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- PDB-4iur: crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 ... -

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Basic information

Entry
Database: PDB / ID: 4iur
Titlecrystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide
Components
  • Histone H3.2, H3(1-15)K9me3
  • SHH1 SAWADEE
KeywordsGENE REGULATION / tandem tudor / zinc finger / H3K9me3 / mediate interaction / histone / methylation
Function / homology
Function and homology information


chromocenter / DNA methylation-dependent heterochromatin formation / regulatory ncRNA-mediated gene silencing / plastid / : / structural constituent of chromatin / nucleosome / protein heterodimerization activity / chromatin binding / DNA binding ...chromocenter / DNA methylation-dependent heterochromatin formation / regulatory ncRNA-mediated gene silencing / plastid / : / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 ...SAWADEE domain / Protein SAWADEE HOMEODOMAIN HOMOLOG 1/2 / SAWADEE domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / SH3 type barrels. - #140 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / SH3 type barrels. / 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: 2.501 Å
AuthorsPatel, D.J. / Du, 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
B: SHH1 SAWADEE
C: Histone H3.2, H3(1-15)K9me3
A: SHH1 SAWADEE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2617
Polymers33,1693
Non-polymers1,0924
Water1,08160
1
B: SHH1 SAWADEE
C: Histone H3.2, H3(1-15)K9me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9344
Polymers17,3892
Non-polymers5462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-6 kcal/mol
Surface area8790 Å2
MethodPISA
2
A: SHH1 SAWADEE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3273
Polymers15,7811
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.341, 56.152, 58.936
Angle α, β, γ (deg.)90.00, 93.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SHH1 SAWADEE / 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: F9L1.16, At1g15215, AT1G15215 / 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: 1607.877 Da / Num. of mol.: 1 / Fragment: H3(1-15) K9me3 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 / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
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: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2011
RadiationMonochromator: SI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 12209 / Num. obs: 12197 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 32.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1202 / Rsym value: 0.541 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IUP

4iup


Resolution: 2.501→40.572 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 580 4.76 %RANDOM
Rwork0.2147 ---
obs0.2166 12173 99.75 %-
all-12753 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.138 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.9995 Å20 Å2-3.1421 Å2
2--12.1652 Å20 Å2
3----0.1657 Å2
Refinement stepCycle: LAST / Resolution: 2.501→40.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 46 60 2353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052334
X-RAY DIFFRACTIONf_angle_d0.9463148
X-RAY DIFFRACTIONf_dihedral_angle_d14.748898
X-RAY DIFFRACTIONf_chiral_restr0.063342
X-RAY DIFFRACTIONf_plane_restr0.003408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5009-2.75250.39541510.31152877X-RAY DIFFRACTION100
2.7525-3.15070.36621380.24582875X-RAY DIFFRACTION100
3.1507-3.9690.23931470.21342890X-RAY DIFFRACTION100
3.969-40.57710.19291440.18232951X-RAY DIFFRACTION100
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)
10.8339-0.5310.05920.53230.09420.11370.0303-0.25880.137-0.13110.0646-0.10740.12650.16650.11560.16610.06960.03160.21590.01690.1796-35.27351.9161-19.4214
20.65850.359-0.09790.3337-0.1640.2427-0.131-0.28320.00280.07930.06550.1721-0.04110.06420.04040.24030.0373-0.00870.2210.07250.2972-37.5655-0.1393-17.7361
30.3269-0.06370.34840.5728-0.24170.36740.0119-0.43980.03470.2264-0.2838-0.572-0.20540.2859-0.08640.21050.0252-0.12370.54780.2145-0.0336-17.3512-1.9753-10.5338
40.24360.3087-0.10580.7031-0.2160.15130.026-0.2526-0.2220.1507-0.0089-0.1595-0.04170.30170.09930.3462-0.0682-0.01960.48310.110.2866-16.7993.3712-7.6901
50.03920.1228-0.09220.4216-0.29920.21640.0491-0.1092-0.06340.0774-0.1722-0.3821-0.01660.25770.19060.37650.01040.010.78750.22960.616-4.1766-8.5861-8.6128
60.24530.06690.23360.1586-0.07140.4487-0.0884-0.27630.15230.2917-0.1011-0.0514-0.07430.12170.1070.2752-0.0385-0.06420.52020.09240.2598-17.05752.6711-7.0739
71.7419-0.0047-0.21421.24750.46221.5138-0.06410.19430.28070.0558-0.1272-0.120.46730.05310.08630.30150.0085-0.10280.48280.02770.3609-28.0571-7.439-6.3475
80.1816-0.2070.24530.3569-0.19460.4550.1112-0.0762-0.0898-0.0787-0.2896-0.12220.0820.01850.09670.1893-0.06240.01250.28160.0220.3313-5.5520.3884-22.8286
90.6361-0.5370.32550.88360.51481.61530.1474-0.3224-0.1225-0.06820.1237-0.194-0.1648-0.3526-0.02910.11520.00660.0090.13890.02490.2335-18.515623.274-23.1103
100.45270.10390.08610.13380.34951.0036-0.17910.0568-0.233-0.24370.0076-0.45340.46940.02620.16740.5855-0.02410.12630.4292-0.03190.9653-10.186610.1468-27.9292
110.9252-0.08580.21160.13130.21790.4043-0.2748-0.28780.20230.03150.1946-0.00440.17210.0602-0.00320.24550.0060.00260.25730.01930.17312.784122.3807-17.4877
121.4185-0.03690.12530.52690.21070.1527-0.0963-0.41060.01240.2817-0.04170.19160.1798-0.17550.04750.28540.04160.01610.2503-0.03860.19476.343519.5588-10.4307
132.2616-0.7109-0.98560.5160.75551.2107-0.0363-0.99030.02190.1720.1739-0.15780.41650.6226-0.05730.2120.0173-0.03450.3681-0.02110.23311.869720.8931-12.6593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 124:155)
2X-RAY DIFFRACTION2chain 'B' and (resseq 156:181)
3X-RAY DIFFRACTION3chain 'B' and (resseq 182:209)
4X-RAY DIFFRACTION4chain 'B' and (resseq 210:221)
5X-RAY DIFFRACTION5chain 'B' and (resseq 222:232)
6X-RAY DIFFRACTION6chain 'B' and (resseq 233:256)
7X-RAY DIFFRACTION7chain 'C'
8X-RAY DIFFRACTION8chain 'A' and (resseq 125:145)
9X-RAY DIFFRACTION9chain 'A' and (resseq 146:162)
10X-RAY DIFFRACTION10chain 'A' and (resseq 163:170)
11X-RAY DIFFRACTION11chain 'A' and (resseq 171:208)
12X-RAY DIFFRACTION12chain 'A' and (resseq 209:221)
13X-RAY DIFFRACTION13chain 'A' and (resseq 222:257)

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