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- PDB-7ef1: crystal structure of maize SHH2 SAWADEE domain in complex with an... -

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Basic information

Entry
Database: PDB / ID: 7ef1
Titlecrystal structure of maize SHH2 SAWADEE domain in complex with and H3K9me1 peptide
Components
  • HB transcription factor
  • Histone H3.2
KeywordsGENE REGULATION / SAWADEE domain / Maize / SHH2
Function / homology
Function and homology information


chromocenter / structural constituent of chromatin / nucleosome / protein heterodimerization activity / chromatin binding / DNA binding / metal ion binding / nucleus
Similarity search - Function
SAWADEE domain / Protein SAWADEE HOMEODOMAIN HOMOLOG 1/2 / SAWADEE domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / SH3 type barrels. - #140 / Homeobox-like domain superfamily / SH3 type barrels. ...SAWADEE domain / Protein SAWADEE HOMEODOMAIN HOMOLOG 1/2 / SAWADEE domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / SH3 type barrels. - #140 / Homeobox-like domain superfamily / SH3 type barrels. / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
HB transcription factor / Histone H3.2
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, Y. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770782 China
CitationJournal: J Integr Plant Biol / Year: 2021
Title: Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2.
Authors: Wang, Y. / Zhou, X. / Luo, J. / Lv, S. / Liu, R. / Du, X. / Jia, B. / Yuan, F. / Zhang, H. / Du, J.
History
DepositionMar 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: 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: HB transcription factor
B: HB transcription factor
P: Histone H3.2
Q: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2866
Polymers38,1554
Non-polymers1312
Water4,216234
1
A: HB transcription factor
P: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1433
Polymers19,0782
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint0 kcal/mol
Surface area9410 Å2
MethodPISA
2
B: HB transcription factor
Q: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1433
Polymers19,0782
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-5 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.821, 68.563, 80.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HB transcription factor / Protein SAWADEE HOMEODOMAIN HOMOLOG 2


Mass: 17914.150 Da / Num. of mol.: 2 / Mutation: R235G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100279552, HB131, ZEAMMB73_Zm00001d005584 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7ZYP9
#2: Protein/peptide Histone H3.2


Mass: 1163.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize) / References: UniProt: P69246
#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.: 234 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH7.5, 70% MPD

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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: Jun 28, 2015
RadiationMonochromator: silicon crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 29252 / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.055 / Rrim(I) all: 0.116 / Χ2: 1.043 / Net I/σ(I): 7.4 / Num. measured all: 116568
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.973.90.75728830.7410.4210.8690.77199.5
1.97-2.0540.59328620.8310.320.6760.84699.3
2.05-2.144.10.46928730.8790.2480.5320.86299.4
2.14-2.2540.34128920.9340.1810.3880.93299.8
2.25-2.394.10.26328770.9620.140.2990.95199.6
2.39-2.5840.20529090.9710.110.2331.00699.8
2.58-2.8440.14929420.980.0810.171.21599.9
2.84-3.2540.0929580.9930.050.1031.33100
3.25-4.093.90.04629510.9980.0260.0531.27499
4.09-503.90.03431050.9980.0190.041.22799.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EEZ

7eez


Resolution: 1.9→34.863 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 1476 5.09 %
Rwork0.1912 27505 -
obs0.193 28981 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.44 Å2 / Biso mean: 32.5679 Å2 / Biso min: 12.66 Å2
Refinement stepCycle: final / Resolution: 1.9→34.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 2 234 2714
Biso mean--26.36 38.91 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052525
X-RAY DIFFRACTIONf_angle_d0.8773399
X-RAY DIFFRACTIONf_chiral_restr0.034358
X-RAY DIFFRACTIONf_plane_restr0.003451
X-RAY DIFFRACTIONf_dihedral_angle_d13.941953
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.96130.23311130.2157248399
1.9613-2.03140.22651490.207242699
2.0314-2.11270.22641470.20432425100
2.1127-2.20890.23361430.20082486100
2.2089-2.32530.22011240.18382479100
2.3253-2.4710.22461260.19062496100
2.471-2.66170.22741460.19572468100
2.6617-2.92940.22131300.19352518100
2.9294-3.3530.25121430.19032516100
3.353-4.22330.19591230.1673253399
4.2233-34.8630.23361320.2001267599
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)
13.57114.406-1.36095.5862-2.16726.42740.4510.08230.07820.4441-0.09190.39780.1716-0.4351-0.33530.2649-0.0097-0.02780.2212-0.00730.2558-21.416810.4273-14.566
26.15532.44652.02182.29072.29935.15940.21930.00660.4003-0.1426-0.32340.0893-0.2531-0.14660.02420.20890.0356-0.01710.11550.0330.2003-15.241820.2432-17.8686
33.88471.08810.69585.14191.49646.5945-0.03430.5806-0.2365-0.29830.5048-0.87170.03190.7711-0.26450.2744-0.04340.00710.3076-0.11710.2526-12.259210.5333-31.958
43.4795-0.03850.16766.93841.22365.06340.31460.24890.6267-0.8245-0.33530.0102-1.0542-0.6242-0.00140.37610.0691-0.04270.25240.00160.2142-19.699322.4316-23.5541
53.783-0.20960.02331.9645-1.22222.0941-0.04160.0323-0.0994-0.17930.04080.04490.2051-0.1960.02550.1585-0.0098-0.02460.1344-0.00340.163-15.199113.1714-15.7726
63.8157-1.21420.36772.8371-0.97494.0049-0.1727-0.17910.19940.15850.0407-0.0202-0.329-0.01110.09590.14870.0083-0.02250.1476-0.04960.1484-10.506118.616-1.7203
76.30642.2351-0.59261.1564-1.71996.7861-0.5211-1.33951.03851.35830.6860.5949-0.2366-0.3969-0.01950.50270.09460.09640.4361-0.03660.3508-17.154618.016913.4689
84.75911.452-2.5724.9108-1.82927.15450.0103-0.43240.54370.1258-0.0514-0.1964-0.28420.39550.09470.12940.003-0.0450.1522-0.03820.2048-3.793520.3943-2.036
91.45280.84890.55043.32732.08233.8104-0.0405-0.02290.15460.15760.1041-0.172-0.18740.0835-0.05940.17210.0522-0.00140.1705-0.02130.1906-12.328119.18640.1364
105.50875.0124-5.21226.8372-5.04188.5150.1593-0.053-0.26980.70820.31960.7394-0.1461-0.7382-0.37760.2343-0.00820.05120.28060.07720.3288-19.69030.88713.1207
119.21188.29132.12869.14981.68794.55930.13220.0969-0.5166-0.2033-0.13150.02910.3126-0.19240.15030.2142-0.00530.02390.3010.04970.2272-8.9862-8.21525.1225
124.61853.077-2.2993.4197-2.32885.6077-0.0388-0.4946-0.17990.0741-0.2916-0.25150.06160.87180.13380.17930.05240.02340.32550.07220.21352.4501-6.93848.4988
135.3250.9593-1.77673.7231-1.02757.53430.3512-0.35070.51320.2614-0.3061-0.5533-0.0671.0721-0.15610.1906-0.03270.01990.40360.07960.2718-0.2478-7.388217.6962
143.03740.44922.08121.9109-1.69067.61280.0752-0.2753-0.11440.0257-0.0002-0.0307-0.1576-0.0856-0.07920.1379-0.00450.0360.21140.02530.226-3.7899-3.93356.6104
154.26650.2415-0.31213.58450.56323.1268-0.0187-0.0841-0.3296-0.2451-0.043-0.22430.03550.55810.02130.14970.00460.06730.2158-0.00250.18872.8128-0.8441-7.3777
164.4807-0.96861.4083.34844.8989.07680.36750.6803-0.3756-0.8694-0.5874-0.0628-0.3751-0.16150.11160.37010.03260.02970.2892-0.0860.2735-0.0424-5.8242-23.013
173.91570.3220.6932.46860.56734.0707-0.18740.1781-0.087-0.35760.2955-0.3012-0.10610.3962-0.12160.1682-0.02040.06850.1545-0.05420.19725.30191.0335-8.5336
182.5369-0.94812.14038.1939-1.45293.99550.16810.3807-0.5226-0.59760.01021.19360.4063-1.0461-0.27690.2321-0.0554-0.03050.3466-0.05030.3569-13.8402-1.1031-8.1172
197.17641.4091-2.59957.7121-4.63883.43090.5007-0.82570.11240.71750.01331.2033-0.38310.294-0.40290.3635-0.03710.01690.2509-0.00490.3554-19.129725.064-8.8026
202.32340.37280.28367.49890.17252.8526-0.23270.451-1.5905-1.13410.239-0.87450.3961.41-0.0990.42060.08870.1160.4413-0.0180.53295.4642-12.4818-2.5644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 131 through 139 )A131 - 139
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 152 )A140 - 152
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 163 )A153 - 163
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 177 )A164 - 177
5X-RAY DIFFRACTION5chain 'A' and (resid 178 through 194 )A178 - 194
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 228 )A195 - 228
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 239 )A229 - 239
8X-RAY DIFFRACTION8chain 'A' and (resid 240 through 250 )A240 - 250
9X-RAY DIFFRACTION9chain 'A' and (resid 251 through 262 )A251 - 262
10X-RAY DIFFRACTION10chain 'A' and (resid 263 through 278 )A263 - 278
11X-RAY DIFFRACTION11chain 'B' and (resid 131 through 139 )B131 - 139
12X-RAY DIFFRACTION12chain 'B' and (resid 140 through 152 )B140 - 152
13X-RAY DIFFRACTION13chain 'B' and (resid 153 through 177 )B153 - 177
14X-RAY DIFFRACTION14chain 'B' and (resid 178 through 194 )B178 - 194
15X-RAY DIFFRACTION15chain 'B' and (resid 195 through 228 )B195 - 228
16X-RAY DIFFRACTION16chain 'B' and (resid 229 through 239 )B229 - 239
17X-RAY DIFFRACTION17chain 'B' and (resid 240 through 261 )B240 - 261
18X-RAY DIFFRACTION18chain 'B' and (resid 262 through 272 )B262 - 272
19X-RAY DIFFRACTION19chain 'P' and (resid 2 through 10 )P2 - 10
20X-RAY DIFFRACTION20chain 'Q' and (resid 3 through 8 )Q3 - 8

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