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- PDB-3sow: Structure of UHRF1 PHD finger in complex with histone H3K4me3 1-9... -

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Basic information

Entry
Database: PDB / ID: 3sow
TitleStructure of UHRF1 PHD finger in complex with histone H3K4me3 1-9 peptide
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Histone H3
KeywordsLIGASE / Zn coordinated PHD finger / Histone binding / Histone H3
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation / : / positive regulation of protein metabolic process ...histone H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation / : / positive regulation of protein metabolic process / mitotic spindle assembly / heterochromatin / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / replication fork / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / euchromatin / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / RING-type E3 ubiquitin transferase / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / Transcriptional regulation of granulopoiesis / HCMV Early Events / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / histone binding / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / nucleic acid binding / protein ubiquitination / cadherin 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 / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane
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 / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / 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 H3.1 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9501 Å
AuthorsRajakumara, E. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2011
Title: PHD Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression.
Authors: Rajakumara, E. / Wang, Z. / Ma, H. / Hu, L. / Chen, H. / Lin, Y. / Guo, R. / Wu, F. / Li, H. / Lan, F. / Shi, Y.G. / Xu, Y. / Patel, D.J. / Shi, Y.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Sep 13, 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_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_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_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: Histone H3
D: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,57612
Polymers18,0534
Non-polymers5238
Water84747
1
A: E3 ubiquitin-protein ligase UHRF1
C: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2886
Polymers9,0262
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-34 kcal/mol
Surface area5060 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UHRF1
D: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2886
Polymers9,0262
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-32 kcal/mol
Surface area4920 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-96 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.622, 42.622, 183.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsHalf of the content in the asymmetric unit that contains protein-peptide complex

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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: 7920.976 Da / Num. of mol.: 2 / Fragment: UHRF1 (UNP Residues 298-367)
Source method: isolated from a genetically manipulated source
Details: PreScission protease cleavable N-terminal GST tag / Source: (gene. exp.) Homo sapiens (human) / Gene: ICBP90, NP95, RNF106, UHRF1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Histone H3


Mass: 1105.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: 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: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% w/v polyethylene glycol 8,000, 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: Mirrors
RadiationMonochromator: Cryo-cooled double Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 13122 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Rmerge(I) obs: 0.12 / Χ2: 2.338 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.95-1.9813.70.7813.235911.17396.1
1.98-2.0213.20.736381.17695.8
2.02-2.0613.80.6036021.17998
2.06-2.113.80.486351.36498.1
2.1-2.1513.20.4146501.37598.2
2.15-2.2140.3556181.4997.6
2.2-2.2513.20.3116591.54898.4
2.25-2.3113.40.2826161.64899
2.31-2.3813.40.2316511.66497.9
2.38-2.4613.30.2176301.74499.1
2.46-2.54130.1866631.87899.3
2.54-2.65130.1636542.10198.6
2.65-2.7713.30.1436382.2499.1
2.77-2.91130.1176612.799.8
2.91-3.112.80.1056753.203100
3.1-3.3312.80.0876753.45799.9
3.33-3.6712.50.0796714.02899.9
3.67-4.212.50.0656954.094100
4.2-5.2913.20.067154.06499.9
5.29-5014.30.0557853.89498.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3SOU CHAIN A

3sou


Resolution: 1.9501→19.778 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8331 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.09 / σ(I): 2 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 605 4.95 %RANDOM
Rwork0.203 ---
obs0.2052 12220 92.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.842 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 71.46 Å2 / Biso mean: 29.5322 Å2 / Biso min: 15.08 Å2
Baniso -1Baniso -2Baniso -3
1-5.7793 Å20 Å2-0 Å2
2--5.7793 Å2-0 Å2
3----11.5585 Å2
Refinement stepCycle: LAST / Resolution: 1.9501→19.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 8 47 1188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081157
X-RAY DIFFRACTIONf_angle_d1.1151563
X-RAY DIFFRACTIONf_chiral_restr0.073162
X-RAY DIFFRACTIONf_plane_restr0.004206
X-RAY DIFFRACTIONf_dihedral_angle_d19.233451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9501-2.14610.29271370.20742517265483
2.1461-2.45610.22981630.19882759292291
2.4561-3.09260.25271510.20363030318197
3.0926-19.77950.23821540.20223309346399

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