0527-0.0574-0.03450.11830.07110.1217-6.361118.35378.2693
42.5038-1.62880.17424.5078-1.55896.9785-0.24630.10250.06890.0787-0.15860.0007-0.3632-0.25310.40490.0629-0.0052-0.0380.0996-0.04030.1794-11.901617.247914.9356
511.3249-3.625-5.18174.06811.60617.0747-0.2831-0.2697-0.0673-0.1324-0.0802-0.10580.74050.77480.36340.09170.07440.07040.12890.04870.1038-4.25657.88411.0391
64.7484-0.00560.43583.76531.17362.65760.0263-0.48720.3509-0.0648-0.05040.222-0.0473-0.11940.0240.0132-0.01160.01320.1282-0.06060.1115-23.843611.202121.6717
73.11731.8366-3.58012.7111-4.1018.8565-0.16260.0681-0.1137-0.60440.0237-0.08220.80730.05610.13890.17980.00890.04140.0728-0.00660.08-12.17745.30257.566
85.64070.67740.86350.86610.26553.6555-0.00420.1008-0.3434-0.2123-0.02280.02410.302-0.04430.0270.1282-0.0447-0.02220.0547-0.00550.1264-24.34530.49612.4608
96.4074.2405-4.163514.7774-6.892513.948-0.23620.72510.3016-0.81880.5690.40510.6396-0.8552-0.33280.1263-0.1125-0.05490.16370.07260.0026-18.716610.4012-0.9208
1018.43233.109-5.0293.9654-3.20667.40730.22140.59130.32820.1441-0.26830.0751-0.27870.28380.04680.0838-0.0308-0.02030.0984-0.00530.0642-20.046713.6979.2667
117.1173-1.2005-0.3282.49-0.55752.79050.12690.0937-0.3414-0.3104-0.07440.13140.1498-0.471-0.05250.0714-0.0625-0.04870.1026-0.04360.0876-33.18261.929411.0101
128.7971-1.11642.23211.0455-0.45336.22870.0578-0.3716-0.49790.16350.10990.40960.4402-0.5847-0.16770.04-0.07980.01090.13690.0350.1476-34.72861.701321.8491
1316.3371.1207-3.09521.8606-0.857513.20580.351-0.9838-0.86130.6466-0.1175-0.25370.3797-0.1501-0.23350.1137-0.0495-0.03850.2110.09140.0828-22.83851.412427.6713
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA21 - 2722 - 28
2X-RAY DIFFRACTION2AA40 - 5141 - 52
3X-RAY DIFFRACTION3AA52 - 6053 - 61
4X-RAY DIFFRACTION4AA61 - 7362 - 74
5X-RAY DIFFRACTION5AA74 - 8175 - 82
6X-RAY DIFFRACTION6AA82 - 9683 - 97
7X-RAY DIFFRACTION7AA97 - 11898 - 119
8X-RAY DIFFRACTION8AA119 - 132120 - 133
9X-RAY DIFFRACTION9AA133 - 143134 - 144
10X-RAY DIFFRACTION10AA144 - 156145 - 157
11X-RAY DIFFRACTION11AA157 - 173158 - 174
12X-RAY DIFFRACTION12AA174 - 188175 - 189
13X-RAY DIFFRACTION13AA189 - 193190 - 194

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