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- PDB-3fl2: Crystal structure of the ring domain of the E3 ubiquitin-protein ... -

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Basic information

Entry
Database: PDB / ID: 3fl2
TitleCrystal structure of the ring domain of the E3 ubiquitin-protein ligase UHRF1
ComponentsE3 ubiquitin-protein ligase UHRF1
KeywordsLIGASE / CELL CYCLE / DNA DAMAGE / DNA REPAIR / RING FINGER DOMAIN / METAL BINDING / DNA REPLICATION / TRANSCRIPTIONAL SILENCING / CHROMATIN / PHOSPHORYLATION / TRANSCRIPTION / TRANSCRIPTION REGULATION / UBL CONJUGATION / UBL CONJUGATION PATHWAY / ZINC / ZINC-FINGER / EPIGENETICS / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly ...histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly / protein autoubiquitination / heterochromatin / cis-regulatory region sequence-specific DNA binding / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / positive regulation of protein metabolic process / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / euchromatin / nuclear matrix / spindle / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / nucleic acid binding / protein ubiquitination / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / PUA-like superfamily ...: / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / PUA-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of the Ring Domain of the E3 Ubiquitin-Protein Ligase Uhrf1
Authors: Walker, J.R. / Avvakumov, G.V. / Xue, S. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionDec 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1343
Polymers14,0031
Non-polymers1312
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.736, 46.916, 48.409
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 UHRF1 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / Ubiquitin-like-containing PHD and ...Ubiquitin-like PHD and RING finger domain-containing protein 1 / Ubiquitin-like-containing PHD and RING finger domains protein 1 / Inverted CCAAT box-binding protein of 90 kDa / Transcription factor ICBP90 / Nuclear zinc finger protein Np95 / Nuclear protein 95 / HuNp95 / RING finger protein 106


Mass: 14002.911 Da / Num. of mol.: 1 / Fragment: ring domain (UNP residues 672-793)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ICBP90, NP95, RNF106, UHRF1 / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.88 Å3/Da / Density % sol: 34.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 27% PEG MME 2000, 0.1 M TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Dec 11, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 11019 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rsym value: 0.04 / Net I/σ(I): 43.78
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 10.761 / Num. unique all: 1068 / Rsym value: 0.178 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
REFMAC5.5.0063refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z6U

1z6u


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.655 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.138 / 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
Rfree0.24976 525 4.8 %RANDOM
Rwork0.1834 ---
obs0.18654 10426 99.84 %-
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: 15.852 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å20 Å2
2--0.37 Å20 Å2
3---1.56 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 2 100 1009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022932
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9581250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8595114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20624.09144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98115155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.983157
X-RAY DIFFRACTIONr_chiral_restr0.0980.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021708
X-RAY DIFFRACTIONr_mcbond_it1.7273580
X-RAY DIFFRACTIONr_mcangle_it2.4194935
X-RAY DIFFRACTIONr_scbond_it3.9515352
X-RAY DIFFRACTIONr_scangle_it5.6657315
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 30 -
Rwork0.193 754 -
obs--99.87 %
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)
10.27361.0348-0.53510.9231-0.883320.7779-0.09450.1958-0.1522-0.2294-0.0592-0.1880.22760.34480.15360.215-0.02440.01190.3401-0.0850.244115.981515.27352.6265
25.2810.55631.60034.4344-0.14729.0049-0.13440.4740.1745-0.1597-0.04130.2118-0.35260.35430.17570.139-0.00140.00040.09780.0560.158418.67621.723812.9025
30.2923-0.532-0.63315.08843.41812.62070.0267-0.1010.0067-0.29820.2274-0.4159-0.18490.2218-0.25410.2630.01940.02160.26410.02710.251826.087511.48135.8139
40.6879-0.4589-0.26361.33271.41538.85350.07040.0955-0.007-0.1283-0.1333-0.18870.3080.17550.06290.14610.0430.03260.13920.00070.177423.48478.203814.288
56.0461-1.44427.68947.1059-3.487320.44860.2852-0.0104-0.5213-0.0176-0.1334-0.25320.9210.4155-0.15180.1304-0.00910.01940.1375-0.00170.172619.83155.2724.193
68.38054.1293.28214.97092.15041.5620.0355-0.17530.26930.0702-0.08220.1596-0.0055-0.13980.04670.11050.01720.03380.0578-0.01550.089917.480216.831725.3834
77.9783.6333-0.29544.086-0.78811.2527-0.0435-0.33450.14890.0923-0.0205-0.07240.0558-0.0830.0640.11060.01020.0050.1032-0.00670.1118.957514.229326.7629
89.9313-0.60462.84284.74591.720416.3730.0799-0.3412-0.23550.2934-0.1060.38820.3993-0.65120.02610.13940.00470.01480.14460.00730.145614.990710.244833.8324
95.0618-0.5487-4.02199.3367-5.079811.99610.0018-0.2175-0.2011-0.0124-0.05070.42970.3891-0.44090.0490.1855-0.01780.01590.2267-0.02670.134517.418813.646940.5327
107.7393-3.0225-1.70654.1404-0.56753.83050.0484-0.44350.26580.26670.0787-0.0038-0.1884-0.0217-0.12710.1278-0.00890.01730.125-0.03790.131725.378117.634134.3644
111.9233-0.014-2.316.59472.541614.86640.0206-0.2141-0.19440.034-0.0750.12660.3534-0.43450.05440.1758-0.01130.02440.20420.00190.208314.784521.404234.5975
122.29450.53512.6185.87221.20959.827-0.0291-0.0030.12850.0664-0.00390.2241-0.2154-0.35150.03290.09060.0240.02080.10420.01390.135212.147516.578217.9303
137.11641.0416-2.01972.28810.35362.47190.00340.276-0.2324-0.1665-0.0725-0.09480.14580.03610.0690.11570.0134-0.00140.081-0.03270.121411.5596.521615.9121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A675 - 680
2X-RAY DIFFRACTION2A681 - 693
3X-RAY DIFFRACTION3A694 - 711
4X-RAY DIFFRACTION4A712 - 725
5X-RAY DIFFRACTION5A726 - 731
6X-RAY DIFFRACTION6A732 - 740
7X-RAY DIFFRACTION7A741 - 745
8X-RAY DIFFRACTION8A746 - 751
9X-RAY DIFFRACTION9A752 - 757
10X-RAY DIFFRACTION10A758 - 767
11X-RAY DIFFRACTION11A768 - 773
12X-RAY DIFFRACTION12A774 - 781
13X-RAY DIFFRACTION13A782 - 793

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