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- PDB-3t6r: Structure of UHRF1 in complex with unmodified H3 N-terminal tail -

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Basic information

Entry
Database: PDB / ID: 3t6r
TitleStructure of UHRF1 in complex with unmodified H3 N-terminal tail
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Histone H3.1t N-terminal peptide
KeywordsTRANSCRIPTION / Zinc Finger / Histone binding
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / H3K9me3 modified histone binding / 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 / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / H3K9me3 modified histone binding / 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 / cis-regulatory region sequence-specific DNA binding / protein autoubiquitination / heterochromatin / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / positive regulation of protein metabolic process / Meiotic synapsis / methylated histone binding / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / euchromatin / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / Meiotic recombination / nuclear matrix / spindle / ubiquitin-protein transferase activity / structural constituent of chromatin / ubiquitin protein ligase activity / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / Processing of DNA double-strand break ends / histone binding / ubiquitin-dependent protein catabolic process / nucleic acid binding / chromosome, telomeric region / protein ubiquitination / protein heterodimerization activity / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / 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 ...: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / Histone H3 signature 1. / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1t / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsXie, S. / Jakoncic, J. / Qian, C.M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: UHRF1 double tudor domain and the adjacent PHD finger act together to recognize K9me3-containing histone H3 tail
Authors: Xie, S. / Jakoncic, J. / Qian, C.M.
History
DepositionJul 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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
D: Histone H3.1t N-terminal peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,56912
Polymers17,0213
Non-polymers5489
Water84747
1
A: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4086
Polymers8,1221
Non-polymers2865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase UHRF1
D: Histone H3.1t N-terminal peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1616
Polymers8,8992
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-1 kcal/mol
Surface area4950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.028, 41.028, 183.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein E3 ubiquitin-protein ligase UHRF1 / Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein ...Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein Np95 / HuNp95 / RING finger protein 106 / Transcription factor ICBP90 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 8122.240 Da / Num. of mol.: 2 / Fragment: UNP residues 299-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q96T88
#2: Protein/peptide Histone H3.1t N-terminal peptide / H3/t / H3t / H3/g


Mass: 776.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16695
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris-HCl, 25% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.2569 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2011
RadiationMonochromator: 100 degree with 1 degree oscillation / Protocol: SAD at Zinc high energy remote / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2569 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 12342 / Num. obs: 12220 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.95→2 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0087refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→24.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.051 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22881 582 4.8 %RANDOM
Rwork0.19355 ---
all0.197 12342 --
obs0.19524 11575 --
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: 29.224 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 9 47 1179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211190
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9691613
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2275150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11424.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07115204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8371510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022946
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1321.5737
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0321194
X-RAY DIFFRACTIONr_scbond_it2.9783453
X-RAY DIFFRACTIONr_scangle_it5.044.5415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 42 -
Rwork0.192 805 -
obs--100 %

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