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- PDB-3zvy: PHD finger of human UHRF1 in complex with unmodified histone H3 N... -

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Basic information

Entry
Database: PDB / ID: 3zvy
TitlePHD finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail
Components
  • E3 UBIQUITIN-PROTEIN LIGASE UHRF1
  • HISTONE H3.1Histone H3
KeywordsLIGASE/PEPTIDE / LIGASE-PEPTIDE COMPLEX / HISTONE READER / EPIGENETICS
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 / negative regulation of gene expression via chromosomal CpG island methylation / regulation of epithelial cell proliferation / methyl-CpG binding / 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 / 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 / Chromatin modifying enzymes / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / telomere organization / positive regulation of protein metabolic process / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / replication fork / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / double-strand break repair via homologous recombination / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RING-type E3 ubiquitin transferase / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nucleic acid binding / 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 / zinc ion binding / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus
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-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / 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 / SAD / Resolution: 1.95 Å
AuthorsLallous, N. / Birck, C. / Mc Ewen, A.G. / Legrand, P. / Samama, J.P.
CitationJournal: Plos One / Year: 2011
Title: The Phd Finger of Human Uhrf1 Reveals a New Subgroup of Unmethylated Histone H3 Tail Readers.
Authors: Lallous, N. / Legrand, P. / Mcewen, A.G. / Ramon-Maiques, S. / Samama, J.P. / Birck, C.
History
DepositionJul 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.temp

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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 H3.1
D: HISTONE H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,12116
Polymers18,2834
Non-polymers83812
Water1,42379
1
B: E3 UBIQUITIN-PROTEIN LIGASE UHRF1
D: HISTONE H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5969
Polymers9,1412
Non-polymers4557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-43.8 kcal/mol
Surface area4830 Å2
MethodPISA
2
A: E3 UBIQUITIN-PROTEIN LIGASE UHRF1
C: HISTONE H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5257
Polymers9,1412
Non-polymers3845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-27 kcal/mol
Surface area5070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.300, 42.300, 182.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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: 8207.351 Da / Num. of mol.: 2 / Fragment: PHD FINGER, RESIDUES 296-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA 2
References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide HISTONE H3.1 / Histone H3 / HISTONE H3/A / HISTONE H3/B / HISTONE H3/C / HISTONE H3/D / HISTONE H3/F / HISTONE H3/H / HISTONE ...HISTONE H3/A / HISTONE H3/B / HISTONE H3/C / HISTONE H3/D / HISTONE H3/F / HISTONE H3/H / HISTONE H3/I / HISTONE H3/J / HISTONE H3/K / HISTONE H3/L


Mass: 934.075 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-9 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431

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Non-polymers , 4 types, 91 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.41 Å3/Da / Density % sol: 48.61 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: CRYSTALS WERE OBTAINED AT 17 DEGREES USING THE VAPOR DIFFUSION METHOD BY MIXING A PROTEIN SOLUTION AT A CONCENTRATION OF 606 MICROM (IN 20 MM TRIS PH 7, 150 MM NACL, 0.5 MM TCEP, 25 MICROM ...Details: CRYSTALS WERE OBTAINED AT 17 DEGREES USING THE VAPOR DIFFUSION METHOD BY MIXING A PROTEIN SOLUTION AT A CONCENTRATION OF 606 MICROM (IN 20 MM TRIS PH 7, 150 MM NACL, 0.5 MM TCEP, 25 MICROM ZNCL2 AND 0.1 MM PMSF) AND 10-FOLD EXCESS OF PEPTIDE WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M TRIS PH 8.5, 0.2 M MGCL2, 30 % PEG 4000). CRYSTALS WERE CRYOPROTECTED WITH 15 % MPD AND FLASH FROZEN IN LIQUID NITROGEN.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.284
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.284 Å / Relative weight: 1
ReflectionResolution: 1.95→38.4 Å / Num. obs: 22160 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 4.96 % / Biso Wilson estimate: 34.47 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.46
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.12 / % possible all: 83.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.95→41.21 Å / SU ML: 0.23 / σ(F): 1.48 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1176 5.1 %
Rwork0.1813 --
obs0.1836 22160 99.68 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.733 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.101 Å20 Å20 Å2
2--3.101 Å20 Å2
3----6.2019 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 26 79 1194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071137
X-RAY DIFFRACTIONf_angle_d1.1071540
X-RAY DIFFRACTIONf_dihedral_angle_d12.328441
X-RAY DIFFRACTIONf_chiral_restr0.076161
X-RAY DIFFRACTIONf_plane_restr0.004203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.03880.28961460.25512737X-RAY DIFFRACTION99
2.0388-2.14620.24011480.21672742X-RAY DIFFRACTION100
2.1462-2.28070.27321480.19982712X-RAY DIFFRACTION100
2.2807-2.45680.23581460.1922744X-RAY DIFFRACTION100
2.4568-2.7040.22961480.19222741X-RAY DIFFRACTION100
2.704-3.09510.29761450.19352736X-RAY DIFFRACTION100
3.0951-3.89910.24811480.17682751X-RAY DIFFRACTION100
3.8991-41.21910.16711470.15642706X-RAY DIFFRACTION99
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)
10.9489-0.29541.61443.31240.69193.13240.26310.3024-0.1280.45180.1328-0.3730.18120.5162-0.3520.29240.0836-0.11660.3089-0.07660.272540.563716.6928149.9603
21.4773-0.71010.73482.4891-1.61851.93040.298-0.0384-0.11210.41120.02620.0954-0.0345-0.1943-0.21710.3390.0284-0.06010.2219-0.00540.225620.82939.7726152.0925
32.82863.66910.81636.71692.47552.1689-0.3570.8663-0.319-0.37050.7318-0.4105-0.31130.5722-0.41460.38060.0065-0.0030.8104-0.15760.45345.844110.8248145.0354
40.1879-0.45290.18411.1485-0.47860.20170.04950.05010.1649-0.19510.37290.14250.4451-0.4166-0.04590.39160.1241-0.04740.4819-0.12460.413714.864315.6987148.7195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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