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- PDB-3l4h: Helical box domain and second WW domain of the human E3 ubiquitin... -

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Basic information

Entry
Database: PDB / ID: 3l4h
TitleHelical box domain and second WW domain of the human E3 ubiquitin-protein ligase HECW1
ComponentsE3 ubiquitin-protein ligase HECW1
KeywordsPROTEIN BINDING / E3 ligase / WW domain / UBL-conjugation pathway / structural genomics / Structural Genomics Consortium / SGC / Coiled coil / Cytoplasm / Ligase / helical box domain
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / regulation of dendrite morphogenesis / Degradation of DVL / negative regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase HECW1/2, N-terminal / E3 ubiquitin-protein ligase HECW, C2 domain / E3 ubiquitin-protein ligase HECW1, helical box domain / N-terminal domain of E3 ubiquitin-protein ligase HECW1 and 2 / Helical box domain of E3 ubiquitin-protein ligase HECW1 / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. ...E3 ubiquitin-protein ligase HECW1/2, N-terminal / E3 ubiquitin-protein ligase HECW, C2 domain / E3 ubiquitin-protein ligase HECW1, helical box domain / N-terminal domain of E3 ubiquitin-protein ligase HECW1 and 2 / Helical box domain of E3 ubiquitin-protein ligase HECW1 / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
ACETIC ACID / E3 ubiquitin-protein ligase HECW1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsWalker, J.R. / Qiu, L. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The tandem helical box and second WW domains of human HECW1
Authors: Walker, J.R. / Qiu, L. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionDec 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HECW1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0362
Polymers12,9751
Non-polymers601
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.079, 44.082, 39.610
Angle α, β, γ (deg.)90.00, 92.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein E3 ubiquitin-protein ligase HECW1 / HECT / C2 and WW domain-containing protein 1 / NEDD4-like E3 ubiquitin-protein ligase 1 / hNEDL1


Mass: 12975.484 Da / Num. of mol.: 1
Fragment: helical box and second WW domain (UNP residues 948-1056)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HECW1, KIAA0322, NEDL1 / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) V2R
References: UniProt: Q76N89, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE COMPLETE SEQUENCE USED FOR CRYSTALLIZATION IS: ...THE COMPLETE SEQUENCE USED FOR CRYSTALLIZATION IS: GSEAESSQSSLDLRREGSLSPVNSQKITLLLQSPAVKFITNPEFFTVLHAN YSAYRVFTSSTCLKHMILKVRRDARNFERYQHNRDLVNFINMFADTRLELP RGWEIKTDQQGKSFFVDHNSRATTFIDPRIPLQNG. THE PROTEIN WAS CRYSTALLIZED IN THE PRESENCE OF TRYPSIN AND THE ACTUAL CRYSTALLIZED PROTEIN SEQUENCE MAY BE SHORTER. ONLY THE ORDERED PART OF THE PROTEIN IS REPORTED IN SEQRES RECORDS.

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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: 1.75 Å3/Da / Density % sol: 29.83 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, sitting drop / pH: 8
Details: equal volumes of protein (10 mg/ml) [containing 0.1 MM actetic acid PH 3.0] was mixed with crystallization buffer (1.0 M sodium citrate, 0.1 MM immidazole PH 8.0), along with trypsin at a ...Details: equal volumes of protein (10 mg/ml) [containing 0.1 MM actetic acid PH 3.0] was mixed with crystallization buffer (1.0 M sodium citrate, 0.1 MM immidazole PH 8.0), along with trypsin at a concentration of 1 mg trypsin/500 mg protein. cryoprotected with 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291.1K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2009 / Details: MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 8513 / Num. obs: 8513 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rsym value: 0.066 / Net I/σ(I): 31.0366
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 5.462 / Num. unique all: 412 / Rsym value: 0.256 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.45 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.608 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.13 / 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
Rfree0.19956 413 4.9 %RANDOM
Rwork0.14995 ---
obs0.15228 7986 99.79 %-
all-8513 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.812 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 4 72 978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022960
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9361303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19522.65349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80415163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.024159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021749
X-RAY DIFFRACTIONr_mcbond_it0.7381.5573
X-RAY DIFFRACTIONr_mcangle_it1.2632935
X-RAY DIFFRACTIONr_scbond_it2.353387
X-RAY DIFFRACTIONr_scangle_it3.644.5368
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 30 -
Rwork0.149 589 -
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)
19.7368.868-0.220715.8897-2.85516.4823-0.61360.97080.2713-0.5010.3734-0.0326-0.19280.60340.24020.1798-0.0895-0.0010.23640.06630.07954.754637.156824.7555
23.87920.1214-0.74552.6155-0.55982.547-0.0246-0.01180.09260.00080.01690.0177-0.0728-0.08170.00770.04-0.0056-0.00240.0594-0.00830.06-3.446635.16434.9054
34.8463-3.05521.354912.2587-5.47161.3046-0.0369-0.07530.10910.3280.18250.2135-0.1703-0.0699-0.14550.0818-0.0030.02010.08780.01660.0776-5.912825.338942.6929
41.89631.8583-0.3472.1659-3.62493.54270.1464-0.33270.04410.3397-0.2879-0.1317-0.07420.33010.14150.1995-0.0052-0.02080.20450.0140.17691.036225.66145.8829
50.9663.784-0.975311.4177-1.725511.78170.1151-0.4125-0.02930.1568-0.0103-0.39360.36970.3607-0.10470.0608-0.0073-0.02590.1703-0.01440.06797.854931.989242.3917
69.61860.3672-2.28227.12191.38374.59020.0902-0.3550.60610.3315-0.0638-0.2816-0.09080.4036-0.02640.0461-0.012-0.00630.0699-0.02080.08966.737839.913837.7875
713.9809-5.5865-5.21861.16711.47787.3890.14040.20360.3769-0.11460.0893-0.1297-0.44460.0186-0.22980.09680.00620.01680.11890.01790.09410.210137.650630.836
85.02472.54721.96358.34041.06942.9955-0.13810.3261-0.198-0.57740.171-0.22190.02260.099-0.03290.08540.00010.02030.0919-0.00720.062612.518730.948931.6424
920.93999.6864-0.972410.8167-0.09955.35840.12130.1191-0.88770.2915-0.0753-0.50830.40660.133-0.0460.09730.0116-0.00340.0432-0.0080.06488.224623.108434.5828
103.5722-0.7293-1.32490.3934-1.41342.79980.0128-0.1308-0.1295-0.01240.0330.0819-0.0997-0.1088-0.04580.1174-0.00540.01760.0973-0.01340.0841-0.645924.614134.1363
1116.22563.985-5.89637.9297-2.10237.80410.1670.2638-0.2971-0.28580.15660.34670.6597-1.1905-0.32360.1159-0.0466-0.03290.2443-0.05640.1686-9.127521.233924.1135
125.33161.5429-1.97177.60420.77747.81950.11720.610.0696-0.29340.02950.0648-0.0706-0.3595-0.14670.08460.0345-0.01370.1326-0.0228-0.0008-0.38624.411517.3068
1310.30576.2670.529721.678-10.548815.655-0.0033-0.1674-0.7251-0.30520.0855-0.15470.97060.4032-0.08220.28620.1266-0.02760.2374-0.10440.23116.719216.2721.1762
147.20743.0157-1.08029.2656-5.605514.9580.05860.81140.5855-0.20160.22380.5435-0.68470.19-0.28240.1730.01090.0410.18010.01910.08954.074527.12116.9582
155.97022.7049-8.26349.2634-8.743730.37710.02610.35350.6156-0.7289-0.0841-0.345-0.49820.89460.0580.1237-0.03570.01990.19530.0170.15097.596726.890922.1749
165.9083-1.7245-2.33312.34451.68262.91610.10330.2820.0581-0.0347-0.0761-0.0176-0.0417-0.141-0.02730.06990.0067-0.01110.09250.00420.0187-4.81130.20426.927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A948 - 953
2X-RAY DIFFRACTION2A954 - 966
3X-RAY DIFFRACTION3A967 - 973
4X-RAY DIFFRACTION4A974 - 980
5X-RAY DIFFRACTION5A981 - 988
6X-RAY DIFFRACTION6A989 - 993
7X-RAY DIFFRACTION7A994 - 998
8X-RAY DIFFRACTION8A999 - 1003
9X-RAY DIFFRACTION9A1004 - 1008
10X-RAY DIFFRACTION10A1009 - 1014
11X-RAY DIFFRACTION11A1015 - 1019
12X-RAY DIFFRACTION12A1020 - 1026
13X-RAY DIFFRACTION13A1027 - 1035
14X-RAY DIFFRACTION14A1036 - 1040
15X-RAY DIFFRACTION15A1041 - 1047
16X-RAY DIFFRACTION16A1048 - 1056

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