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- PDB-3pt3: Crystal structure of the C-terminal lobe of the human UBR5 HECT domain -

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Basic information

Entry
Database: PDB / ID: 3pt3
TitleCrystal structure of the C-terminal lobe of the human UBR5 HECT domain
ComponentsE3 ubiquitin-protein ligase UBR5
KeywordsLIGASE / UBR5 / EDD / hHYD / mixed alpha-beta fold / ubiquitin ligase
Function / homology
Function and homology information


heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / DNA repair-dependent chromatin remodeling / ubiquitin-ubiquitin ligase activity / progesterone receptor signaling pathway / protein K48-linked ubiquitination / ubiquitin binding / protein polyubiquitination / positive regulation of protein import into nucleus / positive regulation of canonical Wnt signaling pathway ...heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / DNA repair-dependent chromatin remodeling / ubiquitin-ubiquitin ligase activity / progesterone receptor signaling pathway / protein K48-linked ubiquitination / ubiquitin binding / protein polyubiquitination / positive regulation of protein import into nucleus / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / DNA repair / DNA damage response / positive regulation of gene expression / perinuclear region of cytoplasm / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / : / E3 ubiquitin ligase EDD, ubiquitin-associated domain / E3 ubiquitin ligase EDD / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain ...Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / : / E3 ubiquitin ligase EDD, ubiquitin-associated domain / E3 ubiquitin ligase EDD / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMatta-Camacho, E. / Kozlov, G. / Menade, M. / Gehring, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the HECT C-lobe of the UBR5 E3 ubiquitin ligase.
Authors: Matta-Camacho, E. / Kozlov, G. / Menade, M. / Gehring, K.
History
DepositionDec 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
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 UBR5
B: E3 ubiquitin-protein ligase UBR5


Theoretical massNumber of molelcules
Total (without water)27,0372
Polymers27,0372
Non-polymers00
Water1,38777
1
A: E3 ubiquitin-protein ligase UBR5


Theoretical massNumber of molelcules
Total (without water)13,5191
Polymers13,5191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase UBR5


Theoretical massNumber of molelcules
Total (without water)13,5191
Polymers13,5191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.240, 39.070, 44.170
Angle α, β, γ (deg.)90.04, 84.59, 81.77
Int Tables number1
Space group name H-MP1
DetailsA / B

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Components

#1: Protein E3 ubiquitin-protein ligase UBR5 / E3 ubiquitin-protein ligase / HECT domain-containing 1 / Hyperplastic discs protein homolog / hHYD ...E3 ubiquitin-protein ligase / HECT domain-containing 1 / Hyperplastic discs protein homolog / hHYD / Progestin-induced protein


Mass: 13518.530 Da / Num. of mol.: 2 / Fragment: C-terminal lobe of HECT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBR5, EDD, EDD1, HYD, KIAA0896 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O95071, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 1.84 Å3/Da / Density % sol: 33.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 0.2M NaCl, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9779
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 5, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 12853 / Num. obs: 11665 / % possible obs: 90.76 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.97→2.01 Å / % possible all: 93.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1c4z

1c4z


Resolution: 1.97→23.11 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.885 / SU B: 9.001 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27619 627 5.1 %RANDOM
Rwork0.2192 ---
obs0.22209 11665 90.76 %-
all-12853 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.736 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.06 Å20.12 Å2
2--0.11 Å20.05 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.97→23.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 0 77 1579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221546
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.962099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4445185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58724.15465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1115278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.614158
X-RAY DIFFRACTIONr_chiral_restr0.090.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021132
X-RAY DIFFRACTIONr_nbd_refined0.1970.2639
X-RAY DIFFRACTIONr_nbtor_refined0.30.21045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.264
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.28
X-RAY DIFFRACTIONr_mcbond_it0.5141.5982
X-RAY DIFFRACTIONr_mcangle_it0.8621529
X-RAY DIFFRACTIONr_scbond_it1.4143683
X-RAY DIFFRACTIONr_scangle_it2.1734.5568
LS refinement shellResolution: 1.973→2.024 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 43 -
Rwork0.235 761 -
obs--82.21 %
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)
11.2471-0.46490.33271.59271.95283.12740.075-0.03840.02070.0351-0.22860.25530.1331-0.3480.1536-0.0259-0.00170.00660.0489-0.00920.0698-12.812-12.1285-10.5271
20.92860.70840.08255.00852.43933.3517-0.04760.09680.1363-0.2994-0.24220.2991-0.2531-0.38030.28980.08010.0397-0.03420.02290.00710.0115-13.2895-16.0397-26.4134
32.42112.64121.18914.28053.15253.88850.06410.0386-0.1237-0.1872-0.0247-0.13730.03350.326-0.03940.03960.0446-0.00160.03330.0110.0293-5.9734-18.3296-16.7489
41.80870.67020.50722.58290.66022.22940.04480.05730.004-0.1079-0.0105-0.0611-0.03710.0134-0.03420.04290.00740.00960.04720.0010.0193-6.3543-16.7282-19.1653
57.12754.64042.47323.34292.737527.65710.19010.3897-0.2613-0.2989-0.2892-0.3451-0.44330.24560.09910.06080.02360.0037-0.00350.0647-0.0544-3.685-15.7814-27.276
63.8138-2.20642.03413.1519-1.29132.34260.0270.02760.1739-0.1414-0.0626-0.25040.0360.22360.0356-0.01170.00160.0380.0641-0.00820.06639.19461.7343-6.1023
73.8692-0.3715-0.1194.2533-4.539816.24840.0205-0.05430.26480.24610.0593-0.4918-0.45230.3694-0.0798-0.0033-0.0427-0.0150.026-0.01940.09699.09016.61641.5918
88.85358.09333.984915.63344.74915.69690.3338-0.0581-0.2841.09420.1365-0.62320.08170.3755-0.47030.03390.0269-0.02570.01850.00170.00043.2339-2.955411.0107
91.6047-0.5505-0.31745.2659-1.27094.12340.0472-0.0266-0.11370.0443-0.04860.18560.0175-0.1030.00150.0133-0.0381-0.01170.0643-0.01740.0886-0.514-1.0818-2.1617
101.2839-0.1856-0.22934.43570.36041.47090.0097-0.08010.05210.11640.0019-0.0577-0.07890.0536-0.01170.00480.0007-0.00570.0681-0.00560.0649-0.83842.57150.7313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2693 - 2710
2X-RAY DIFFRACTION2A2711 - 2734
3X-RAY DIFFRACTION3A2735 - 2761
4X-RAY DIFFRACTION4A2762 - 2785
5X-RAY DIFFRACTION5A2786 - 2792
6X-RAY DIFFRACTION6B2786 - 2708
7X-RAY DIFFRACTION7B2709 - 2721
8X-RAY DIFFRACTION8B2722 - 2732
9X-RAY DIFFRACTION9B2733 - 2763
10X-RAY DIFFRACTION10B2764 - 2792

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