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- PDB-5y20: Crystal structure of AL1 PHD finger bound to H3K4me3 -

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Basic information

Entry
Database: PDB / ID: 5y20
TitleCrystal structure of AL1 PHD finger bound to H3K4me3
Components
  • PEPTIDE FROM HISTONE H3
  • PHD finger protein ALFIN-LIKE 1
KeywordsTRANSCRIPTION / zinc finger
Function / homology
Function and homology information


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 / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) ...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 / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / transcription cis-regulatory region binding / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus / membrane
Similarity search - Function
Alfin, N-terminal / Alfin1-like, PHD finger / Alfin / Alfin / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. ...Alfin, N-terminal / Alfin1-like, PHD finger / Alfin / Alfin / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Zinc finger, FYVE/PHD-type / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / PHD finger protein ALFIN-LIKE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.409 Å
AuthorsZhao, S. / Zhang, B. / Li, H.
CitationJournal: Cell Rep / Year: 2018
Title: Systematic Profiling of Histone Readers in Arabidopsis thaliana.
Authors: Zhao, S. / Zhang, B. / Yang, M. / Zhu, J. / Li, H.
History
DepositionJul 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein ALFIN-LIKE 1
P: PEPTIDE FROM HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8174
Polymers6,6862
Non-polymers1312
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-15 kcal/mol
Surface area4030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.168, 46.168, 70.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PHD finger protein ALFIN-LIKE 1 / Protein AL1


Mass: 5866.727 Da / Num. of mol.: 1 / Fragment: PHD finger, UNP residues 185-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AL1, At5g05610, MOP10.15 / Plasmid: pGEX6p / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9FFF5
#2: Protein/peptide PEPTIDE FROM HISTONE H3


Mass: 818.961 Da / Num. of mol.: 1 / Fragment: H3 peptide 1-15 / Source method: obtained synthetically / Details: chemically synthesized H3K4ac peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8., 3.0M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2016 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 3265 / % possible obs: 100 % / Redundancy: 26.5 % / Biso Wilson estimate: 27.61 Å2 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.043 / Rrim(I) all: 0.225 / Χ2: 1.161 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2
2.4-2.4427.70.8440.9870.1620.8590.769
2.44-2.4928.10.8520.9650.1630.8680.766
2.49-2.5327.40.7510.9530.1450.7650.804
2.53-2.5927.50.7060.9760.1360.7190.825
2.59-2.6428.20.6240.9540.1190.6350.842
2.64-2.727.20.5340.9850.1030.5440.863
2.7-2.7727.80.5910.9770.1140.6020.827
2.77-2.8527.80.5160.980.0990.5250.901
2.85-2.93270.3770.9960.0730.3841.004
2.93-3.0227.50.330.9910.0630.3360.996
3.02-3.1326.90.310.9940.0610.3161.004
3.13-3.2627.10.2430.9940.0470.2471.14
3.26-3.41270.2250.9910.0440.2291.185
3.41-3.5826.70.180.9970.0350.1831.408
3.58-3.8126.50.1620.9960.0320.1651.551
3.81-4.125.80.1290.9980.0260.1311.749
4.1-4.5225.70.1270.9970.0250.1291.839
4.52-5.1724.70.110.9980.0220.1121.552
5.17-6.5123.70.110.9920.0230.1121.274
6.51-5021.40.0870.9990.0180.0891.95

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXphenix.refine: 1.9_1692refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FSA

2fsa


Resolution: 2.409→38.568 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.08
RfactorNum. reflection% reflection
Rfree0.2151 448 13.86 %
Rwork0.1611 --
obs0.1685 3233 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.14 Å2 / Biso mean: 29.9686 Å2 / Biso min: 19.29 Å2
Refinement stepCycle: final / Resolution: 2.409→38.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms459 0 2 28 489
Biso mean--25.98 31.72 -
Num. residues----59
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007468
X-RAY DIFFRACTIONf_angle_d1.002632
X-RAY DIFFRACTIONf_chiral_restr0.04167
X-RAY DIFFRACTIONf_plane_restr0.00578
X-RAY DIFFRACTIONf_dihedral_angle_d14.481167
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4088-2.75730.24741550.16728811036
2.7573-3.47350.19151370.17519201057
3.4735-38.57260.21761560.15179841140

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