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- PDB-3fde: Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crysta... -

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Basic information

Entry
Database: PDB / ID: 3fde
TitleMouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution
Components
  • 5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'
  • 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'
  • E3 ubiquitin-protein ligase UHRF1
KeywordsLIGASE / SRA domain / base flipping / DNA CpG methylation / Cell cycle / Developmental protein / DNA damage / DNA repair / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / hemi-methylated DNA-binding / negative regulation of gene expression via chromosomal CpG island methylation / regulation of epithelial cell proliferation / methyl-CpG binding / mitotic spindle assembly / protein autoubiquitination / heterochromatin / cis-regulatory region sequence-specific DNA binding / heterochromatin formation ...histone H3 ubiquitin ligase activity / hemi-methylated DNA-binding / negative regulation of gene expression via chromosomal CpG island methylation / regulation of epithelial cell proliferation / methyl-CpG binding / mitotic spindle assembly / protein autoubiquitination / heterochromatin / cis-regulatory region sequence-specific DNA binding / heterochromatin formation / methylated histone binding / positive regulation of protein metabolic process / replication fork / euchromatin / RING-type E3 ubiquitin transferase / nuclear matrix / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / nucleic acid binding / DNA repair / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
SRA-YDG / PUA domain-like / : / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. ...SRA-YDG / PUA domain-like / : / 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. / 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 / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / 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
Unknown ligand / DNA / DNA (> 10) / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsHashimoto, H. / Horton, J.R. / Zhang, X. / Cheng, X.
Citation
Journal: Epigenetics / Year: 2009
Title: UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.
Authors: Hashimoto, H. / Horton, J.R. / Zhang, X. / Cheng, X.
#1: Journal: Nature / Year: 2008
Title: The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
Authors: Hashimoto, H. / Horton, J.R. / Zhang, X. / Bostick, M. / Jacobsen, S.E. / Cheng, X.
History
DepositionNov 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq / 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.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 / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_2 / _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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: 5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'
E: 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'
C: 5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'
F: 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,97141
Polymers62,5136
Non-polymers1,45735
Water12,250680
1
A: E3 ubiquitin-protein ligase UHRF1
D: 5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'
E: 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,98518
Polymers31,2573
Non-polymers72915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-15.4 kcal/mol
Surface area13640 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UHRF1
C: 5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'
F: 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,98523
Polymers31,2573
Non-polymers72920
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-15.4 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.678, 103.691, 149.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsAsymmetric unit contains two SRA-DNA complexes.

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Components

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Protein , 1 types, 2 molecules AB

#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 / Nuclear zinc finger protein Np95 / Nuclear protein 95


Mass: 23915.711 Da / Num. of mol.: 2 / Fragment: YDG domain: UNP residues 419-628
Source method: isolated from a genetically manipulated source
Details: hexahistidine-SUMO-tagged construct / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Np95, Uhrf1 / Plasmid: pXC666 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8VDF2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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DNA chain , 2 types, 4 molecules DCEF

#2: DNA chain 5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'


Mass: 3637.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA oligo
#3: DNA chain 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'


Mass: 3703.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA oligo

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Non-polymers , 4 types, 715 molecules

#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 9 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 3350, 0.4M NaCl, pH 7.0, VAPOR DIFFUSION, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2NaClSodium chloride11
3PEG 335012
4NaClSodium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→32.79 Å / Num. obs: 121098 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.9
Reflection shellResolution: 1.41→1.45 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→32.79 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.047 / SU ML: 0.035 / Isotropic thermal model: PDB entry 2ZO0 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18632 6067 5 %RANDOM
Rwork0.14906 ---
obs0.15093 114952 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.522 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2---0.08 Å20 Å2
3---0.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.057 Å0.06 Å
Luzzati sigma a-0.035 Å
Refinement stepCycle: LAST / Resolution: 1.41→32.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 1016 114 680 5159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0214662
X-RAY DIFFRACTIONr_angle_refined_deg2.122.2286454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5635436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39922.528178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58115550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8631540
X-RAY DIFFRACTIONr_chiral_restr0.2050.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213326
X-RAY DIFFRACTIONr_mcbond_it2.1891.52117
X-RAY DIFFRACTIONr_mcangle_it3.16123380
X-RAY DIFFRACTIONr_scbond_it4.07532476
X-RAY DIFFRACTIONr_scangle_it5.4944.53035
X-RAY DIFFRACTIONr_rigid_bond_restr2.61334658
X-RAY DIFFRACTIONr_sphericity_free10.0953704
X-RAY DIFFRACTIONr_sphericity_bonded6.56134454
LS refinement shellResolution: 1.41→1.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 279 -
Rwork0.481 5243 -
obs-5243 60.41 %

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