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- PDB-3asl: Structure of UHRF1 in complex with histone tail -

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Basic information

Entry
Database: PDB / ID: 3asl
TitleStructure of UHRF1 in complex with histone tail
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Histone H3.3H3F3A
KeywordsLIGASE/DNA BINDING PROTEIN / histone reader module / epigenetic regulation / histone H3 / LIGASE-DNA BINDING PROTEIN complex
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 / negative regulation of gene expression via chromosomal CpG island methylation / oocyte maturation / nucleus organization / spermatid development / mitotic spindle assembly / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / nucleosomal DNA binding / protein autoubiquitination / heterochromatin / cis-regulatory region sequence-specific DNA binding / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / Inhibition of DNA recombination at telomere / telomere organization / positive regulation of protein metabolic process / embryo implantation / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / 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) / HCMV Late Events / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / HDACs deacetylate histones / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RING-type E3 ubiquitin transferase / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / multicellular organism growth / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / 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 / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / 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 / cadherin binding / 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
Similarity search - Function
: / 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 ...: / 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/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 / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / 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 / Histone H3.3 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.41 Å
AuthorsArita, K. / Sugita, K. / Unoki, M. / Hamamoto, R. / Sekiyama, N. / Tochio, H. / Ariyoshi, M. / Shirakawa, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1
Authors: Arita, K. / Isogai, S. / Oda, T. / Unoki, M. / Sugita, K. / Sekiyama, N. / Kuwata, K. / Hamamoto, R. / Tochio, H. / Sato, M. / Ariyoshi, M. / Shirakawa, M.
History
DepositionDec 16, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Mar 13, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,68210
Polymers9,1722
Non-polymers5108
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-2 kcal/mol
Surface area5480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.210, 36.137, 34.175
Angle α, β, γ (deg.)90.00, 110.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein E3 ubiquitin-protein ligase UHRF1


Mass: 7920.976 Da / Num. of mol.: 1 / Fragment: PHD finger domain
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 Histone H3.3 / H3F3A


Mass: 1251.436 Da / Num. of mol.: 1 / Fragment: residues in UNP 2-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243, UniProt: P68431*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10mM sodium citrate, 42% PEGMME2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11.28221
SYNCHROTRONPhoton Factory BL-17A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDNov 12, 2008
ADSC QUANTUM 2702CCDJan 22, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.282211
211
ReflectionResolution: 1.4→50 Å / Num. obs: 14019 / % possible obs: 92.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.4→1.45 Å / % possible all: 79.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.41→31.97 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.917 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19621 702 5 %RANDOM
Rwork0.1588 ---
all0.16052 14019 --
obs0.16052 13317 93.05 %-
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: 12.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20.46 Å2
2---0.25 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.41→31.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms604 0 20 72 696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021628
X-RAY DIFFRACTIONr_bond_other_d0.0020.02461
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.977837
X-RAY DIFFRACTIONr_angle_other_deg0.95431115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24823.87131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24515108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.99156
X-RAY DIFFRACTIONr_chiral_restr0.0920.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02117
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_it1.2391.5386
X-RAY DIFFRACTIONr_mcbond_other0.3741.5149
X-RAY DIFFRACTIONr_mcangle_it1.9132621
X-RAY DIFFRACTIONr_scbond_it3.1043242
X-RAY DIFFRACTIONr_scangle_it4.3414.5216
X-RAY DIFFRACTIONr_rigid_bond_restr1.17631089
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.406→1.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 52 -
Rwork0.167 856 -
obs--82.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.2775-6.5767-0.25788.0261.183513.14480.1879-0.3118-0.71730.29590.01810.46451.0213-0.3201-0.2060.163-0.0591-0.00340.08840.03540.0861-2.61615.0809-4.4428
21.35443.1211-2.31738.9009-1.655211.923-0.14490.08830.0051-0.1410.15410.02170.5669-0.1997-0.00920.0892-0.02850.01290.10310.00280.0669-1.15216.9578-12.7044
33.91021.52662.62042.15580.978613.4497-0.0231-0.03870.23960.0111-0.10660.2242-0.1688-0.63320.12970.03410.0120.00820.10410.01620.0813-0.755214.9403-9.6025
42.21062.1429-2.30053.83390.77557.62730.1161-0.03150.1165-0.06940.04160.0719-0.31390.0262-0.15770.0623-0.02260.03590.10540.01170.07853.787718.5812-6.4981
53.20120.35280.33750.59621.28753.49180.10760.18540.02640.04970.0462-0.04010.11430.0167-0.15380.0455-0.00410.01290.08730.00290.06838.510613.8244-11.8972
63.4295-1.9074-0.57933.06912.71328.21590.09870.05690.09220.04780.0012-0.15610.15570.1247-0.10.0734-0.00240.00940.0939-0.02520.086813.815116.34-5.329
711.36720.68784.88065.41462.92749.8475-0.006-0.3316-0.28080.39230.07340.18870.3404-0.4853-0.06740.2368-0.10320.00750.130.00390.11247.457917.60684.9347
82.18732.46840.76082.86741.31763.0495-0.05150.02690.2148-0.13290.03230.2108-0.3716-0.03280.01920.0811-0.01710.03540.076-0.02040.112210.84622.0256-7.2026
99.0145-9.93250.208113.3287-1.90396.0176-0.04260.01250.3717-0.0364-0.0079-0.2922-0.56670.23110.05050.1205-0.05640.00180.089-0.01320.137315.864727.6825-6.4922
106.925-0.9552-3.39478.01033.101614.6387-0.2401-0.1708-0.11540.51750.0394-0.0725-0.03180.15560.20080.0656-0.0063-0.01790.0922-0.02640.128919.995420.33993.5807
119.43541.23651.06418.17762.83584.81470.06950.01520.38870.4705-0.1271-0.0267-0.0826-0.29420.05760.1231-0.02590.00540.1116-0.02570.11529.076726.21174.7952
121.6995-1.31281.44915.08571.49514.68940.16370.02870.0368-0.2606-0.0815-0.01320.07810.2596-0.08220.02710.01010.00260.0488-0.00840.028318.114510.3716-5.1104
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A299 - 304
2X-RAY DIFFRACTION2A305 - 310
3X-RAY DIFFRACTION3A311 - 315
4X-RAY DIFFRACTION4A316 - 321
5X-RAY DIFFRACTION5A322 - 327
6X-RAY DIFFRACTION6A328 - 332
7X-RAY DIFFRACTION7A333 - 338
8X-RAY DIFFRACTION8A339 - 345
9X-RAY DIFFRACTION9A346 - 351
10X-RAY DIFFRACTION10A352 - 357
11X-RAY DIFFRACTION11A358 - 366
12X-RAY DIFFRACTION12B1 - 9

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