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- PDB-7cce: crystal structure of Arabidopsis AIPP3 BAH domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 7cce
Titlecrystal structure of Arabidopsis AIPP3 BAH domain in complex with an H3K27me3 peptide
Components
  • Bromo-adjacent homology (BAH) domain-containing protein
  • Histone H3.2
KeywordsGENE REGULATION / BAH domain / AIPP3 / H3K27me3 / histone modification / epigenetcis
Function / homology
Function and homology information


chromocenter / plastid / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / DNA-templated transcription / chromatin binding / DNA binding / extracellular region ...chromocenter / plastid / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / DNA-templated transcription / chromatin binding / DNA binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. ...Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / 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
Histone H3.1 / Bromo-adjacent homology (BAH) domain-containing protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsYuan, J. / Du, J.
CitationJournal: Nat Commun / Year: 2020
Title: Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis.
Authors: Zhang, Y.Z. / Yuan, J. / Zhang, L. / Chen, C. / Wang, Y. / Zhang, G. / Peng, L. / Xie, S.S. / Jiang, J. / Zhu, J.K. / Du, J. / Duan, C.G.
History
DepositionJun 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Bromo-adjacent homology (BAH) domain-containing protein
P: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6023
Polymers21,4802
Non-polymers1221
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-9 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.599, 78.599, 72.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Bromo-adjacent homology (BAH) domain-containing protein


Mass: 19677.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g11560, F25E4.180, F25E4_180 / Plasmid: pMal-p2X-His / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q8RXT5
#2: Protein/peptide Histone H3.2 / Histone H3.1


Mass: 1802.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, pH 7.0, and 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 26, 2018
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 10478 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 71.93 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.02 / Rrim(I) all: 0.084 / Χ2: 1.481 / Net I/σ(I): 7.3 / Num. measured all: 200614
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4418.71.1215370.950.2651.1520.468100
2.44-2.4919.10.9265010.950.2170.9520.501100
2.49-2.5318.50.8385130.9520.1990.8610.508100
2.53-2.5918.70.7825170.9580.1850.8040.541100
2.59-2.6419.90.6224990.9710.1420.6380.617100
2.64-2.720.50.4675360.9880.1050.4790.715100
2.7-2.7720.60.3585010.9880.0810.3670.726100
2.77-2.85200.315140.9890.0710.3180.846100
2.85-2.9319.80.2555220.9910.0590.2621.034100
2.93-3.0219.30.215170.9910.0490.2161.254100
3.02-3.1318.10.175220.9920.0420.1751.493100
3.13-3.2619.40.1545040.9950.0360.1581.75100
3.26-3.4120.10.1325290.9970.0310.1362.079100
3.41-3.5819.50.1115240.9980.0260.1142.418100
3.58-3.8119.50.0995170.9980.0230.1022.529100
3.81-4.118.10.0855300.9980.0210.0882.708100
4.1-4.5219.10.0755350.9980.0180.0772.824100
4.52-5.1719.40.0665310.9990.0150.0672.43499.6
5.17-6.5117.80.0625410.9990.0150.0642.199100
6.51-5017.20.0495880.9980.0120.051.939100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FT2

4ft2


Resolution: 2.404→24.849 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 35.94
RfactorNum. reflection% reflection
Rfree0.266 466 4.46 %
Rwork0.2185 --
obs0.2206 10440 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.92 Å2 / Biso mean: 90.7241 Å2 / Biso min: 47.89 Å2
Refinement stepCycle: final / Resolution: 2.404→24.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 8 3 1408
Biso mean--93.56 63.33 -
Num. residues----171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4043-2.75180.37061550.30053276
2.7518-3.46550.31631570.28263299
3.4655-24.80.23791540.1913399
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)
19.43254.1671.71082.85761.97875.55050.6437-0.6221.3090.452-0.5143-0.4884-0.4670.7103-0.22910.589-0.08290.03580.8584-0.0020.654629.652635.29944.4127
27.7874-0.59375.31535.7887-5.33417.97950.5489-0.4013-0.3461-0.3612-0.78660.7439-0.71480.10230.34280.64710.12560.13880.7120.02630.498222.684628.86322.2984
33.73913.0678-1.63153.70530.69475.4133-0.00910.0618-3.92020.33410.5947-0.86162.010.7686-0.66891.3530.1179-0.32621.1494-0.21721.341728.788911.55960.5524
44.82460.18894.6516.32861.40075.8604-0.137-1.02310.02090.2602-0.0389-0.1106-0.39770.12910.16090.41220.0380.08230.90380.01420.444127.847226.85898.3122
55.60071.2638-1.43378.4039-2.09554.52980.1943-0.4741-0.53210.2232-0.3533-0.545-0.0990.87050.20820.63190.1638-0.02510.91780.05580.579429.207321.37048.4205
64.56-0.10895.42032.8837-0.73688.51450.583-0.4284-1.14610.2850.15070.32351.6116-0.643-0.66610.89580.19530.0541.09740.27690.959217.99629.750514.203
70.14940.03971.14557.7969-3.38628.3422-0.0043-0.3737-0.2781-0.04670.20440.03380.25090.8816-0.14150.35130.0868-0.00430.7534-0.00250.522623.653223.77714.9559
83.22931.20072.22788.7036-4.0594.4718-0.5071-0.8688-0.8154-0.74580.31851.09721.0823-4.7470.10120.6627-0.061-0.15351.49080.19041.12583.226118.84848.5543
95.0741-6.33073.6819.3745-4.20862.7666-1.0139-1.282-1.31821.06251.61861.62060.2132-1.1651-0.52040.80170.08880.01810.9160.32210.847815.338415.123515.0657
103.6347-3.29580.83183.53880.01246.2197-0.5311-3.2055-1.96681.58450.98110.1390.2955-0.2457-0.30340.77030.07070.05441.01730.241.061320.833112.025723.1552
118.56095.2089-3.5968.88072.45025.33580.5129-1.8745-2.74562.4031.1155-0.00820.84251.2105-0.60271.17930.27860.1261.65660.56261.119215.800919.632727.2763
124.2887-4.24092.84455.0973-4.30764.2507-0.9926-2.86011.54360.43380.5603-0.4015-1.0782-1.53890.34130.86960.33650.03831.5260.05050.863814.75227.333119.7891
135.4794-0.20372.17889.7557-4.87933.1353-0.06220.53051.18180.2569-0.73390.0521-1.2244-1.33490.73011.17550.10610.08681.54030.22111.15890.530624.639712.7754
140.72570.61380.56234.23661.20750.53431.09090.58250.0688-1.46620.06030.86510.73421.1614-1.61820.8320.3673-0.06981.2252-0.03860.784933.154415.37819.3582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 119 through 126 )A119 - 126
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 139 )A127 - 139
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 148 )A140 - 148
4X-RAY DIFFRACTION4chain 'A' and (resid 149 through 158 )A149 - 158
5X-RAY DIFFRACTION5chain 'A' and (resid 159 through 176 )A159 - 176
6X-RAY DIFFRACTION6chain 'A' and (resid 177 through 198 )A177 - 198
7X-RAY DIFFRACTION7chain 'A' and (resid 199 through 215 )A199 - 215
8X-RAY DIFFRACTION8chain 'A' and (resid 216 through 230 )A216 - 230
9X-RAY DIFFRACTION9chain 'A' and (resid 231 through 238 )A231 - 238
10X-RAY DIFFRACTION10chain 'A' and (resid 239 through 246 )A239 - 246
11X-RAY DIFFRACTION11chain 'A' and (resid 247 through 253 )A247 - 253
12X-RAY DIFFRACTION12chain 'A' and (resid 254 through 268 )A254 - 268
13X-RAY DIFFRACTION13chain 'A' and (resid 269 through 277 )A269 - 277
14X-RAY DIFFRACTION14chain 'P' and (resid 22 through 33 )P22 - 33

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