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- PDB-6l1f: Crystal structure of PHF20L1 Tudor1 in complex with K142me1 DNMT1 -

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Basic information

Entry
Database: PDB / ID: 6l1f
TitleCrystal structure of PHF20L1 Tudor1 in complex with K142me1 DNMT1
Components
  • PHD finger protein 20-like protein 1
  • the K142me1 DNMT1 peptide
KeywordsMETAL BINDING PROTEIN/PEPTIDE / PHF20L1 / Tudor / apo / METAL BINDING PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


methylation-dependent protein binding / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins ...methylation-dependent protein binding / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / STAT3 nuclear events downstream of ALK signaling / female germ cell nucleus / methyl-CpG binding / NSL complex / negative regulation of gene expression via chromosomal CpG island methylation / Formation of WDR5-containing histone-modifying complexes / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Nuclear events stimulated by ALK signaling in cancer / pericentric heterochromatin / positive regulation of vascular associated smooth muscle cell proliferation / DNA methylation / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / promoter-specific chromatin binding / cellular response to amino acid stimulus / NoRC negatively regulates rRNA expression / negative regulation of protein catabolic process / methylation / negative regulation of gene expression / DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / PHD finger protein 20-like protein 1 / PHD finger protein 20-like / Agenet domain, plant type / Tudor-like domain present in plant sequences. / PhD finger domain / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain ...: / PHD finger protein 20-like protein 1 / PHD finger protein 20-like / Agenet domain, plant type / Tudor-like domain present in plant sequences. / PhD finger domain / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / mbt repeat / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / CXXC zinc finger domain / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
PHD finger protein 20-like protein 1 / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLv, M.Q. / Gao, J.
CitationJournal: J Phys Chem Lett / Year: 2020
Title: Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1.
Authors: Lv, M. / Gao, J. / Li, M. / Ma, R. / Li, F. / Liu, Y. / Liu, M. / Zhang, J. / Yao, X. / Wu, J. / Shi, Y. / Tang, Y. / Pan, Y. / Zhang, Z. / Ruan, K.
History
DepositionSep 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: the K142me1 DNMT1 peptide
B: PHD finger protein 20-like protein 1


Theoretical massNumber of molelcules
Total (without water)9,3582
Polymers9,3582
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-2 kcal/mol
Surface area5030 Å2
Unit cell
Length a, b, c (Å)42.702, 52.932, 31.394
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide the K142me1 DNMT1 peptide


Mass: 663.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MLZ represent mono-methylated lysine / Source: (synth.) Homo sapiens (human) / References: UniProt: P26358
#2: Protein PHD finger protein 20-like protein 1 / Plant Homeodomain (PHD) Finger Protein 20-like 1


Mass: 8693.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF20L1, CGI-72 / Production host: Escherichia coli (E. coli) / References: UniProt: A8MW92
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 35.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% PEG MME 2000, 0.1M sodium cacodylate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→33.24 Å / Num. obs: 5921 / % possible obs: 99.01 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 16.9
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 553

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SD4

3sd4


Resolution: 1.9→33.235 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.98
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 553 9.34 %RANDOM
Rwork0.1922 ---
obs0.196 5921 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.8 Å2 / Biso mean: 27.3073 Å2 / Biso min: 11.78 Å2
Refinement stepCycle: final / Resolution: 1.9→33.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms635 0 0 32 667
Biso mean---32.35 -
Num. residues----73
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-2.0910.27541110.196129097
2.091-2.39350.25031240.19561343100
2.3935-3.01520.27251540.21431326100
3.0152-33.23030.20171640.181140999
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)
14.2223-0.8179-1.13041.72171.97972.3681-0.3157-0.48210.60960.9015-0.01970.347-0.1589-0.0047-0.04790.37370.00670.02280.2877-0.04560.3607-16.435923.573-1.6503
21.58950.17940.49652.21560.34691.2420.014-0.0228-0.0231-0.00880.00020.00830.0281-0.08040.00340.13340.0085-0.00930.14730.00360.1374-9.57210.0745-13.9429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 140 through 145)A140 - 145
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 69)B3 - 69

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