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- PDB-4gy5: Crystal structure of the tandem tudor domain and plant homeodomai... -

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Basic information

Entry
Database: PDB / ID: 4gy5
TitleCrystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Peptide from Histone H3.3
KeywordsLIGASE / Histone binding
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 / negative regulation of chromosome condensation / hemi-methylated DNA-binding / Barr body / regulation of centromere complex assembly / homologous recombination / muscle cell differentiation ...histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / negative regulation of chromosome condensation / hemi-methylated DNA-binding / Barr body / regulation of centromere complex assembly / homologous recombination / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / regulation of epithelial cell proliferation / methyl-CpG binding / oocyte maturation / negative regulation of gene expression via chromosomal CpG island methylation / nucleus organization / spermatid development / mitotic spindle assembly / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin formation / epigenetic regulation of gene expression / nucleosomal DNA binding / Inhibition of DNA recombination at telomere / methylated histone binding / positive regulation of protein metabolic process / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / 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) / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / 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 / multicellular organism growth / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin-protein transferase activity / male gonad development / ubiquitin protein ligase activity / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / histone binding / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell population proliferation / nucleic acid binding / chromosome, telomeric region / protein ubiquitination / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / extracellular exosome / 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. / Zinc finger RING-type profile. / Histone H3 / Histone H3/CENP-A / 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 H3.3 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.956 Å
AuthorsCheng, J. / Yang, Y. / Fang, J. / Xiao, J. / Zhu, T. / Chen, F. / Wang, P. / Xu, Y.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing ...Title: Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) protein
Authors: Cheng, J. / Yang, Y. / Fang, J. / Xiao, J. / Zhu, T. / Chen, F. / Wang, P. / Li, Z. / Yang, H. / Xu, Y.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Structure summary
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: Peptide from Histone H3.3
F: Peptide from Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,35913
Polymers114,9016
Non-polymers4587
Water18010
1
A: E3 ubiquitin-protein ligase UHRF1
E: Peptide from Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8535
Polymers29,6562
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-6 kcal/mol
Surface area13330 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UHRF1
F: Peptide from Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8535
Polymers29,6562
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-6 kcal/mol
Surface area13130 Å2
MethodPISA
3
C: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8602
Polymers27,7941
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: E3 ubiquitin-protein ligase UHRF1


Theoretical massNumber of molelcules
Total (without water)27,7941
Polymers27,7941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)145.940, 145.940, 125.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein
E3 ubiquitin-protein ligase UHRF1 / UHRF1


Mass: 27794.279 Da / Num. of mol.: 4 / Fragment: Tudor PHD domain, UNP residues 134-366
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 Peptide from Histone H3.3


Mass: 1862.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / 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


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.956→50 Å / Num. all: 27861 / Num. obs: 27861 / % possible obs: 100 % / Biso Wilson estimate: 82.9 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_353)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DB3, 3SHB

3db3

3shb


Resolution: 2.956→45.377 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7655 / SU ML: 0.39 / σ(F): 0.16 / Phase error: 29.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 1401 5.03 %
Rwork0.2549 --
all0.2549 27861 -
obs0.2565 27861 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.719 Å2 / ksol: 0.279 e/Å3
Displacement parametersBiso max: 229.78 Å2 / Biso mean: 97.4127 Å2 / Biso min: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.956→45.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6121 0 7 10 6138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036240
X-RAY DIFFRACTIONf_angle_d0.7018426
X-RAY DIFFRACTIONf_chiral_restr0.054878
X-RAY DIFFRACTIONf_plane_restr0.0091119
X-RAY DIFFRACTIONf_dihedral_angle_d13.462416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9556-3.06120.38131160.35992347246386
3.0612-3.18370.35391430.32572423256691
3.1837-3.32860.36671410.29692547268894
3.3286-3.5040.33481240.292619274396
3.504-3.72350.32571460.26392654280098
3.7235-4.01080.30991490.2522677282698
4.0108-4.41410.23791740.22082708288299
4.4141-5.05210.23781470.2022751289899
5.0521-6.36240.26571420.230828032945100
6.3624-45.38260.27531190.26052931305098

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