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- PDB-7yta: crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide -

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Basic information

Entry
Database: PDB / ID: 7yta
Titlecrystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide
Components
  • AGDP3 AGD1-2
  • H3(1-15)K9me2 peptide
KeywordsGENE REGULATION / AGENET domain / ROS1 / H3K9me2 binding
Function / homology
Function and homology information


chromocenter / plastid / structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
Protein of unknown function DUF724 / Protein of unknown function (DUF724) / Agenet domain, plant type / Tudor-like domain present in plant sequences. / Agenet-like domain / Agenet domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A ...Protein of unknown function DUF724 / Protein of unknown function (DUF724) / Agenet domain, plant type / Tudor-like domain present in plant sequences. / Agenet-like domain / Agenet domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
uncharacterized protein LOC107817772 isoform X2 / Histone H3.1
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsZhou, X. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentJCYJ20200109110403829 China
CitationJournal: J Integr Plant Biol / Year: 2022
Title: The H3K9me2-binding protein AGDP3 limits DNA methylation and transcriptional gene silencing in Arabidopsis.
Authors: Zhou, X. / Wei, M. / Nie, W. / Xi, Y. / Peng, L. / Zheng, Q. / Tang, K. / Satheesh, V. / Wang, Y. / Luo, J. / Du, X. / Liu, R. / Yang, Z. / La, H. / Zhong, Y. / Yang, Y. / Zhu, J.K. / Du, J. / Lei, M.
History
DepositionAug 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGDP3 AGD1-2
P: H3(1-15)K9me2 peptide
B: AGDP3 AGD1-2
Q: H3(1-15)K9me2 peptide
C: AGDP3 AGD1-2
R: H3(1-15)K9me2 peptide


Theoretical massNumber of molelcules
Total (without water)56,7856
Polymers56,7856
Non-polymers00
Water1,26170
1
A: AGDP3 AGD1-2
P: H3(1-15)K9me2 peptide


Theoretical massNumber of molelcules
Total (without water)18,9282
Polymers18,9282
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-5 kcal/mol
Surface area8870 Å2
MethodPISA
2
B: AGDP3 AGD1-2
Q: H3(1-15)K9me2 peptide


Theoretical massNumber of molelcules
Total (without water)18,9282
Polymers18,9282
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-8 kcal/mol
Surface area9500 Å2
MethodPISA
3
C: AGDP3 AGD1-2
R: H3(1-15)K9me2 peptide


Theoretical massNumber of molelcules
Total (without water)18,9282
Polymers18,9282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-7 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.741, 70.741, 217.989
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 AGDP3 AGD1-2 / uncharacterized protein LOC107817772 isoform X2


Mass: 17335.512 Da / Num. of mol.: 3 / Mutation: L12I,T13A,A16S,V17I,L110M,E137Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: LOC107817772 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1S4CD95
#2: Protein/peptide H3(1-15)K9me2 peptide


Mass: 1592.843 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 25% PEG 1500, 0.1 M sodium chloride and 0.1 M bis-Tris propane, pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 25, 2019
RadiationMonochromator: silicon crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 25568 / % possible obs: 100 % / Redundancy: 24.6 % / Biso Wilson estimate: 28.62 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.019 / Rrim(I) all: 0.092 / Χ2: 0.495 / Net I/σ(I): 3.9 / Num. measured all: 629775
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.38210.97925050.9770.2151.0030.416100
2.38-2.4822.80.87324660.9850.1860.8930.421100
2.48-2.5925.50.7925040.9910.1580.8060.422100
2.59-2.7326.70.57725260.9910.1130.5890.451100
2.73-2.926.50.33524970.9970.0660.3420.455100
2.9-3.1225.70.19325310.9990.0390.1970.49100
3.12-3.4424.50.111253710.0230.1140.539100
3.44-3.9326.50.078258010.0160.0790.593100
3.93-4.95240.045261210.0090.0460.56199.9
4.95-5023.10.03828100.9990.0080.0390.58299.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZWX

5zwx


Resolution: 2.31→27.47 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 29.02 / Stereochemistry target values: ML
Details: During refinment, the anisotropic correction was applied to truncate the data resolution in different axis. The finally used data were truncated to a*=2.7, b*=2.7, c*=2.3.
RfactorNum. reflection% reflection
Rfree0.2708 980 5.11 %
Rwork0.2474 18213 -
obs0.2487 19193 75.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.34 Å2 / Biso mean: 43.0766 Å2 / Biso min: 11.64 Å2
Refinement stepCycle: final / Resolution: 2.31→27.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 0 70 3677
Biso mean---30.81 -
Num. residues----444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.430.2607120.312433734910
2.43-2.580.3401680.31561134120234
2.58-2.780.33651680.32562895306386
2.78-3.060.33571660.295734123578100
3.06-3.50.27111860.265334133599100
3.5-4.410.24192030.21634473650100
4.41-27.470.23811770.20683575375297
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)
11.3816-0.03310.81151.4444-1.04611.24930.01280.08170.1033-0.21010.08210.1109-0.0357-0.3371-0.18910.41570.13480.0840.4180.19390.03198.130861.710966.4174
23.38640.8387-1.70011.22750.15863.0567-0.35210.3403-0.5154-0.2346-0.0666-0.32851.37790.75170.4890.46380.27690.13490.57980.08060.192617.831347.281370.7588
32.41180.10981.14762.4741-2.28953.22020.00160.13560.153-0.133-0.05210.0205-0.155-0.0361-0.12550.35740.06980.11130.48510.14530.093213.787860.715464.8661
47.9384-0.9222.37693.0831-3.49114.63460.28471.3162-0.6029-1.8186-0.17350.61140.7518-1.0806-0.1391.088-0.2189-0.22721.1776-0.12640.52782.664951.85355.5766
52.83360.5586-0.50942.40180.02833.178-0.18460.1919-0.129-0.4801-0.1374-0.6207-0.08190.86880.1140.42750.14570.21830.85410.21690.269422.127259.342461.892
60.3614-0.44970.54640.5703-0.69040.82050.11370.04490.0259-0.1799-0.1149-0.0163-0.43230.06750.02710.39180.0208-0.02010.4417-0.0046-0.084312.326657.358379.0395
70.5407-0.1958-0.49862.10040.05661.33230.02890.39550.1476-0.2775-0.082-0.1627-0.16540.4293-0.01510.0662-0.10160.09650.60950.1863-0.018920.961754.015884.2434
80.73010.0573-0.88694.12840.63215.06110.0143-0.05170.03680.2233-0.0115-0.1361-0.19590.5231-0.03460.1431-0.12490.00810.62290.05190.074324.046152.132788.9044
92.356-0.6041.61762.6068-0.64423.4117-0.0697-0.07440.03740.23270.0105-0.2986-0.29560.70050.18570.1863-0.0507-0.03020.53460.03010.05122.179756.476586.2812
104.6785-0.91992.17153.9548-1.81815.21820.0143-0.3041-0.0544-0.15390.12250.3502-0.0948-0.3667-0.0480.07670.0868-0.02790.48220.06910.14294.474353.723779.7909
111.26990.8544-1.38770.7166-0.36743.7743-0.22720.4223-0.0674-0.50760.1588-0.58760.42750.40110.10610.53790.27260.30721.21880.1580.610527.699551.572670.4192
121.3711-0.06111.20531.1950.43674.62720.0923-0.30550.04590.41020.01670.01540.14420.1319-0.01320.7504-0.1430.07430.5917-0.22060.129916.728964.0155130.3617
132.1108-0.2306-0.03941.67542.85126.7179-0.118-0.23730.259-0.07170.2231-0.1092-0.85940.295-0.03460.8728-0.34390.00290.5989-0.10720.150218.945171.0698135.7398
140.9788-0.0252-0.8350.6320.27854.33350.03040.2902-0.0018-0.21910.0384-0.0571-0.00340.38430.02670.6825-0.2181-0.00640.6936-0.13660.145320.90963.2826127.2299
153.03930.1455-0.34032.39620.98026.22460.0766-0.2440.30610.0024-0.08120.1333-0.9351-0.04020.05820.55530.0508-0.01510.4213-0.07280.062212.339363.1341111.1774
164.53250.06380.27043.55162.15635.7384-0.1373-0.03040.26950.1343-0.04290.283-0.9832-0.74370.36550.74110.08150.01990.4177-0.10710.08969.428565.5765110.4297
173.31582.97160.07634.1566-0.27630.08130.2763-0.0083-0.38520.3660.1345-0.68170.36280.805-0.3090.63950.1775-0.24080.7686-0.11340.327620.048352.5527120.0722
182.971.48871.82767.53314.86353.4706-0.248-1.09410.91841.6759-0.65091.1219-0.226-0.74560.92641.26430.2713-0.09891.1453-0.32320.72865.647773.2541126.8503
193.02681.6844-3.4022.9718-0.34565.00310.1533-0.14550.15280.79340.18540.6887-0.3992-1.4609-0.39220.39570.11160.12970.70980.22920.25035.592937.5866119.3214
202.97361.2609-1.36532.6156-1.42755.09170.1103-0.2507-0.05510.3094-0.0043-0.1129-0.20090.28750.07470.27290.0457-0.09580.40980.07360.06517.210939.0424115.2196
212.9345-0.1529-0.07462.657-0.11886.9198-0.1962-0.52020.06160.55130.38420.0166-0.0566-0.1908-0.11070.48630.1669-0.02960.43430.09560.125915.634933.7528122.6557
220.4422-0.2432-0.42671.0825-0.70034.1439-0.1304-0.0948-0.06320.20740.20440.12810.22-0.5324-0.16410.18620.0042-0.07270.47010.10120.018210.628238.4328105.3198
231.17240.59650.15951.9977-1.65274.55560.19690.1727-0.12820.00540.028-0.09760.35090.4719-0.38240.096-0.0228-0.08540.389-0.04120.056616.297638.314195.6789
241.9636-0.3102-1.34483.113-2.05892.6040.11080.623-0.0705-0.5459-0.09370.09060.53420.1187-0.30420.18440.0609-0.12330.520.05320.048518.645136.87493.3996
255.2706-0.4345-0.92074.14821.08475.71130.18080.5359-0.1803-0.6882-0.2431-0.09310.3950.3287-0.06440.3015-0.0023-0.06270.32260.05390.023715.070134.53396.6138
268.1932-1.0035-2.87146.50853.97245.61910.19550.19180.4316-0.0734-0.03080.4486-0.5419-0.911-0.14060.08520.10180.05950.48470.08690.19545.061247.871105.6589
276.69331.55673.68321.5081.83022.8537-0.00760.07020.09950.113-0.5646-0.5137-0.39561.27220.64560.48850.0927-0.1150.52910.06950.154425.478532.6289110.8182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 20 )A10 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 31 )A21 - 31
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 39 )A32 - 39
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 47 )A40 - 47
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 66 )A48 - 66
6X-RAY DIFFRACTION6chain 'A' and (resid 67 through 91 )A67 - 91
7X-RAY DIFFRACTION7chain 'A' and (resid 92 through 110 )A92 - 110
8X-RAY DIFFRACTION8chain 'A' and (resid 111 through 123 )A111 - 123
9X-RAY DIFFRACTION9chain 'A' and (resid 124 through 135 )A124 - 135
10X-RAY DIFFRACTION10chain 'A' and (resid 136 through 147 )A136 - 147
11X-RAY DIFFRACTION11chain 'P' and (resid 1 through 10 )P1 - 10
12X-RAY DIFFRACTION12chain 'B' and (resid 11 through 31 )B11 - 31
13X-RAY DIFFRACTION13chain 'B' and (resid 32 through 66 )B32 - 66
14X-RAY DIFFRACTION14chain 'B' and (resid 67 through 84 )B67 - 84
15X-RAY DIFFRACTION15chain 'B' and (resid 85 through 110 )B85 - 110
16X-RAY DIFFRACTION16chain 'B' and (resid 111 through 135 )B111 - 135
17X-RAY DIFFRACTION17chain 'B' and (resid 136 through 150 )B136 - 150
18X-RAY DIFFRACTION18chain 'Q' and (resid 2 through 10 )Q2 - 10
19X-RAY DIFFRACTION19chain 'C' and (resid 10 through 20 )C10 - 20
20X-RAY DIFFRACTION20chain 'C' and (resid 21 through 39 )C21 - 39
21X-RAY DIFFRACTION21chain 'C' and (resid 40 through 66 )C40 - 66
22X-RAY DIFFRACTION22chain 'C' and (resid 67 through 99 )C67 - 99
23X-RAY DIFFRACTION23chain 'C' and (resid 100 through 110 )C100 - 110
24X-RAY DIFFRACTION24chain 'C' and (resid 111 through 123 )C111 - 123
25X-RAY DIFFRACTION25chain 'C' and (resid 124 through 135 )C124 - 135
26X-RAY DIFFRACTION26chain 'C' and (resid 136 through 149 )C136 - 149
27X-RAY DIFFRACTION27chain 'R' and (resid 1 through 10 )R1 - 10

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