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- PDB-2pb7: Crystal Structure of the SRA domain of the human UHRF1 protein -

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Basic information

Entry
Database: PDB / ID: 2pb7
TitleCrystal Structure of the SRA domain of the human UHRF1 protein
ComponentsE3 ubiquitin-protein ligase UHRF1
KeywordsLIGASE / beta barrel / new fold
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 / 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 / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / 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 / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / positive regulation of protein metabolic process / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / double-strand break repair via homologous recombination / euchromatin / RING-type E3 ubiquitin transferase / nuclear matrix / spindle / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / nucleic acid binding / protein ubiquitination / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus
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 domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsDelagoutte, B. / Birck, C. / Samama, J.P.
CitationJournal: To be Published
Title: The mammalian SRA domain is a new nucleosome binding motif
Authors: Delagoutte, B. / Atmanene, C. / Birck, C. / Sanglier, S. / Mantovani, R. / Bonapace, I.M. / Oudet, P. / Van Dorsselaer, A. / Moras, D. / Samama, J.P.
History
DepositionMar 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF1


Theoretical massNumber of molelcules
Total (without water)26,7921
Polymers26,7921
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.929, 53.929, 161.995
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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 / Inverted CCAAT box-binding protein of 90 kDa / Transcription factor ICBP90 / Nuclear zinc finger protein Np95 / Nuclear protein 95 / HuNp95 / RING finger protein 106


Mass: 26791.812 Da / Num. of mol.: 1 / Fragment: SRA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Plasmid: pHGWA (home made based on pET22b) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14-19% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8730, 0.9791, 0.9795, 0.9757
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 1, 2006 / Details: Si (111) monochromator and Pt coated mirrors
RadiationMonochromator: Si (111) monochromator and Pt coated mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8731
20.97911
30.97951
40.97571
ReflectionResolution: 1.9→50 Å / Num. all: 22424 / Num. obs: 22424 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.081 / Net I/σ(I): 5
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.35 / Num. unique all: 3220 / Rsym value: 0.351 / % possible all: 95.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SOLVEphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD
Starting model: MAD model

Resolution: 1.9→10 Å / Isotropic thermal model: anisotropic / Cross valid method: sigmaa / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1088 -random
Rwork0.205 ---
all0.206 22207 --
obs0.206 22207 99 %-
Displacement parametersBiso mean: 33.19 Å2
Baniso -1Baniso -2Baniso -3
1--5.858 Å2-3.183 Å20 Å2
2---5.858 Å20 Å2
3---11.716 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 0 91 1579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0102
X-RAY DIFFRACTIONc_dihedral_angle_d24.407
X-RAY DIFFRACTIONc_improper_angle_d0.911
X-RAY DIFFRACTIONc_angle_deg1.375
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection
Rfree0.305 66
Rwork0.274 -
obs-1013

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