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- PDB-3g1n: Catalytic domain of the human E3 ubiquitin-protein ligase HUWE1 -

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Basic information

Entry
Database: PDB / ID: 3g1n
TitleCatalytic domain of the human E3 ubiquitin-protein ligase HUWE1
ComponentsE3 ubiquitin-protein ligase HUWE1
KeywordsLIGASE / ALPHA AND BETA PROTEIN (A + B) / E3 LIGASE / HECT DOMAIN / UBL-CONJUGATION PATHWAY / Alternative splicing / Chromosomal rearrangement / Cytoplasm / Differentiation / Disease mutation / DNA-binding / Mental retardation / Nucleus / Phosphoprotein / Ubl conjugation pathway / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair ...negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / secretory granule lumen / ficolin-1-rich granule lumen / membrane fusion / cell differentiation / Golgi membrane / Neutrophil degranulation / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) ...Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Armadillo-type fold / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWalker, J.R. / Qiu, L. / Li, Y. / Davis, T. / Tempel, W. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. ...Walker, J.R. / Qiu, L. / Li, Y. / Davis, T. / Tempel, W. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Hect Domain of Human HUWE1/MULE
Authors: Walker, J.R. / Qiu, L. / Li, Y. / Davis, T. / Tempel, W. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Dhe-Paganon, S.
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: 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

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HUWE1
B: E3 ubiquitin-protein ligase HUWE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1034
Polymers91,0572
Non-polymers462
Water2,522140
1
A: E3 ubiquitin-protein ligase HUWE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5512
Polymers45,5291
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase HUWE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5512
Polymers45,5291
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)176.530, 72.213, 77.238
Angle α, β, γ (deg.)90.00, 106.94, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein E3 ubiquitin-protein ligase HUWE1 / HECT / UBA and WWE domain-containing protein 1 / Upstream regulatory element-binding protein 1 / ...HECT / UBA and WWE domain-containing protein 1 / Upstream regulatory element-binding protein 1 / URE-binding protein 1 / URE-B1 / Mcl-1 ubiquitin ligase E3 / Mule / ARF-binding protein 1 / ARF-BP1 / Large structure of UREB1 / LASU1 / Homologous to E6AP carboxyl terminus homologous protein 9 / HectH9


Mass: 45528.500 Da / Num. of mol.: 2 / Fragment: HECT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPC272, HUWE1, KIAA0312, KIAA1578, UREB1 / Plasmid: PET28A-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) V2R
References: UniProt: Q7Z6Z7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG-4000, 10% ISOPROPANOL, 0.1 M TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 21, 2009 / Details: MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 28536 / Num. obs: 28536 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.133 / Net I/σ(I): 10.851
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.96 / Num. unique all: 2629 / Rsym value: 0.441 / % possible all: 91.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0063refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ND7

1nd7


Resolution: 2.6→29.3 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.873 / SU B: 29.614 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 1.219 / ESU R Free: 0.361 / 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
Rfree0.27919 1443 5.1 %RANDOM
Rwork0.214 ---
obs0.21726 27053 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20.06 Å2
2--0.09 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 0 2 141 6415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226428
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.958686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0515770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52623.228347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.993151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.591559
X-RAY DIFFRACTIONr_chiral_restr0.0930.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214999
X-RAY DIFFRACTIONr_mcbond_it0.2771.53786
X-RAY DIFFRACTIONr_mcangle_it0.54326119
X-RAY DIFFRACTIONr_scbond_it0.87932642
X-RAY DIFFRACTIONr_scangle_it1.4644.52567
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2986 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.420.5
Bmedium thermal0.362
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 101 -
Rwork0.33 1819 -
obs--90.91 %
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)
13.0182-3.03940.98295.2916-0.85413.6590.1254-0.066-0.04950.02780.0718-0.16350.3492-0.2153-0.19720.1595-0.1156-0.05140.1905-0.02740.149119.4826-17.9409-5.9373
23.24351.85590.5092.0422.49085.92840.108-0.1370.2209-0.1499-0.17570.288-0.4772-0.65420.06760.1060.0769-0.03580.33240.05180.203413.3192-7.2852-3.2967
38.80865.6081.54433.57571.01710.5033-0.34220.12680.5673-0.25670.09690.3816-0.26040.1720.24530.4084-0.0259-0.02550.25930.06320.272120.9072-5.6198-11.9093
47.87910.5102-0.00531.52521.21481.001-0.2264-0.07330.2503-0.18020.18730.0324-0.18120.1340.03910.30370.0072-0.00210.18220.00920.119534.607-0.74161.6189
51.7904-0.5877-0.06151.81051.19994.21540.01140.12130.0868-0.0299-0.0008-0.0532-0.1350.0202-0.01060.1817-0.01530.04390.040.02720.084328.6124-9.162.6669
69.19329.00760.97788.96420.33652.91240.01930.16020.4673-0.0967-0.05010.46960.61220.88260.03080.30110.1184-0.05170.29990.00660.31446.1562-15.37858.284
72.5961-4.11052.06376.7256-2.01389.1324-0.0860.12360.11950.1055-0.1996-0.1144-0.24780.12980.28560.1296-0.0685-0.00220.161-0.01140.257353.7452-5.98112.5879
89.2659-3.04981.14091.3147-1.53484.8940.01390.13360.47350.016-0.1499-0.26270.03960.34660.1360.1919-0.102-0.05270.08260.05160.303349.5925-11.599624.014
92.24830.7157-0.55661.0744-0.61921.49710.0127-0.0461-0.0317-0.1241-0.0401-0.10380.0961-0.19560.02740.10480.0051-0.00820.1070.02920.132932.72-16.47425.0697
102.5866-0.99470.26953.0364-0.74863.2356-0.03280.0991-0.1151-0.076-0.0419-0.05340.02170.20030.07470.1229-0.031-0.00680.0264-0.0120.075154.5283-12.1327-13.6647
112.17380.7322-1.41332.04340.79492.00860.0713-0.09180.08560.27940.107-0.39950.01460.1972-0.17830.2183-0.0593-0.10610.155-0.03710.314956.3617-8.1123-5.155
120.6922-0.84160.68093.8535-0.37941.6330.0182-0.1852-0.14410.06160.15130.13820.39160.339-0.16950.29180.1526-0.05340.38210.03690.223158.5999-18.9379-7.2758
132.1565-0.41450.67964.1823-1.07382.43840.1903-0.1028-0.52150.1109-0.1453-0.17150.47090.3167-0.0450.26840.0212-0.00010.1711-0.01070.199456.0681-8.3688-29.3376
143.2135-1.2864-0.00314.06930.28762.02270.0924-0.110.2399-0.00750.0703-0.2731-0.06050.1145-0.16270.1481-0.06170.02780.11070.00410.143455.27483.2315-32.6667
152.53640.03982.54670.56450.71593.37660.2068-0.29080.1585-0.0577-0.2438-0.06680.1307-0.56190.03690.2519-0.01270.02010.2131-0.00030.160641.7360.5775-33.6778
162.22980.90440.54140.6221-0.27483.1612-0.04280.09580.21-0.0115-0.00160.008-0.13470.14010.04440.1790.01950.03030.0374-0.01430.117742.6133-5.8043-40.8191
174.55743.32421.59232.70042.37946.237-0.0128-0.2716-0.1999-0.0408-0.1954-0.04650.0496-0.11160.20810.1710.0132-0.04480.17180.04630.202339.9209-15.4468-36.6894
188.74292.59781.95717.75962.72563.42090.126-0.0303-0.10570.46190.056-0.27610.14370.1754-0.1820.0556-0.01050.01810.12820.01330.066523.9217-23.6601-47.315
195.70416.06520.71137.74260.39650.9268-0.39750.9632-0.252-0.38480.52030.1225-0.0076-0.0597-0.12290.1506-0.06490.08230.5284-0.18120.152929.5988-22.9214-61.007
203.6494-0.5947-0.43528.2444-0.74890.14110.01710.0269-0.59290.1473-0.1377-0.5018-0.02220.05760.12070.1867-0.01080.04040.3409-0.06280.257232.3559-26.9736-53.0849
210.82030.58690.21610.60480.33842.3405-0.09290.0875-0.19220.06480.035-0.0128-0.07040.00270.05780.14040.00310.08790.1477-0.02070.165645.3574-16.2962-39.1261
221.54880.0572-0.2152.20310.33551.793-0.0202-0.1922-0.09530.1220.0231-0.10090.0726-0.0164-0.00290.06930.0050.0140.10640.02170.069623.5455-22.5076-21.4589
234.24270.7875-0.40522.4498-0.85911.26360.0360.0599-0.0456-0.3714-0.15370.2026-0.0439-0.16160.11770.150.0243-0.04440.1696-0.00880.115420.4051-20.2273-30.124
242.67530.1628-0.92922.2494-1.01662.385-0.2671-0.0215-0.4688-0.1043-0.0019-0.28020.22330.23760.2690.13290.03020.01380.1233-0.01660.182124.6728-30.7618-26.9822
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3993 - 4025
2X-RAY DIFFRACTION2A4026 - 4056
3X-RAY DIFFRACTION3A4057 - 4070
4X-RAY DIFFRACTION4A4071 - 4093
5X-RAY DIFFRACTION5A4094 - 4136
6X-RAY DIFFRACTION6A4137 - 4147
7X-RAY DIFFRACTION7A4148 - 4160
8X-RAY DIFFRACTION8A4161 - 4211
9X-RAY DIFFRACTION9A4212 - 4254
10X-RAY DIFFRACTION10A4255 - 4306
11X-RAY DIFFRACTION11A4307 - 4340
12X-RAY DIFFRACTION12A4341 - 4366
13X-RAY DIFFRACTION13B3996 - 4025
14X-RAY DIFFRACTION14B4026 - 4059
15X-RAY DIFFRACTION15B4060 - 4082
16X-RAY DIFFRACTION16B4083 - 4122
17X-RAY DIFFRACTION17B4123 - 4140
18X-RAY DIFFRACTION18B4141 - 4164
19X-RAY DIFFRACTION19B4165 - 4202
20X-RAY DIFFRACTION20B4203 - 4213
21X-RAY DIFFRACTION21B4214 - 4255
22X-RAY DIFFRACTION22B4256 - 4305
23X-RAY DIFFRACTION23B4306 - 4340
24X-RAY DIFFRACTION24B4341 - 4366

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