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- PDB-3h6z: Crystal Structure of the Four MBT Repeats of Drosophila melanogas... -

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Basic information

Entry
Database: PDB / ID: 3h6z
TitleCrystal Structure of the Four MBT Repeats of Drosophila melanogaster Sfmbt in Complex with Peptide RHR (me)K VLR
Components
  • 'HR(MLZ)VLR
  • Polycomb protein Sfmbt
KeywordsTRANSCRIPTION / MBT / MBR repeat / aromatic cage / Chromatin regulator / DNA-binding / Metal-binding / Nucleus / Repressor / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


Transcriptional Regulation by E2F6 / imaginal disc growth / SUMOylation of chromatin organization proteins / PcG protein complex / oogenesis / heterochromatin formation / methylated histone binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding ...Transcriptional Regulation by E2F6 / imaginal disc growth / SUMOylation of chromatin organization proteins / PcG protein complex / oogenesis / heterochromatin formation / methylated histone binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Sfmbt, SAM domain / : / : / : / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. ...Sfmbt, SAM domain / : / : / : / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SH3 type barrels. - #140 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
sucrose / Polycomb protein Sfmbt
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGrimm, C. / Mueller, C.W.
CitationJournal: Embo J. / Year: 2009
Title: Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt
Authors: Grimm, C. / Matos, R. / Ly-Hartig, N. / Steuerwald, U. / Lindner, D. / Rybin, V. / Muller, J. / Muller, C.W.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 28, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / reflns / struct_conn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 16, 2019Group: Data collection / Refinement description / Category: refine / reflns / reflns_shell
Item: _refine.ls_number_reflns_all / _reflns.B_iso_Wilson_estimate ..._refine.ls_number_reflns_all / _reflns.B_iso_Wilson_estimate / _reflns.pdbx_redundancy / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.pdbx_redundancy
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycomb protein Sfmbt
L: 'HR(MLZ)VLR
B: Polycomb protein Sfmbt
M: 'HR(MLZ)VLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7538
Polymers102,3844
Non-polymers1,3694
Water1,17165
1
A: Polycomb protein Sfmbt
L: 'HR(MLZ)VLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8764
Polymers51,1922
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-1 kcal/mol
Surface area21430 Å2
MethodPISA
2
B: Polycomb protein Sfmbt
M: 'HR(MLZ)VLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8764
Polymers51,1922
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-1 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.800, 97.040, 214.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Polycomb protein Sfmbt / Scm-like with four MBT domain-containing protein 1 / dSfmbt


Mass: 50366.723 Da / Num. of mol.: 2 / Fragment: UNP residues 535-977 / Mutation: K185D, R356S, R370D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sfmbt / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9VK33
#2: Protein/peptide 'HR(MLZ)VLR


Mass: 825.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Peptide synthesis / Source: (synth.) synthetic construct (others)
#3: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.59 Å3/Da / Density % sol: 65.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 3.7M NaCl, pH7, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2007
RadiationMonochromator: ESRF ID14-4 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 37129 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.137 / Net I/σ(I): 12.3
Reflection shellResolution: 2.8→3 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.551 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0065refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.46 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 1 / SU B: 28.518 / SU ML: 0.258 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.646 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1884 5.1 %RANDOM
Rwork0.221 ---
obs0.223 35240 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.44 Å2 / Biso mean: 37.931 Å2 / Biso min: 19.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.77 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6958 0 92 65 7115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227254
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9549876
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30223.626342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.798151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9151542
X-RAY DIFFRACTIONr_chiral_restr0.0920.21068
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215556
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3571.54348
X-RAY DIFFRACTIONr_mcangle_it0.68127018
X-RAY DIFFRACTIONr_scbond_it0.80532906
X-RAY DIFFRACTIONr_scangle_it1.3364.52858
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 133 -
Rwork0.326 2522 -
all-2655 -
obs--99.59 %
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)
15.2574-2.1043.40843.55080.33738.2616-0.1833-0.37310.50660.07590.1044-0.278-0.6927-0.12870.0789-0.1685-0.12910.0958-0.1278-0.0374-0.010634.982640.506142.1275
21.915-0.7041-3.86982.41243.853810.56440.07190.04430.1417-0.2863-0.24180.2712-0.2174-0.46420.1699-0.08460.0043-0.0013-0.002-0.02370.06419.886140.615948.6745
34.99-0.5365-2.78530.50041.7736.45940.1943-0.65470.3588-0.2048-0.1070.0129-0.74450.7854-0.0873-0.0213-0.08830.07220.0785-0.10940.036927.143845.103157.4147
46.3173.6201-1.57452.4831-2.56077.1250.0427-0.5306-0.13590.2844-0.1357-0.26170.24170.35610.0931-0.17920.021-0.0249-0.0026-0.15920.104422.361340.15464.4392
50.8909-1.4065-3.08852.22054.87610.7069-0.26630.114-0.10370.3557-0.10280.42560.2675-0.24180.3691-0.0249-0.0670.04220.1626-0.05880.111117.265936.199650.5018
61.85190.36880.70161.98020.874.40640.1638-0.1547-0.0663-0.00180.0123-0.27680.35950.2276-0.176-0.0817-0.0514-0.0266-0.10540.006-0.022533.909116.942425.6369
74.29971.6073-0.10852.9040.36954.67320.02610.1976-0.0517-0.2548-0.11510.16460.196-0.19280.089-0.0713-0.10750.0084-0.0757-0.0019-0.096223.008613.322117.1605
82.98551.64440.23498.4552-1.67558.27010.00540.5130.1525-0.06050.22970.3601-0.1383-0.152-0.2351-0.14770.0110.0794-0.07230.0886-0.083535.327433.404910.2798
95.14274.56560.17096.752-1.24691.9822-0.12580.2316-0.1481-0.24160.0894-0.24040.1490.26010.0364-0.0921-0.01050.0324-0.01190.0934-0.114936.406431.918210.1737
102.9867-0.175-2.30722.0628-1.26727.2332-0.00970.65440.2804-0.2258-0.1742-0.0251-0.2928-0.38760.1839-0.0863-0.0157-0.056-0.06030.06680.004334.744941.96798.8403
110.90810.2551.4732.9868-0.71132.92410.21910.16160.2018-0.2901-0.1827-0.2014-0.09680.2504-0.0364-0.1072-0.06030.0396-0.0479-0.0308-0.038438.323438.177229.8467
1210.09741.7197-1.57432.5102-1.27932.15570.289-0.19390.29390.2894-0.12810.00280.1760.0505-0.1609-0.0821-0.0431-0.0213-0.0576-0.01-0.073939.828432.372541.8791
134.3182-0.4655-2.83193.7167-0.31289.21330.078-0.3578-0.5774-0.0602-0.17380.05940.7279-0.08860.0958-0.1617-0.1232-0.1096-0.09170.0684-0.02010.5967-22.560338.0593
141.4348-0.06853.02773.0774-3.589110.24850.09150.1696-0.1226-0.3044-0.2608-0.20230.54210.58920.1694-0.09150.0078-0.0144-0.0352-0.00130.037815.6117-22.659844.7797
154.568-1.97832.80341.6729-1.77583.95870.1588-0.4236-0.3328-0.2070.126-0.00731.0388-0.5634-0.2849-0.0321-0.0478-0.09640.0260.12450.038.3078-27.426153.3334
164.83292.08742.55053.56742.42196.3338-0.0124-0.240.17510.4852-0.035-0.0272-0.0711-0.32180.0474-0.17850.0267-0.0063-0.07450.07090.019112.9427-22.568560.5101
170.7933-1.41062.9072.5082-5.16910.6525-0.2970.10240.16760.190.0001-0.3896-0.20780.08340.2969-0.1-0.0601-0.04660.10490.00940.080918.1601-18.252646.7464
181.29590.4555-0.7192.6858-2.26967.2376-0.0755-0.15510.0723-0.04720.13930.305-0.3351-0.4222-0.0638-0.0815-0.0421-0.011-0.1166-0.0081-0.03731.57971.418322.1659
192.4567-0.02751.01855.648-1.04842.71770.12040.07540.0257-0.1811-0.1703-0.4669-0.26040.11910.0499-0.0661-0.12920.0426-0.0282-0.0179-0.103912.6665.4214.2212
201.98411.9941-3.8554.9954-0.966710.3163-0.12780.065-0.4080.01830.0504-0.20370.1412-0.08430.0774-0.0906-0.0252-0.0758-0.0470.0031-0.05860.7811-14.52546.4992
215.92685.0343-0.88217.45880.53913.798-0.19960.22320.2188-0.42130.12820.39460.0222-0.47240.0714-0.0321-0.1032-0.00520.0567-0.0541-0.1947-0.6184-13.30016.2737
222.5353-0.65073.0910.167-0.78279.8348-0.12040.4708-0.41290.00540.10160.09880.51470.05960.01890.0638-0.0769-0.009-0.0892-0.02340.03791.2494-23.22324.7419
231.9171-1.3079-1.7482.60861.11894.17070.10080.1709-0.1682-0.2448-0.04420.13250.2201-0.4108-0.0566-0.0883-0.121-0.037-0.02440.0597-0.0759-2.6251-19.977525.796
249.9211-0.30872.51440.82141.14154.75150.1166-0.1398-0.19430.3371-0.1343-0.021-0.09890.04080.0177-0.0504-0.091-0.0069-0.14010.0159-0.1333-4.3308-14.476437.95
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A531 - 559
2X-RAY DIFFRACTION2A560 - 576
3X-RAY DIFFRACTION3A593 - 621
4X-RAY DIFFRACTION4A622 - 659
5X-RAY DIFFRACTION5A660 - 686
6X-RAY DIFFRACTION6A687 - 747
7X-RAY DIFFRACTION7A748 - 794
8X-RAY DIFFRACTION8A795 - 817
9X-RAY DIFFRACTION9A818 - 873
10X-RAY DIFFRACTION10A874 - 908
11X-RAY DIFFRACTION11A909 - 963
12X-RAY DIFFRACTION12A964 - 977
13X-RAY DIFFRACTION13B531 - 559
14X-RAY DIFFRACTION14B560 - 576
15X-RAY DIFFRACTION15B593 - 621
16X-RAY DIFFRACTION16B622 - 659
17X-RAY DIFFRACTION17B660 - 686
18X-RAY DIFFRACTION18B687 - 747
19X-RAY DIFFRACTION19B748 - 794
20X-RAY DIFFRACTION20B795 - 816
21X-RAY DIFFRACTION21B817 - 873
22X-RAY DIFFRACTION22B874 - 908
23X-RAY DIFFRACTION23B909 - 963
24X-RAY DIFFRACTION24B964 - 977

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