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- PDB-9m4r: crystal structure of Arabidopsis thaliana ING1 PHD finger in comp... -

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Basic information

Entry
Database: PDB / ID: 9m4r
Titlecrystal structure of Arabidopsis thaliana ING1 PHD finger in complex with an H3K4me3 peptide
Components
  • Histone H3.1
  • PHD finger protein ING1
KeywordsGENE REGULATION / histone modification / epigenetic regulation / H3K4me3 / ING1
Function / homology
Function and homology information


chromocenter / plastid / : / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / DNA binding / extracellular region / zinc ion binding ...chromocenter / plastid / : / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / DNA binding / extracellular region / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type ...Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3.1 / PHD finger protein ING1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsLi, X. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32325008 China
CitationJournal: Nat Commun / Year: 2025
Title: A pair of readers of histone H3K4 methylation recruit Polycomb repressive complex 2 to regulate photoperiodic flowering.
Authors: Luo, X. / Li, X. / Chen, Z. / Tian, S. / Liu, Y. / Shang, Z. / Chen, L. / Sun, Y. / Du, J. / He, Y.
History
DepositionMar 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: 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 ING1
P: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5104
Polymers9,3792
Non-polymers1312
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-3 kcal/mol
Surface area3950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.830, 41.830, 69.435
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PHD finger protein ING1 / Protein INHIBITOR OF GROWTH 1 / Protein AtING1


Mass: 8186.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ING1, At3g24010, F14O13.20 / Plasmid: pMal / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LIQ6
#2: Protein/peptide Histone H3.1


Mass: 1192.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: H3K4me3 peptide / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226
#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.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.87 Å3/Da / Density % sol: 34.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 40% PEG400, 5% PEG3000, and 0.1M MES, 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: 1.2824 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 2, 2017
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 8189 / % possible obs: 99.9 % / Redundancy: 18.2 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.7617.80.228130.9910.9980.0540.2272.421100
1.76-1.8318.10.2037840.9920.9980.0490.2092.89699.6
1.83-1.9118.60.178060.9940.9980.0420.1763.177100
1.91-2.0218.20.1558040.9950.9990.0390.163.80199.9
2.02-2.1417.50.1417980.9970.9990.0350.1454.3799.8
2.14-2.3118.80.1278190.9960.9990.0310.1314.708100
2.31-2.5418.30.1227980.9960.9990.030.1265.254100
2.54-2.9118.60.18280.9970.9990.0240.1035.20199.6
2.91-3.6618.30.088340.99810.0190.0824.75699.9
3.66-5017.60.0759050.9970.9990.0180.0774.59599.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→36.226 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.74 / Phase error: 19.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 689 4.61 %
Rwork0.1568 --
obs0.1586 8139 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→36.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms444 0 2 60 506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019455
X-RAY DIFFRACTIONf_angle_d1.712615
X-RAY DIFFRACTIONf_dihedral_angle_d16.103162
X-RAY DIFFRACTIONf_chiral_restr0.07862
X-RAY DIFFRACTIONf_plane_restr0.01278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.83130.18021740.14982804X-RAY DIFFRACTION100
1.8313-2.01560.1971140.14682886X-RAY DIFFRACTION100
2.0156-2.30720.18961470.14952846X-RAY DIFFRACTION100
2.3072-2.90670.20381320.17432847X-RAY DIFFRACTION100
2.9067-36.2260.20591220.15372875X-RAY DIFFRACTION100
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)
13.8851-2.7325-1.7933.4051.09481.07720.16110.14460.3496-0.0827-0.08130.315-0.3785-0.45450.0810.2167-0.00460.02870.22110.02490.2356-5.504429.940333.7882
22.32190.0379-2.02933.1164-0.72468.98670.16250.3020.1084-0.18990.01540.1143-0.4044-0.4164-0.15270.20040.02080.00220.18040.01410.21171.214629.902322.9529
34.43420.3079-1.02763.9682-0.0524.08580.0785-0.158-0.31220.1895-0.1235-0.264-0.07050.48750.00870.2149-0.0124-0.00340.1920.01840.20346.746926.465531.8101
43.12820.5214-0.76777.00262.87399.08330.04140.2495-1.14780.24560.2562-0.18761.1923-0.067-0.01960.2998-0.0226-0.00610.18290.00410.22172.911122.242822.5556
54.1537-3.7957-5.88895.51634.91728.50890.2315-0.59580.57630.37950.07720.0937-0.32630.31-0.2560.293-0.06240.03760.22060.00610.33425.286134.481532.554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 177 through 190 )
2X-RAY DIFFRACTION2chain 'A' and (resid 191 through 202 )
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 218 )
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 226 )
5X-RAY DIFFRACTION5chain 'P' and (resid 1 through 6 )

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