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- PDB-3db4: Crystal structure of the tandem tudor domains of the E3 ubiquitin... -

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Basic information

Entry
Database: PDB / ID: 3db4
TitleCrystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1
ComponentsE3 ubiquitin-protein ligase UHRF1
KeywordsLIGASE / CELL CYCLE / DNA DAMAGE / DNA REPAIR / TANDEM TUDOR DOMAINS / METAL BINDING / DNA REPLICATION / TRANSCRIPTIONAL SILENCING / CHROMATIN / PHOSPHORYLATION / TRANSCRIPTION / TRANSCRIPTION REGULATION / UBL CONJUGATION PATHWAY / ZINC-FINGER / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / DNA-binding / Metal-binding / Nucleus / 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 / 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. / SH3 type barrels. - #30 ...: / 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. / SH3 type barrels. - #30 / SH3 type barrels. - #140 / 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 / SH3 type barrels. / 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
E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Dong, A. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Dong, A. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein.
Authors: Nady, N. / Lemak, A. / Walker, J.R. / Avvakumov, G.V. / Kareta, M.S. / Achour, M. / Xue, S. / Duan, S. / Allali-Hassani, A. / Zuo, X. / Wang, Y.X. / Bronner, C. / Chedin, F. / Arrowsmith, C.H. / Dhe-Paganon, S.
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references

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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)19,1082
Polymers19,0121
Non-polymers961
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.654, 98.654, 43.345
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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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: 19011.543 Da / Num. of mol.: 1 / Fragment: Tandem Tudor Domains (UNP residues 126-285)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Plasmid: pET28-MHL / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Description: DATA SET USED FOR PHASING WAS COLLECTED AT 0.97942
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 % PEG 8000, 0.1 M SODIUM CACODYLATE, 0.2 M AMMONIUM SULFATE, 0.001 M TCEP, pH 6.50, 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: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 5, 2008 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→38.66 Å / Num. all: 9579 / Num. obs: 9579 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Rsym value: 0.105 / Net I/σ(I): 25.55
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 4.76 / Num. unique all: 923 / Rsym value: 0.451 / % possible all: 97.4

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→38.66 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.909 / SU B: 23.059 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.247 / 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
Rfree0.28462 458 4.8 %RANDOM
Rwork0.21695 ---
all0.22008 9579 --
obs0.22008 9112 99.66 %-
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: 55.018 Å2
Baniso -1Baniso -2Baniso -3
1--2.37 Å2-1.19 Å20 Å2
2---2.37 Å20 Å2
3---3.56 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1111 0 5 34 1150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221134
X-RAY DIFFRACTIONr_angle_refined_deg1.0551.9391537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18124.15465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82315189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2591512
X-RAY DIFFRACTIONr_chiral_restr0.0670.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02875
X-RAY DIFFRACTIONr_nbd_refined0.1960.2407
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.23
X-RAY DIFFRACTIONr_mcbond_it0.7233688
X-RAY DIFFRACTIONr_mcangle_it1.18641087
X-RAY DIFFRACTIONr_scbond_it1.6925512
X-RAY DIFFRACTIONr_scangle_it2.2317450
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 36 -
Rwork0.314 633 -
obs--96.82 %
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)
19.9198-2.0448-0.28521.72849.036522.50770.0271-0.36010.65231.5363-0.6761.8289-0.37-0.61270.64890.1809-0.15370.17380.0796-0.22310.42430.0329-4.430212.9678
28.7520.4795-2.955318.38891.95287.5090.5914-0.6660.70441.4368-0.55752.4833-0.1353-0.6448-0.03390.1911-0.09110.24210.1103-0.15580.334829.0582-3.342412.0231
31.58492.1741-0.856516.70174.25392.61110.3877-0.25260.33530.5116-0.40991.0701-0.0107-0.11720.02220.0787-0.0290.02630.1678-0.11850.248133.704-7.84488.6417
410.09045.827-0.680917.00712.16996.5009-0.3780.6861-0.4233-0.8944-0.12870.0581-0.3932-0.03130.50680.02440.0638-0.08190.0942-0.1127-0.003635.0102-20.7329-2.5175
54.50714.2198-1.39014.46480.21324.8926-0.35170.3259-0.7799-0.7555-0.45031.567-0.336-0.3040.80210.02780.0334-0.13980.1248-0.19510.198131.1818-25.066-2.7152
68.0307-12.0455-4.572319.40946.12833.00020.39770.27340.7717-1.734-0.4129-0.8086-0.65040.05240.01520.12710.0109-0.12630.1732-0.22260.203534.2952-28.5171-6.2104
77.37780.1693-2.066711.27821.133613.81840.02971.1032-0.1941-0.7441-0.15541.1895-0.3496-0.47420.12580.1663-0.0444-0.08530.0741-0.13780.091833.2854-21.1984-3.8379
89.2816-2.2258-23.9267.39237.905962.3614-0.3596-2.2040.69411.8782-0.07352.1380.9719-0.96340.43310.4401-0.05680.29860.3836-0.2120.601428.2257-19.05412.3475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA129 - 1485 - 24
2X-RAY DIFFRACTION2AA149 - 18325 - 59
3X-RAY DIFFRACTION3AA184 - 21460 - 90
4X-RAY DIFFRACTION4AA215 - 23791 - 113
5X-RAY DIFFRACTION5AA238 - 248114 - 124
6X-RAY DIFFRACTION6AA249 - 261125 - 137
7X-RAY DIFFRACTION7AA263 - 278139 - 154
8X-RAY DIFFRACTION8AA279 - 283155 - 159

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