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- PDB-9m4s: crystal structure of Arabidopsis thaliana ING2 PHD finger in comp... -

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Basic information

Entry
Database: PDB / ID: 9m4s
Titlecrystal structure of Arabidopsis thaliana ING2 PHD finger in complex with an H3K4me3 peptide
Components
  • Histone H3.1
  • PHD finger protein ING2
KeywordsGENE REGULATION / histone modification / epigenetic regulation / H3K4me3 / ING1
Function / homology
Function and homology information


chromocenter / histone H3K4me3 reader activity / plastid / structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / extracellular region / zinc ion binding / nucleus ...chromocenter / histone H3K4me3 reader activity / plastid / structural constituent of chromatin / nucleosome / 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 / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/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 / PHD-finger / 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
PHD finger protein ING2 / Histone H3.1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 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

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein ING2
P: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9124
Polymers9,7812
Non-polymers1312
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-4 kcal/mol
Surface area5210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.699, 50.699, 55.239
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PHD finger protein ING2 / Protein INHIBITOR OF GROWTH 2 / Protein AtING2


Mass: 8588.702 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ING2, At1g54390, F20D21.22 / Plasmid: pMal / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3H615
#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.: 79 / 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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M NiCl2, 20% PEG2000 MME, and 0.1M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2017
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 10759 / % possible obs: 99.8 % / Redundancy: 8.4 % / CC1/2: 0.946 / CC star: 0.986 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.668.60.33910550.9460.9860.1230.3611.277100
1.66-1.728.40.27910860.960.990.1020.2971.523100
1.72-1.880.23310520.9660.9910.0880.2491.75299.8
1.8-1.98.50.20210830.9750.9940.0730.2152.05199.9
1.9-2.028.50.18210580.980.9950.0660.1932.56299.9
2.02-2.178.10.14710800.9830.9960.0550.1572.75699.8
2.17-2.398.50.12610740.9890.9970.0460.1352.91799.8
2.39-2.748.40.10510840.9920.9980.0390.1122.72799.8
2.74-3.458.60.08410880.9950.9990.030.092.699100
3.45-508.30.06510990.9960.9990.0240.0692.4599.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.601→43.907 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 514 4.8 %
Rwork0.1851 --
obs0.187 10700 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.601→43.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms556 0 2 79 637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016571
X-RAY DIFFRACTIONf_angle_d1.501775
X-RAY DIFFRACTIONf_dihedral_angle_d19.647208
X-RAY DIFFRACTIONf_chiral_restr0.0879
X-RAY DIFFRACTIONf_plane_restr0.01100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.601-1.68490.19981720.20012835X-RAY DIFFRACTION100
1.6849-1.79050.25851140.19142905X-RAY DIFFRACTION100
1.7905-1.92870.25121360.19662829X-RAY DIFFRACTION100
1.9287-2.12280.22961240.18622850X-RAY DIFFRACTION100
2.1228-2.42990.19791230.17842888X-RAY DIFFRACTION100
2.4299-3.06140.23161930.19662785X-RAY DIFFRACTION100
3.0614-43.9070.22131430.17612849X-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)
15.15972.044-2.80952.1989-1.82281.8924-0.1431-0.16660.50490.6740.253-0.6602-0.32841.2577-0.14640.5843-0.0024-0.41210.4238-0.12080.691916.574629.652521.8201
26.5447-1.24780.3523.5397-0.12693.3002-0.1050.04790.38350.02370.0507-0.3517-0.07940.29120.06840.197-0.0064-0.01380.161-0.0010.17218.631922.236314.8838
39.00290.074-1.33983.385-1.44115.81910.1646-0.5266-0.0137-0.0022-0.1695-0.09670.1270.16910.00280.1611-0.0045-0.00110.1782-0.0020.13072.455913.267921.7873
45.654-1.52950.95223.237-0.6115.42810.02660.41140.2688-0.1785-0.0789-0.0959-0.06120.14710.08460.198-0.02120.00320.14960.00830.17862.53721.22079.0686
52.22913.1085-3.32614.9592-5.23625.5340.3063-0.01390.49040.2115-0.07710.4647-0.8903-0.581-0.22410.29490.0332-0.0060.3121-0.00520.268-7.837121.394410.243
67.0253-1.93430.4365.20950.0724.6011-0.12180.015-0.5894-0.07380.01230.26770.3581-0.08170.08270.19140.0030.03650.1562-0.00990.16960.30967.621215.1189
77.54011.11020.27526.8914-0.15635.5128-0.01020.12360.71320.0392-0.0435-0.399-0.77250.20650.02650.3319-0.0067-0.03040.2014-0.00280.28131.936127.847714.5001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 201 through 205 )
2X-RAY DIFFRACTION2chain 'A' and (resid 206 through 221 )
3X-RAY DIFFRACTION3chain 'A' and (resid 222 through 231 )
4X-RAY DIFFRACTION4chain 'A' and (resid 232 through 243 )
5X-RAY DIFFRACTION5chain 'A' and (resid 244 through 248 )
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 260 )
7X-RAY DIFFRACTION7chain 'P' and (resid 1 through 9 )

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