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- PDB-21ed: Crystal structure of human PHF20L1(85-142) -

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Basic information

Entry
Database: PDB / ID: 21ed
TitleCrystal structure of human PHF20L1(85-142)
ComponentsPHD finger protein 20-like protein 1
KeywordsPROTEIN BINDING / Tudor domain / Histone binding / Epigenetic reader / Methyl lysine recognition / Protein protein interaction / Chromatin regulation / Nuclear protein / Structural biology
Function / homology
Function and homology information


methylation-dependent protein binding / NSL complex / Formation of WDR5-containing histone-modifying complexes / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein catabolic process / regulation of transcription by RNA polymerase II / nucleoplasm / zinc 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 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor 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 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / 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
Similarity search - Domain/homology
PHD finger protein 20-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsLiu, Y. / Huang, X. / Shang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271309 China
CitationJournal: J.Biol.Chem. / Year: 2026
Title: A revised model for PHF20L1 Tudor function: DNA binding overrides methylation selectivity on nucleosomes.
Authors: Huang, X. / Xiao, Q. / Liu, X. / Shang, X. / Wang, Z. / Hu, H. / Zhou, Y. / Huang, Q. / Jiang, T. / Qin, S. / Huang, Y. / Li, J.B. / Liu, Y.
History
DepositionDec 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein 20-like protein 1


Theoretical massNumber of molelcules
Total (without water)6,8981
Polymers6,8981
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.849, 55.849, 93.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PHD finger protein 20-like protein 1


Mass: 6897.953 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 5.27 Å3/Da / Density % sol: 76.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.2 M Magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.31→47.9 Å / Num. obs: 6920 / % possible obs: 100 % / Redundancy: 1.8 % / CC1/2: 0.999 / Net I/σ(I): 13.5
Reflection shellResolution: 2.31→2.39 Å / Num. unique obs: 652 / CC1/2: 0.974

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→36.36 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.727 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2878 337 4.9 %RANDOM
Rwork0.2745 ---
obs-6581 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.132 Å2
Baniso -1Baniso -2Baniso -3
1-4.29 Å20 Å20 Å2
2--4.29 Å20 Å2
3----8.58 Å2
Refinement stepCycle: 1 / Resolution: 2.31→36.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms448 0 0 3 451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012481
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0581.661645
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.99556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.35854
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0791088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1370.266
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02360
X-RAY DIFFRACTIONr_gen_planes_other
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_it7.7266.869227
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.7112.28282
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it11.1447.236254
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined16.5969.81675
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 22 -
Rwork0.414 466 -
obs--100 %

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