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- PDB-3ask: Structure of UHRF1 in complex with histone tail -

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Basic information

Entry
Database: PDB / ID: 3ask
TitleStructure of UHRF1 in complex with histone tail
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Histone H3.3H3F3A
KeywordsLIGASE/DNA BINDING PROTEIN / histone reader modules / epigenetic regulation / histone H3 / trimethylaion of lysine residue / LIGASE-DNA BINDING PROTEIN complex
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 / negative regulation of gene expression via chromosomal CpG island methylation / regulation of epithelial cell proliferation / methyl-CpG binding / nucleosomal DNA binding ...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 / negative regulation of gene expression via chromosomal CpG island methylation / regulation of epithelial cell proliferation / methyl-CpG binding / nucleosomal DNA binding / mitotic spindle assembly / RNA polymerase II core promoter sequence-specific DNA binding / protein autoubiquitination / heterochromatin / cis-regulatory region sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / Inhibition of DNA recombination at telomere / telomere organization / positive regulation of protein metabolic process / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / replication fork / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / double-strand break repair via homologous recombination / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RING-type E3 ubiquitin transferase / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / spindle / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / histone binding / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / nucleic acid binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
SH3 type barrels. - #1150 / : / 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. - #1150 / : / 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-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Histone H3.3 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.904 Å
AuthorsArita, K. / Sugita, K. / Unoki, M. / Hamamoto, R. / Sekiyama, N. / Tochio, H. / Ariyoshi, M. / Shirakawa, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1
Authors: Arita, K. / Isogai, S. / Oda, T. / Unoki, M. / Sugita, K. / Sekiyama, N. / Kuwata, K. / Hamamoto, R. / Tochio, H. / Sato, M. / Ariyoshi, M. / Shirakawa, M.
History
DepositionDec 16, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Jun 5, 2013Group: 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: E3 ubiquitin-protein ligase UHRF1
C: E3 ubiquitin-protein ligase UHRF1
D: E3 ubiquitin-protein ligase UHRF1
P: Histone H3.3
Q: Histone H3.3
R: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,49514
Polymers109,0377
Non-polymers4587
Water724
1
A: E3 ubiquitin-protein ligase UHRF1
P: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8075
Polymers27,6112
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-5 kcal/mol
Surface area13620 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UHRF1
Q: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8075
Polymers27,6112
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-7 kcal/mol
Surface area13170 Å2
MethodPISA
3
C: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2692
Polymers26,2041
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: E3 ubiquitin-protein ligase UHRF1
R: Histone H3.3


Theoretical massNumber of molelcules
Total (without water)27,6112
Polymers27,6112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.178, 145.178, 125.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 133:161 or resseq 179:299 )A133 - 161
121chain A and (resseq 133:161 or resseq 179:299 )A179 - 299
211chain B and (resseq 133:161 or resseq 180:299 )B133 - 161
221chain B and (resseq 133:161 or resseq 180:299 )B180 - 299
311chain C and (resseq 133:161 or resseq 179:299 )C133 - 161
321chain C and (resseq 133:161 or resseq 179:299 )C179 - 299
411chain D and (resseq 133:161 or resseq 179:299 )D133 - 161
421chain D and (resseq 133:161 or resseq 179:299 )D179 - 299

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Components

#1: Protein
E3 ubiquitin-protein ligase UHRF1


Mass: 26203.588 Da / Num. of mol.: 4
Fragment: tandem Tudor domain, PHD finger (residues 134-366)
Mutation: residues 167-175 was deleted.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Histone H3.3 / H3F3A


Mass: 1407.620 Da / Num. of mol.: 3 / Fragment: residues in UNP 2-14 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 29627 / Num. obs: 29627 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.9→2.95 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.904→40.265 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.778 / SU ML: 1.04 / σ(F): 1.38 / Phase error: 28.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2924 9.93 %random
Rwork0.2435 ---
all0.2478 29627 --
obs0.2478 29455 97.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.121 Å2 / ksol: 0.279 e/Å3
Displacement parametersBiso max: 177.84 Å2 / Biso mean: 73.1257 Å2 / Biso min: 27.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.4092 Å20 Å20 Å2
2---1.4092 Å2-0 Å2
3---2.8183 Å2
Refinement stepCycle: LAST / Resolution: 2.904→40.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6130 0 7 4 6141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096268
X-RAY DIFFRACTIONf_angle_d1.1578424
X-RAY DIFFRACTIONf_chiral_restr0.075875
X-RAY DIFFRACTIONf_plane_restr0.0091118
X-RAY DIFFRACTIONf_dihedral_angle_d17.5122383
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1228X-RAY DIFFRACTIONPOSITIONAL0.079
12B1228X-RAY DIFFRACTIONPOSITIONAL0.079
13C1237X-RAY DIFFRACTIONPOSITIONAL0.069
14D1237X-RAY DIFFRACTIONPOSITIONAL0.069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9035-2.95110.34921350.32721212X-RAY DIFFRACTION96
2.9511-3.0020.3681210.32431211X-RAY DIFFRACTION95
3.002-3.05660.39441310.31791227X-RAY DIFFRACTION96
3.0566-3.11530.36181460.30531210X-RAY DIFFRACTION97
3.1153-3.17890.34551290.28441245X-RAY DIFFRACTION97
3.1789-3.2480.30661230.25891253X-RAY DIFFRACTION97
3.248-3.32350.28711400.25371231X-RAY DIFFRACTION97
3.3235-3.40660.27351380.2421240X-RAY DIFFRACTION98
3.4066-3.49860.30851560.26181237X-RAY DIFFRACTION98
3.4986-3.60150.31171340.25781280X-RAY DIFFRACTION98
3.6015-3.71770.25861350.24561270X-RAY DIFFRACTION99
3.7177-3.85050.31181450.24031248X-RAY DIFFRACTION99
3.8505-4.00450.26241350.22321302X-RAY DIFFRACTION99
4.0045-4.18660.24871370.21281267X-RAY DIFFRACTION99
4.1866-4.4070.25571430.19991278X-RAY DIFFRACTION99
4.407-4.68280.22961420.19041288X-RAY DIFFRACTION99
4.6828-5.04370.24151330.19121300X-RAY DIFFRACTION99
5.0437-5.55010.26141370.22031295X-RAY DIFFRACTION99
5.5501-6.35050.25231660.21251296X-RAY DIFFRACTION99
6.3505-7.99070.27011590.23971318X-RAY DIFFRACTION99
7.9907-40.2690.29811390.26421323X-RAY DIFFRACTION92

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