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- PDB-3bi7: Crystal structure of the SRA domain of E3 ubiquitin-protein ligas... -

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Basic information

Entry
Database: PDB / ID: 3bi7
TitleCrystal structure of the SRA domain of E3 ubiquitin-protein ligase UHRF1
ComponentsE3 ubiquitin-protein ligase UHRF1
KeywordsLIGASE / Cell cycle / DNA damage / DNA repair / DNA-binding / Metal-binding / Nucleus / Phosphorylation / Polymorphism / Transcription / Transcription regulation / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger / Structural Genomics Consortium / SGC / Phosphoprotein
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 / cis-regulatory region sequence-specific DNA binding / heterochromatin / 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 / 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
SRA-YDG / PUA domain-like / : / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. ...SRA-YDG / PUA domain-like / : / 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 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 / Roll / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Li, Y. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Nature / Year: 2008
Title: Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.
Authors: Avvakumov, G.V. / Walker, J.R. / Xue, S. / Li, Y. / Duan, S. / Bronner, C. / Arrowsmith, C.H. / Dhe-Paganon, S.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)24,2557
Polymers23,9101
Non-polymers3446
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.975, 65.975, 96.061
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 23910.240 Da / Num. of mol.: 1 / Fragment: SRA Domain: Residues 414-617
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Plasmid: pNIC-CH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1:1 ratio of protein (34 mg/ml) solution and well solution consisting of 1.4 M Ammonium sulfate, 0.1 M Bis-Tris pH 6.0, 0.2 M NaCl, 1 mM TCEP. Crystals cryoprotected by immersion in the well ...Details: 1:1 ratio of protein (34 mg/ml) solution and well solution consisting of 1.4 M Ammonium sulfate, 0.1 M Bis-Tris pH 6.0, 0.2 M NaCl, 1 mM TCEP. Crystals cryoprotected by immersion in the well solution mixed in 1:1 ratio with a water solution containing 20% (w/v) Sucrose, 4% (w/v) Glucose, 18% (v/v) Glycerol and 18% (v/v) Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97943 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2007 / Details: Mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 27377 / Num. obs: 27377 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rsym value: 0.153 / Net I/σ(I): 24.15
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2670 / Rsym value: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→32.99 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.287 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.09 / 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
Rfree0.19658 1369 5.1 %RANDOM
Rwork0.15851 ---
obs0.16043 25677 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.105 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.38 Å20 Å2
2--0.77 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 28 210 1785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211616
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9422190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1495201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.95823.16579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32615238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6451513
X-RAY DIFFRACTIONr_chiral_restr0.1210.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021280
X-RAY DIFFRACTIONr_nbd_refined0.1990.2724
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.220
X-RAY DIFFRACTIONr_mcbond_it1.0551.51005
X-RAY DIFFRACTIONr_mcangle_it1.47121573
X-RAY DIFFRACTIONr_scbond_it2.2073707
X-RAY DIFFRACTIONr_scangle_it3.2654.5617
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 93 -
Rwork0.207 1868 -
obs--98.49 %
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)
12.2406-2.16070.358410.16970.71562.8855-0.0031-0.05920.23330.3106-0.0496-0.5498-0.21410.49090.05260.001-0.0627-0.02450.08910.00560.05269.485245.761810.7113
22.06890.3008-1.48431.4434-2.03053.4175-0.04220.0097-0.05770.068-0.07180.04160.24590.04630.11390.0479-0.0151-0.00360.06610.00860.04531.783933.466914.8822
38.25070.465-1.75162.9351-0.37257.25640.0964-0.0595-0.26320.0348-0.1539-0.0861-0.28030.34640.05740.0386-0.0437-0.01730.08680.0150.0494.408641.517617.182
43.27820.5194-1.39742.9515-1.72041.3788-0.012-0.33680.03330.3188-0.1486-0.2359-0.42420.0580.16060.1367-0.0595-0.02770.0563-0.0250.0226-0.015950.969415.9232
510.04763.5930.63378.4827-1.60691.96220.085-0.40760.51540.2441-0.01810.9801-0.1111-0.4044-0.06690.0044-0.0110.04120.057-0.02890.0921-9.62642.877411.2704
64.32030.1959-0.64987.70461.71467.66690.0576-0.06710.17920.1872-0.15040.6005-0.07-0.38150.09280.0415-0.03240.02380.0472-0.00390.0975-12.348442.89162.9448
712.22282.81613.30238.1984-0.54263.1302-0.0663-0.82010.7010.6793-0.07180.6893-0.1747-0.41120.13810.1156-0.00130.12860.021-0.06190.0346-12.871456.842215.2162
80.80080.586-1.81852.7181-2.50465.67780.0731-0.0610.18230.13450.00260.0989-0.25440.036-0.07570.0864-0.04460.00170.0056-0.00930.0697-3.153657.80796.2185
97.1148-1.0117-4.48756.77315.452813.33770.21070.24340.3348-0.1681-0.33410.5929-0.7616-0.47880.12340.1304-0.0060.00430.00080.02960.1468-9.404861.81261.7452
101.04311.0795-0.46132.48-0.6721.49860.012-0.04160.0401-0.0006-0.00840.0824-0.0216-0.0837-0.00360.0813-0.02740.00510.0783-0.00510.0951-4.577342.88185.7116
113.24351.01522.64916.2048-2.10019.32390.0738-0.01160.0897-0.0485-0.06750.07680.2133-0.172-0.00630.0804-0.0419-0.00760.042-0.01470.0648-9.840531.91665.9904
120.5961-0.77360.50271.0099-0.74281.81980.0293-0.04410.09150.0031-0.0932-0.0180.01170.07470.06390.0666-0.0370.00020.04750.00570.0715-1.050941.3564.764
1311.3456-0.2768-0.29866.5559-3.39372.401-0.1380.51320.1901-0.04490.18840.4549-0.0881-0.3149-0.05030.0476-0.01490.01710.0197-0.00190.0995-12.696455.9492.8098
1418.67326.7978-16.207711.6614-11.016162.9010.0824-0.16760.33521.0866-0.16350.92891.1327-2.85350.08110.0765-0.14820.20340.1395-0.06530.2135-23.718653.172611.5054
154.4907-3.9983-4.38824.59261.50729.8643-0.17560.4196-0.05120.4164-0.06640.51440.1948-0.49410.2420.0612-0.03630.0730.0214-0.02590.1118-14.633654.31758.2943
162.1781-2.0877-0.42893.93290.49081.00240.03190.0810.021-0.1494-0.094-0.09470.07420.13480.06210.0746-0.02410.00810.0694-0.00280.05040.006538.398-2.4431
179.507-3.6229-0.696514.91981.868515.6251-0.04560.23970.1956-0.3541-0.0312-0.22110.83010.07140.07680.05450.0550.01520.0160.00120.03775.369927.1426-0.7493
1811.89152.2628-12.18125.0766-2.896229.5856-0.3244-0.1798-0.1710.0873-0.0454-0.19871.04831.07950.36980.09190.0634-0.03450.01650.01210.01417.266725.9296.9147
193.0852.9869-1.64649.8277-7.709915.84520.0424-0.0095-0.2726-0.2922-0.2522-0.10860.83640.70770.20980.070.06870.00710.05430.01650.04523.419423.31522.4749
2024.692222.4887-19.166124.5428-7.131541.1245-0.6053-0.0536-0.6604-0.4796-0.5682-0.28191.934-0.54071.17350.16050.020.0452-0.05730.01230.0525-2.727616.521328.3319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA414 - 4242 - 12
2X-RAY DIFFRACTION2AA425 - 43713 - 25
3X-RAY DIFFRACTION3AA438 - 44426 - 32
4X-RAY DIFFRACTION4AA445 - 45833 - 46
5X-RAY DIFFRACTION5AA459 - 46647 - 54
6X-RAY DIFFRACTION6AA467 - 47855 - 66
7X-RAY DIFFRACTION7AA479 - 50467 - 92
8X-RAY DIFFRACTION8AA505 - 51593 - 103
9X-RAY DIFFRACTION9AA516 - 525104 - 113
10X-RAY DIFFRACTION10AA526 - 543114 - 131
11X-RAY DIFFRACTION11AA544 - 551132 - 139
12X-RAY DIFFRACTION12AA552 - 562140 - 150
13X-RAY DIFFRACTION13AA563 - 566151 - 154
14X-RAY DIFFRACTION14AA567 - 573155 - 161
15X-RAY DIFFRACTION15AA574 - 578162 - 166
16X-RAY DIFFRACTION16AA579 - 593167 - 181
17X-RAY DIFFRACTION17AA594 - 599182 - 187
18X-RAY DIFFRACTION18AA600 - 605188 - 193
19X-RAY DIFFRACTION19AA606 - 613194 - 201
20X-RAY DIFFRACTION20AA614 - 619202 - 207

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