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- PDB-3dkm: Crystal structure of the HECTD1 CPH domain -

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Basic information

Entry
Database: PDB / ID: 3dkm
TitleCrystal structure of the HECTD1 CPH domain
ComponentsE3 ubiquitin-protein ligase HECTD1
KeywordsLIGASE / UBL CONJUGATION / UBL CONJUGATION PATHWAY / STRUCTURAL GENOMICS CONSORTIUM / SGC / ANK repeat / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


anatomical structure development / HECT-type E3 ubiquitin transferase / heart valve development / aorta development / ventricular septum development / protein K63-linked ubiquitination / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process ...anatomical structure development / HECT-type E3 ubiquitin transferase / heart valve development / aorta development / ventricular septum development / protein K63-linked ubiquitination / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / metal ion binding
Similarity search - Function
FKBP3, basic tilted helix bundle domain / E3 ubiquitin-protein ligase HECTD1/TRIP12-like / Basic tilted helix bundle domain / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / SUN domain / Sad1 / UNC-like C-terminal / HECT domain ...FKBP3, basic tilted helix bundle domain / E3 ubiquitin-protein ligase HECTD1/TRIP12-like / Basic tilted helix bundle domain / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / SUN domain / Sad1 / UNC-like C-terminal / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / SH3 Domains / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Galactose-binding-like domain superfamily / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / SH3 type barrels. / Armadillo-like helical / Armadillo-type fold / Roll / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HECTD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWalker, J.R. / Qiu, L. / Li, Y. / Bountra, C. / Wolkstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the CPH domain of the E3 ubiquitin-protein ligase HECTD1.
Authors: Walker, J.R. / Qiu, L. / Li, Y. / Bountra, C. / Wolkstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionJun 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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 HECTD1


Theoretical massNumber of molelcules
Total (without water)10,0371
Polymers10,0371
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.710, 45.564, 51.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase HECTD1 / HECT domain-containing protein 1 / E3 ligase for inhibin receptor / EULIR


Mass: 10036.979 Da / Num. of mol.: 1 / Fragment: CPH DOMAIN, UNP residues 1271-1343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HECTD1, KIAA1131 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9ULT8, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.89 Å3/Da / Density % sol: 34.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 % PEG 5000, 0.1 M BIS-TRIS, PH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 10709 / Num. obs: 10709 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Rsym value: 0.073 / Net I/σ(I): 40.84
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 11.103 / Num. unique all: 937 / Rsym value: 0.156 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DK3

2dk3


Resolution: 1.6→27.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.204 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.079 / 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
Rfree0.17788 510 4.8 %RANDOM
Rwork0.1559 ---
obs0.15695 10154 98.16 %-
all-10664 --
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: 26.843 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.92 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms622 0 0 120 742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021641
X-RAY DIFFRACTIONr_angle_refined_deg1.621.929869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.472580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.5224.06232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6561597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.96154
X-RAY DIFFRACTIONr_chiral_restr0.1130.281
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02516
X-RAY DIFFRACTIONr_nbd_refined0.2190.2269
X-RAY DIFFRACTIONr_nbtor_refined0.3210.2432
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.220
X-RAY DIFFRACTIONr_mcbond_it1.5193397
X-RAY DIFFRACTIONr_mcangle_it1.9134614
X-RAY DIFFRACTIONr_scbond_it2.2875295
X-RAY DIFFRACTIONr_scangle_it2.8817255
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 32 -
Rwork0.16 625 -
obs--85.1 %
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)
125.66685.0758-4.48115.94081.45415.01370.0332-1.7666-0.05010.8025-0.1269-1.57530.11951.10130.0937-0.00770.0151-0.04890.11290.0272-0.008526.8211-0.98841.8299
23.2089-6.9514-0.131421.7142-3.12366.5966-0.2975-0.2630.28050.85820.0897-0.7736-0.01520.43740.2079-0.04040.0114-0.0325-0.05690.0131-0.103723.02275.266443.3614
31.4834-1.145-2.22913.37012.84644.9708-0.0423-0.0473-0.03720.02320.06060.01350.07640.0613-0.0183-0.11450.0077-0.0126-0.1180.0007-0.144621.694510.382931.7681
43.6721.5813-0.8223.4993-1.05950.707-0.12030.20820.3055-0.28330.13280.23750.0164-0.0232-0.0124-0.09470.0083-0.003-0.08590.0195-0.123920.545514.290624.2269
51.73082.764-1.494925.0775-1.52981.3267-0.0444-0.1777-0.02580.66720.0410.80330.0247-0.02130.0034-0.11-0.0030.0016-0.06620.0215-0.104112.69878.497238.4891
61.835-0.4532-0.03515.8505-0.47131.15160.0032-0.0256-0.0141-0.0410.02170.0904-0.02170.0258-0.0249-0.1125-0.0044-0.0002-0.1132-0.0001-0.160916.93768.341831.404
712.4503-1.0514-6.988810.81928.12719.21690.0862-1.42480.25740.90820.3803-0.59870.52821.3686-0.4665-0.0395-0.002-0.02280.0804-0.0167-0.072627.469315.775639.9677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1264 - 126910 - 15
2X-RAY DIFFRACTION2AA1270 - 127616 - 22
3X-RAY DIFFRACTION3AA1277 - 128923 - 35
4X-RAY DIFFRACTION4AA1290 - 130136 - 47
5X-RAY DIFFRACTION5AA1302 - 131048 - 56
6X-RAY DIFFRACTION6AA1311 - 133557 - 81
7X-RAY DIFFRACTION7AA1336 - 134282 - 88

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