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- PDB-4iut: crystal structure of SHH1 SAWADEE domain in complex with H3K9me2 ... -

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Basic information

Entry
Database: PDB / ID: 4iut
Titlecrystal structure of SHH1 SAWADEE domain in complex with H3K9me2 peptide
Components
  • Histone H3.2, H3(1-15)K9me3
  • SAWADEE HOMEODOMAIN HOMOLOG 1
KeywordsGENE REGULATION / tandem tudor / zinc finger / H3K9me2 / mediate interaction / histone / methylation
Function / homology
Function and homology information


chromocenter / regulatory ncRNA-mediated gene silencing / plastid / DNA methylation-dependent constitutive heterochromatin formation / structural constituent of chromatin / nucleosome / protein heterodimerization activity / chromatin binding / DNA binding / extracellular region ...chromocenter / regulatory ncRNA-mediated gene silencing / plastid / DNA methylation-dependent constitutive heterochromatin formation / structural constituent of chromatin / nucleosome / protein heterodimerization activity / chromatin binding / DNA binding / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
SAWADEE domain / Protein SAWADEE HOMEODOMAIN HOMOLOG 1/2 / SAWADEE domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / SH3 type barrels. - #140 / SH3 type barrels. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A ...SAWADEE domain / Protein SAWADEE HOMEODOMAIN HOMOLOG 1/2 / SAWADEE domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / SH3 type barrels. - #140 / 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
CYMAL-4 / Histone H3.1 / Protein SAWADEE HOMEODOMAIN HOMOLOG 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDu, J. / Patel, D.J.
CitationJournal: Nature / Year: 2013
Title: Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.
Authors: Law, J.A. / Du, J. / Hale, C.J. / Feng, S. / Krajewski, K. / Palanca, A.M. / Strahl, B.D. / Patel, D.J. / Jacobsen, S.E.
History
DepositionJan 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAWADEE HOMEODOMAIN HOMOLOG 1
B: SAWADEE HOMEODOMAIN HOMOLOG 1
C: Histone H3.2, H3(1-15)K9me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2467
Polymers33,1543
Non-polymers1,0924
Water1,40578
1
A: SAWADEE HOMEODOMAIN HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3273
Polymers15,7811
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SAWADEE HOMEODOMAIN HOMOLOG 1
C: Histone H3.2, H3(1-15)K9me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9194
Polymers17,3732
Non-polymers5462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-42 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.391, 56.706, 59.057
Angle α, β, γ (deg.)90.00, 93.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SAWADEE HOMEODOMAIN HOMOLOG 1 / Uncharacterized protein


Mass: 15780.645 Da / Num. of mol.: 2 / Fragment: SHH1 SAWADEE domain (unp residues 125-258)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g15215, F9L1.16 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9XI47
#2: Protein/peptide Histone H3.2, H3(1-15)K9me3


Mass: 1592.843 Da / Num. of mol.: 1 / Fragment: H3(1-15) K9me2 peptide (unp residues 2-16) / Source method: obtained synthetically / 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: Chemical ChemComp-CVM / CYMAL-4 / 4-CYCLOHEXYLBUTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE


Mass: 480.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H40O11
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2011
RadiationMonochromator: SI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 9812 / Num. obs: 9744 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 9.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.9 / Num. unique all: 964 / Rsym value: 0.56 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IUP

4iup


Resolution: 2.7→40.872 Å / SU ML: 0.81 / σ(F): 1.33 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 469 4.83 %RANDOM
Rwork0.202 ---
obs0.2043 9716 98.97 %-
all-10185 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.091 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1718 Å20 Å2-5.067 Å2
2--7.4669 Å20 Å2
3----4.2952 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 46 78 2379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082342
X-RAY DIFFRACTIONf_angle_d1.5383157
X-RAY DIFFRACTIONf_dihedral_angle_d14.88901
X-RAY DIFFRACTIONf_chiral_restr0.062343
X-RAY DIFFRACTIONf_plane_restr0.002410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7005-3.09110.32711610.26563020X-RAY DIFFRACTION99
3.0911-3.8940.24411470.20373096X-RAY DIFFRACTION99
3.894-40.87680.2141610.17313131X-RAY DIFFRACTION99
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)
11.53522.08021.68453.02951.38547.28260.0340.0645-0.33550.038-0.13040.01810.4760.31790.02680.12360.04450.02390.11650.05320.22585.6478-8.423422.8444
28.52121.086-5.1122.1994-0.37139.01260.29260.9290.5085-0.43820.29130.3941-0.1989-0.2298-0.37990.1779-0.0298-0.05730.20550.00760.240121.8774-3.050821.6402
32.04132.7632-3.51255.2522-2.85277.28710.08270.253-0.72830.06710.07150.17480.1522-0.1089-0.01070.22560.0157-0.05020.1506-0.0390.306613.9111-8.747825.4814
40.4051.1236-0.05913.1393-0.133-0.0055-0.069-0.1345-2.47130.72440.14370.40872.0585-0.2080.07630.63090.0211-0.0480.54780.01360.83479.4309-18.661227.8146
52.0707-2.56282.52913.2735-0.9843.60170.09690.26490.43680.0709-0.3570.16820.21810.33520.16280.15550.0057-0.02030.1337-0.04340.150610.5286-4.304520.387
65.42910.18881.57781.9174-1.17113.5934-0.18840.2227-0.0363-0.18440.10510.0330.3384-0.20250.01710.1649-0.07590.02060.1504-0.0030.0837-8.3792-8.052216.1374
74.8239-2.24740.19513.455-1.59854.03160.26880.4778-0.029-0.6463-0.13460.16110.35950.4004-0.19240.2657-0.0482-0.04510.0912-0.02370.1972-7.0651-8.153310.2441
83.97710.126-1.3263.7951-1.63456.49340.63280.2963-0.2264-0.44830.1810.57070.472-1.118-0.2367-0.3124-0.1992-0.06070.51910.15890.4029-23.3003-7.873816.8247
92.0013-4.15260.78716.48182.7395.90090.35630.84780.3148-0.67380.1955-0.22130.0566-0.0638-0.29510.3306-0.0383-0.08350.2298-0.00240.1813-9.0159-8.53927.0304
104.4103-0.8051-0.14482.3086-0.03523.90250.05860.4440.1209-0.30840.0983-0.06470.3078-0.0637-0.11860.2741-0.0051-0.02870.1580.04830.2172-6.443-8.026312.4414
115.7723-0.9626-1.80320.11170.28530.57210.0794-0.5914-0.36250.35950.1654-0.46530.40880.01830.0908-0.4047-0.30120.53980.4216-0.0556-0.05527.0115-32.339823.3703
123.2167-0.97983.84737.5454-5.11188.9485-0.02350.2810.1795-0.2696-0.02830.231-0.09990.61690.16180.1781-0.10440.03820.2451-0.06220.30933.263-29.191913.5849
130.96761.28380.43691.78070.4830.0131-0.11620.3024-0.0121-0.12890.0608-0.05660.1180.01110.10260.1802-0.06730.03730.17920.01830.201742.1743-23.579822.3051
146.97161.38221.8664.5812-1.24092.8097-0.14730.63770.22530.13290.0709-0.1456-0.03570.27650.01180.1678-0.05130.03680.2264-0.0030.122436.8146-29.203716.9437
153.98560.75141.64630.0830.31221.26250.1956-1.105-0.17890.1132-0.22750.49040.1429-0.61770.05280.2333-0.04270.0170.3588-0.09580.370312.4533-31.799115.898
167.1294-1.35120.35243.9530.35110.9471-0.01530.87970.0986-0.1556-0.1747-0.0449-0.2416-0.00060.03670.40350.0537-0.0720.3185-0.07380.227420.3631-27.38385.4937
178.7578-1.0724.87012.007-3.18673.32560.08310.2073-0.99610.1658-0.2970.36790.5693-0.09440.0750.2903-0.09560.02960.5556-0.21610.43573.9323-37.28898.2537
183.85480.56160.8392.6722-2.46824.1323-0.25620.10320.1222-0.10680.34830.2641-0.2012-0.07730.05430.3418-0.0183-0.08630.3505-0.12910.227117.0019-26.06967.8734
194.29870.4696-0.9860.79390.55851.6419-0.63210.9945-0.8003-0.8120.1341-0.02840.65660.07340.38680.45820.0470.0880.5126-0.12160.284328.1224-36.27056.415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 125:145)
2X-RAY DIFFRACTION2chain 'A' and (resseq 146:155)
3X-RAY DIFFRACTION3chain 'A' and (resseq 156:162)
4X-RAY DIFFRACTION4chain 'A' and (resseq 163:170)
5X-RAY DIFFRACTION5chain 'A' and (resseq 171:181)
6X-RAY DIFFRACTION6chain 'A' and (resseq 182:209)
7X-RAY DIFFRACTION7chain 'A' and (resseq 210:221)
8X-RAY DIFFRACTION8chain 'A' and (resseq 222:232)
9X-RAY DIFFRACTION9chain 'A' and (resseq 233:238)
10X-RAY DIFFRACTION10chain 'A' and (resseq 239:257)
11X-RAY DIFFRACTION11chain 'B' and (resseq 124:132)
12X-RAY DIFFRACTION12chain 'B' and (resseq 133:145)
13X-RAY DIFFRACTION13chain 'B' and (resseq 146:162)
14X-RAY DIFFRACTION14chain 'B' and (resseq 163:181)
15X-RAY DIFFRACTION15chain 'B' and (resseq 182:198)
16X-RAY DIFFRACTION16chain 'B' and (resseq 199:221)
17X-RAY DIFFRACTION17chain 'B' and (resseq 222:232)
18X-RAY DIFFRACTION18chain 'B' and (resseq 233:257)
19X-RAY DIFFRACTION19chain 'C'

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