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- PDB-3db3: Crystal structure of the tandem tudor domains of the E3 ubiquitin... -

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Entry
Database: PDB / ID: 3db3
TitleCrystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Trimethylated histone H3-K9 peptide
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 / cis-regulatory region sequence-specific DNA binding / heterochromatin / Chromatin modifying enzymes / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / positive regulation of protein metabolic process / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / euchromatin / RING-type E3 ubiquitin transferase / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / spindle / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nucleic acid binding / protein ubiquitination / protein heterodimerization activity / Amyloid fiber formation / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / extracellular exosome / extracellular region / 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 / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Histone-fold / 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
Histone H3.2 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
B: Trimethylated histone H3-K9 peptide


Theoretical massNumber of molelcules
Total (without water)19,7182
Polymers19,7182
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-6.4 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.622, 99.622, 41.232
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: Protein/peptide Trimethylated histone H3-K9 peptide


Mass: 706.832 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Trimethylated histone peptide H3-K9 was chemically synthesized. The sequence naturally occurs in Homo sapiens (human)
References: UniProt: Q71DI3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 3 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99987 / Wavelength: 0.99987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2008 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.4→32 Å / Num. all: 9214 / Num. obs: 9214 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rsym value: 0.117 / Net I/σ(I): 22.52
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.62 / Num. unique all: 852 / Rsym value: 0.501 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→31.77 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.886 / SU B: 15.638 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.26 / 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
Rfree0.28198 433 4.7 %RANDOM
Rwork0.21188 ---
obs0.21512 8755 98.5 %-
all-9124 --
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: 35.94 Å2
Baniso -1Baniso -2Baniso -3
1--3.68 Å2-1.84 Å20 Å2
2---3.68 Å20 Å2
3---5.52 Å2
Refinement stepCycle: LAST / Resolution: 2.4→31.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 0 73 1237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221184
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9441604
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4815140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4623.53865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7715196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0091513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02913
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2424
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2767
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.214
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4243726
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17641144
X-RAY DIFFRACTIONr_scbond_it3.0475523
X-RAY DIFFRACTIONr_scangle_it4.6047460
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 22 -
Rwork0.248 569 -
obs--87.82 %
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)
12.42275.75160.558742.376-7.81793.0403-0.7935-0.81420.21441.4511.02062.7258-0.6698-0.1124-0.22710.26820.02750.0737-0.0187-0.11920.033528.0556-0.675220.5866
24.15511.25944.89946.88885.946721.76320.2137-0.01390.1202-0.0331-0.15730.22630.1832-0.3221-0.0564-0.00640.01880.01660.0356-0.05490.210133.0352-6.61957.8505
33.86920.371-3.051211.27895.46799.54820.4256-0.19860.38730.37-0.0336-0.0255-0.3589-0.1399-0.3920.14370.0099-0.0075-0.01960.01310.01632.474-3.165712.075
48.3427-1.8807-5.2855.93410.59449.66710.01450.1132-0.60220.1757-0.10310.2898-0.0301-0.40580.08860.08190.0019-0.0030.0186-0.08040.16233.4396-0.27939.5177
53.09462.3640.06994.85542.22231.54420.101-0.2008-0.10760.59930.0643-0.04750.17970.0606-0.16530.24620.0279-0.04630.043-0.03970.090533.4613-18.4898.7983
65.1187-0.2452-0.49384.84931.33184.37990.07010.28570.0196-0.1337-0.0298-0.0484-0.20410.0792-0.04020.0780.0049-0.06240.0795-0.03360.092733.2903-20.4219-3.1923
74.9679-8.2626-3.032915.31264.0762.44860.01050.2433-0.2258-0.4986-0.2006-0.0044-0.029-0.05090.19010.0438-0.0466-0.04120.058-0.09360.173635.5952-32.889-7.2742
84.5652-0.68661.06985.23641.95928.1511-0.0230.07750.1244-0.1184-0.10950.0842-0.2454-0.43680.13250.098-0.0721-0.00220.0904-0.04720.124531.6191-20.0237-0.4756
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA127 - 1373 - 13
2X-RAY DIFFRACTION2AA138 - 14914 - 25
3X-RAY DIFFRACTION3AA150 - 16226 - 38
4X-RAY DIFFRACTION4AA180 - 19856 - 74
5X-RAY DIFFRACTION5AA199 - 21675 - 92
6X-RAY DIFFRACTION6AA217 - 24693 - 122
7X-RAY DIFFRACTION7AA247 - 258123 - 134
8X-RAY DIFFRACTION8AA259 - 283135 - 159

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