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- PDB-4iuu: Crystal structure of SHH1 SAWADEE domain in complex with H3K9me1 ... -

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Basic information

Entry
Database: PDB / ID: 4iuu
TitleCrystal structure of SHH1 SAWADEE domain in complex with H3K9me1 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 / : / 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: 2.7 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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)34,2327
Polymers33,1403
Non-polymers1,0924
Water97354
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
2
B: SAWADEE HOMEODOMAIN HOMOLOG 1
C: Histone H3.2, H3(1-15)K9me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9054
Polymers17,3592
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-40 kcal/mol
Surface area8860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.759, 118.108, 53.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 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: 1578.816 Da / Num. of mol.: 1 / Fragment: H3(1-15) K9me1 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.: 54 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
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: 10093 / Num. obs: 10043 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 14.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / Num. unique all: 976 / Rsym value: 0.41 / % possible all: 100

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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→48.675 Å / SU ML: 0.76 / σ(F): 1.37 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 483 4.84 %RANDOM
Rwork0.2028 ---
obs0.2059 9971 99.48 %-
all-10454 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.023 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.7725 Å20 Å20 Å2
2---0.3004 Å20 Å2
3----6.4722 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 57 54 2309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042293
X-RAY DIFFRACTIONf_angle_d0.7343089
X-RAY DIFFRACTIONf_dihedral_angle_d16.044886
X-RAY DIFFRACTIONf_chiral_restr0.046342
X-RAY DIFFRACTIONf_plane_restr0.003396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-3.09080.3291720.2563088X-RAY DIFFRACTION100
3.0908-3.89390.27971550.20223147X-RAY DIFFRACTION100
3.8939-48.68310.2351560.18443253X-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)
15.47295.05151.97132.27163.65015.64820.4078-0.0693-0.24560.5593-0.1556-0.42320.2289-0.1217-0.07980.24810.0053-0.02940.2352-0.05240.1805-35.0612-21.10397.2532
22.53160.811-0.00232.8683-2.65334.5264-0.30550.3995-0.33990.1244-0.1769-0.59680.05341.04910.10560.1977-0.0959-0.07280.2065-0.01270.2394-33.6978-24.98787.6545
31.83111.1402-0.07032.65073.91378.44420.18870.04020.03230.6127-0.64160.4826-0.1443-0.86670.29330.27060.02410.00510.2272-0.020.215-40.2125-21.380923.9441
44.7163-0.91720.17095.2719-0.28896.23120.2978-0.3856-0.31260.6388-0.6903-1.18730.02750.43150.29780.10690.00810.02050.37390.02390.2554-32.7194-25.836314.5968
54.1643-0.25742.19654.9343-2.35042.1063-0.12220.1765-0.06880.1819-0.2310.3524-0.20950.26030.32460.2174-0.0078-0.01150.2640.010.2108-38.9318-20.286812.561
62.0801-3.43482.55371.9889-9.45832.0117-0.0740.9689-0.5681-1.00780.12220.82930.3988-0.2116-0.0390.22990.013-0.00350.1952-0.01930.2697-38.2891-23.5391-6.3937
72.7995-2.5478-1.80462.92090.24934.2102-0.1472-0.03240.0593-0.159-0.003-0.1316-0.2707-0.29630.14810.3192-0.04160.02450.12530.02980.2776-35.2907-13.8528-6.9127
82.1665-0.7221.74851.97450.50173.91520.06360.2510.2931-0.4072-0.36680.16580.13730.23950.17260.3331-0.02090.0650.20630.05310.2826-35.5771-13.1754-13.079
94.283-0.88764.46042.13911.20452.04710.0671-0.52080.48580.7391-0.14660.4574-0.52550.12530.53540.5613-0.02080.06930.2438-0.02960.3129-34.4974-5.635-2.9461
103.82561.303-0.69297.8758-0.48856.30720.4441-0.05410.0792-0.7848-0.43120.2906-0.1478-0.3871-0.09910.20540.0394-0.04030.2149-0.0370.1216-36.092-14.8457-7.1191
112.76840.8439-2.13392.6382-2.184.04550.0046-0.05950.2693-0.00250.0205-0.2183-0.15770.199-0.07450.22130.00240.00730.2041-0.04940.2428-14.425-18.333138.4344
122.9874-1.22361.20412.6346-1.60092.9739-0.05440.6397-0.2263-0.5886-0.0878-0.21020.3576-0.0260.1760.2961-0.05090.06980.3516-0.00060.3043-14.6724-17.344822.8088
134.2469-0.1507-0.39114.02631.15593.6004-0.12930.2550.4438-0.4762-0.0489-0.2122-1.3817-0.3936-0.00920.51260.03540.10250.25270.06530.3647-14.8765-5.019622.1598
146.5732-1.5414-2.44082.22842.82326.2592-0.11260.77720.0067-0.7887-0.0461-0.2481-0.12150.08510.05230.63430.00340.18440.46350.15860.5063-13.5876-5.170613.6243
155.8276-4.2258-1.32393.12670.42742.1933-0.22260.9362-0.305-0.9858-0.1215-0.98640.36340.43760.23130.59440.04720.10550.59280.0820.3345-11.3329-14.023818.1479
163.80160.4047-1.49988.17393.97891.9973-0.28230.11420.2071-0.28490.4999-1.2214-0.69620.822-0.64490.45020.2216-0.08080.4935-0.11930.6193-6.1016-6.847129.7914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 125:138)
2X-RAY DIFFRACTION2chain 'A' and (resseq 139:145)
3X-RAY DIFFRACTION3chain 'A' and (resseq 146:155)
4X-RAY DIFFRACTION4chain 'A' and (resseq 156:170)
5X-RAY DIFFRACTION5chain 'A' and (resseq 171:181)
6X-RAY DIFFRACTION6chain 'A' and (resseq 182:187)
7X-RAY DIFFRACTION7chain 'A' and (resseq 188:209)
8X-RAY DIFFRACTION8chain 'A' and (resseq 210:232)
9X-RAY DIFFRACTION9chain 'A' and (resseq 233:243)
10X-RAY DIFFRACTION10chain 'A' and (resseq 244:257)
11X-RAY DIFFRACTION11chain 'B' and (resseq 124:170)
12X-RAY DIFFRACTION12chain 'B' and (resseq 171:198)
13X-RAY DIFFRACTION13chain 'B' and (resseq 199:221)
14X-RAY DIFFRACTION14chain 'B' and (resseq 222:248)
15X-RAY DIFFRACTION15chain 'B' and (resseq 249:257)
16X-RAY DIFFRACTION16chain 'C'

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