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- PDB-7ef3: crystal structure of maize SHH2 SAWADEE domain in complex with H3... -

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Basic information

Entry
Database: PDB / ID: 7ef3
Titlecrystal structure of maize SHH2 SAWADEE domain in complex with H3K9me2 peptide
Components
  • HB transcription factor
  • Histone H3.2
KeywordsGENE REGULATION / SHH2 / maize / H3K9me2 / histone
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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A ...SAWADEE domain / Protein SAWADEE HOMEODOMAIN HOMOLOG 1/2 / SAWADEE domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
HB transcription factor / Histone H3.2
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)38,3146
Polymers38,1834
Non-polymers1312
Water1,802100
1
A: HB transcription factor
P: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1573
Polymers19,0922
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-2 kcal/mol
Surface area9370 Å2
MethodPISA
2
B: HB transcription factor
Q: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1573
Polymers19,0922
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-3 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.906, 67.370, 80.251
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: 1177.378 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 / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
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: Nov 2, 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: 2.1→50 Å / Num. obs: 21207 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.05 / Rrim(I) all: 0.116 / Χ2: 1 / Net I/σ(I): 5.1 / Num. measured all: 111652
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.184.90.7620900.7410.3740.850.48899.5
2.18-2.265.20.58620600.8460.2810.6520.52999.9
2.26-2.375.30.48920810.8910.2320.5430.549100
2.37-2.495.10.40321090.9090.1970.450.60799.9
2.49-2.655.40.29420790.9470.1390.3260.67899.6
2.65-2.855.60.22721130.970.1060.2510.781100
2.85-3.145.40.14621200.9850.0690.1621.0699.9
3.14-3.595.30.10321290.9890.0490.1141.56699.8
3.59-4.525.40.07621700.9920.0370.0851.908100
4.52-5050.06222560.9940.030.0691.7198.8

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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: 2.1→34.13 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 1083 5.14 %
Rwork0.2188 19982 -
obs0.2213 21065 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.31 Å2 / Biso mean: 47.0014 Å2 / Biso min: 22.34 Å2
Refinement stepCycle: final / Resolution: 2.1→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 2 100 2596
Biso mean--40.68 49.99 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022548
X-RAY DIFFRACTIONf_angle_d0.6393432
X-RAY DIFFRACTIONf_chiral_restr0.026360
X-RAY DIFFRACTIONf_plane_restr0.003456
X-RAY DIFFRACTIONf_dihedral_angle_d13.844960
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.19560.30511430.2716242599
2.1956-2.31130.26371420.25152454100
2.3113-2.45610.29191400.24922467100
2.4561-2.64570.36771240.25262462100
2.6457-2.91180.2851370.23182500100
2.9118-3.33280.25791340.21152513100
3.3328-4.19780.22511490.18832507100
4.1978-34.130.27561140.2174265499
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)
14.37154.6413-2.22235.0173-2.80526.6849-0.07570.0269-0.11030.27990.36540.0419-0.3593-1.1544-0.23610.4079-0.0038-0.02030.3945-0.01850.4153-21.194810.5487-14.3705
24.76250.39971.30892.55461.9885.1561-0.2631-0.26630.8305-0.445-0.08620.1078-0.29770.07230.06160.38860.0113-0.04470.28610.04950.4506-15.125720.251-17.541
37.1786-0.5413-0.11085.06391.48096.873-0.90981.17450.5149-0.01130.9108-0.6885-0.03490.7614-0.14240.6109-0.10990.00950.5844-0.07470.3567-12.375911.2256-31.9088
49.0522-2.1085-0.20188.44571.14164.22680.62580.09061.5028-0.9285-0.2901-0.3985-1.24220.12920.01450.6305-0.0240.03740.3640.03220.4023-19.779322.6917-23.3817
55.2987-0.72691.00165.1237-1.49189.6629-0.27470.1509-0.2814-0.17130.0689-0.09440.118-0.3120.15530.1897-0.0546-0.03640.1935-0.01420.31-15.201913.1367-15.7537
64.6134-1.57260.17484.3685-1.054.2324-0.2472-0.36210.04910.31270.1102-0.1658-0.50630.1044-0.12560.30.0318-0.04290.2666-0.09330.3321-10.509618.253-1.4832
74.7824-1.49040.20264.26620.32093.4347-1.4823-1.45671.08692.13170.71940.65250.2974-0.7775-0.11840.82440.20510.12570.6928-0.08740.5228-17.59317.58313.4893
85.35383.4596-0.37257.3664-4.8454.0863-0.10120.06630.37220.19460.1065-0.44720.03290.0209-0.10940.3280.0345-0.00090.263-0.03390.4199-4.035519.9902-1.7447
91.2364-0.76641.60584.21360.95035.0318-0.18760.03690.34720.17610.38-0.2405-0.40480.5410.15590.26460.00910.06640.4249-0.05880.3565-12.375418.73030.376
106.24730.599-1.30445.7563-1.43038.4328-0.5-0.553-0.62610.6513-0.12430.66810.8296-0.44810.23040.4692-0.03840.09670.43030.04930.5744-19.82190.4252.8686
116.60424.07291.98045.26110.74096.33490.07390.9938-1.3440.18080.3080.08140.6726-0.491-0.26290.5401-0.03930.09210.5093-0.01360.5061-8.8594-8.61254.9873
125.532.3559-2.42233.6928-1.93467.60630.1794-0.53510.22850.3163-0.4102-0.0991-0.60571.289-0.42460.4775-0.0538-0.05850.50320.08380.4097-0.6833-4.438115.0012
133.6742-0.11710.86045.74130.59737.64180.1474-0.2998-0.0833-0.3185-0.2485-1.39140.30632.05520.11270.56010.04680.03370.70050.11590.65642.888-12.545914.0062
142.7756-0.3474-0.11932.94-2.69836.6494-0.13010.1239-0.31360.0071-0.0356-0.21260.24710.27860.01610.2592-0.0070.0410.31630.00060.3692-2.8942-2.7439-0.9336
157.72861.21141.75851.3884-2.00784.73921.5346-0.045-0.5729-0.2457-0.112-1.84560.96981.6867-0.22830.48450.13290.19061.16450.07121.404615.5623-7.2123-2.9458
164.1059-0.69710.62564.50231.0147.2249-0.01140.5557-0.0612-0.8083-0.0367-0.0318-0.56760.49210.23080.4485-0.02910.00740.3061-0.08790.41363.34821.9522-6.9929
171.8818-2.2772-0.42788.88692.73266.933-0.01190.01940.0339-0.6968-0.14810.57490.1629-0.19580.31010.5413-0.03520.01660.5654-0.1020.4855-0.4677-5.8191-22.9895
186.20821.14773.83553.7054-0.65753.25730.20290.3125-0.30040.11510.2597-0.14040.21110.6204-0.31040.396-0.0280.05510.341-0.07630.37756.81314.4686-6.7173
197.14311.0092-2.43214.3289-0.13497.0188-0.12330.1794-0.3666-0.49230.1467-0.71640.31740.34010.29670.41380.00570.11740.4552-0.09990.43652.5238-2.7295-9.6332
206.2884-1.66452.09395.93940.49448.67430.09840.8689-1.3309-0.9973-0.28941.31080.675-1.5502-0.17630.5015-0.0373-0.03820.6466-0.12170.7667-16.8049-2.9102-11.6644
214.3622-1.9325-0.72887.6965-1.69342.93690.1924-1.06070.15270.15390.24430.3179-0.6022-0.1367-0.83550.4755-0.10210.01530.4503-0.03840.5804-20.730322.8514-6.616
227.06294.2415-4.46975.8398-2.81052.80891.1412-0.8357-1.6636-0.2234-0.8199-0.9389-0.66740.80791.29351.42070.34790.00561.01510.05450.839410.0901-11.98480.7818
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 163 )B140 - 163
13X-RAY DIFFRACTION13chain 'B' and (resid 164 through 177 )B164 - 177
14X-RAY DIFFRACTION14chain 'B' and (resid 178 through 211 )B178 - 211
15X-RAY DIFFRACTION15chain 'B' and (resid 212 through 217 )B212 - 217
16X-RAY DIFFRACTION16chain 'B' and (resid 218 through 228 )B218 - 228
17X-RAY DIFFRACTION17chain 'B' and (resid 229 through 239 )B229 - 239
18X-RAY DIFFRACTION18chain 'B' and (resid 240 through 250 )B240 - 250
19X-RAY DIFFRACTION19chain 'B' and (resid 251 through 262 )B251 - 262
20X-RAY DIFFRACTION20chain 'B' and (resid 263 through 277 )B263 - 277
21X-RAY DIFFRACTION21chain 'P' and (resid 2 through 8 )P2 - 8
22X-RAY DIFFRACTION22chain 'Q' and (resid 5 through 9 )Q5 - 9

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