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- PDB-2r5m: Crystal Structure of the two MBT repeats from Sex-Comb on Midleg ... -

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Basic information

Entry
Database: PDB / ID: 2r5m
TitleCrystal Structure of the two MBT repeats from Sex-Comb on Midleg (SCM) in complex with peptide R-(me)K-S
Components
  • Polycomb protein Scm
  • peptide R(me)KS
KeywordsTRANSCRIPTION / MBT repeat / Polycomb / Sex Comb on Midleg / Chromatin regulator / Developmental protein / Metal-binding / Nucleus / Repressor / Transcription regulation
Function / homology
Function and homology information


PRC1 complex binding / germarium-derived female germ-line cyst encapsulation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / follicle cell of egg chamber stalk formation / compound eye development / Oxidative Stress Induced Senescence ...PRC1 complex binding / germarium-derived female germ-line cyst encapsulation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / follicle cell of egg chamber stalk formation / compound eye development / Oxidative Stress Induced Senescence / ventral cord development / polytene chromosome / negative regulation of growth / anterior/posterior axis specification / heterochromatin formation / axonogenesis / neurogenesis / histone binding / sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / zinc ion binding / identical protein binding / nucleus
Similarity search - Function
Zinc finger, MYM-type / MYM-type Zinc finger with FCS sequence motif / : / SLED domain / SLED domain superfamily / SLED domain / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. ...Zinc finger, MYM-type / MYM-type Zinc finger with FCS sequence motif / : / SLED domain / SLED domain superfamily / SLED domain / 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
Polycomb protein Scm
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGrimm, C. / Steuerwald, U. / Mueller, C.W.
CitationJournal: Embo Rep. / Year: 2007
Title: Structural and functional analyses of methyl-lysine binding by the malignant brain tumour repeat protein Sex comb on midleg.
Authors: Grimm, C. / de Ayala Alonso, A.G. / Rybin, V. / Steuerwald, U. / Ly-Hartig, N. / Fischle, W. / Muller, J. / Muller, C.W.
History
DepositionSep 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 Scm
L: peptide R(me)KS


Theoretical massNumber of molelcules
Total (without water)29,8032
Polymers29,8032
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.710, 82.710, 76.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-466-

HOH

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Components

#1: Protein Polycomb protein Scm / Sex comb on midleg protein


Mass: 29398.307 Da / Num. of mol.: 1 / Fragment: UNP residues:175-435 / Mutation: R277C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Scm / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VHA0
#2: Protein/peptide peptide R(me)KS


Mass: 404.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.3
Details: 15% (w/v) PEG3350, 100 mM calcium acetate and 3% ethanol, pH 7.3, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. all: 0 / Num. obs: 9984 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 4.1
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1112 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 21.99 / SU ML: 0.247 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 2.357 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24467 377 4.8 %RANDOM
Rwork0.16942 ---
all0.17295 0 --
obs0.17295 7531 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.991 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å20 Å2
2--2.65 Å20 Å2
3----5.3 Å2
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 0 173 1862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221738
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3031.9532359
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5265213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56524.64384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79315278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7161510
X-RAY DIFFRACTIONr_chiral_restr0.1240.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021366
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.2800
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21174
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8561.51100
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46921735
X-RAY DIFFRACTIONr_scbond_it2.3193731
X-RAY DIFFRACTIONr_scangle_it3.5714.5624
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 28 -
Rwork0.207 544 -
obs--100 %
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)
111.1071-8.7856-4.101523.13372.816310.21780.504-0.29320.4249-0.56060.0255-1.4945-0.08331.8162-0.5294-0.0146-0.06770.10520.1931-0.17680.0486-8.397-10.466-27.015
24.0336-1.2287-1.54643.1735-0.37163.17510.0267-0.69670.5404-0.20820.2479-0.6056-0.31480.164-0.27460.2823-0.12350.04490.0746-0.1770.0092-26.9793.881-11.687
37.9403-2.1375-2.35275.4813-0.02313.0926-0.15-0.54210.0174-0.37290.1361-0.6406-0.1775-0.0290.01390.2126-0.05940.01310.0581-0.1466-0.1269-28.7510.701-11.173
48.485113.6642-3.363745.9066-11.87795.277-0.0561-0.71460.83070.08710.50450.3284-0.8959-0.0873-0.44850.295-0.03130.05650.1097-0.1858-0.0731-39.15412.167-12.669
524.45023.6428-2.177529.120411.337519.04160.5832-2.42991.014-1.2310.05451.6066-0.7514-3.1375-0.6378-0.01850.149-0.14950.67030.1537-0.2684-47.4992.711-5.985
612.0715-0.3013-7.57754.28951.73369.36750.4945-0.85121.05220.00270.0117-0.641-1.41070.2452-0.50620.39340.01930.0264-0.0381-0.17430.0327-29.0169.701-6.804
78.5214-4.0193-0.35033.05983.688410.67860.68240.69840.4001-0.9472-0.5482-0.4379-1.20540.8124-0.13420.28820.03470.2245-0.0153-0.1130.0605-16.269-4.47-31.415
87.3808-0.5088-2.70547.839-1.707519.35970.41760.6323-0.6131-0.498-0.03230.15590.6716-0.8894-0.3853-0.00230.11170.0145-0.0431-0.14270.0622-22.863-12.339-27.638
92.86692.1485-0.77753.82491.97255.02920.71620.03810.4346-0.5732-0.5770.1353-0.86740.0877-0.13920.30370.01760.1675-0.0112-0.11780.0836-21.595-2.983-27.557
109.0056-1.66620.90196.83791.146615.03870.5301-0.459-0.39050.4838-0.1493-0.56650.89161.0971-0.38080.12910.07850.02140.0119-0.07860.1117-13.984-12.3-17.795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA174 - 1954 - 25
2X-RAY DIFFRACTION2AA196 - 22726 - 57
3X-RAY DIFFRACTION3AA228 - 26358 - 93
4X-RAY DIFFRACTION4AA264 - 27494 - 104
5X-RAY DIFFRACTION5AA275 - 283105 - 113
6X-RAY DIFFRACTION6AA284 - 308114 - 138
7X-RAY DIFFRACTION7AA309 - 324139 - 154
8X-RAY DIFFRACTION8AA325 - 356155 - 186
9X-RAY DIFFRACTION9AA357 - 369187 - 199
10X-RAY DIFFRACTION10AA370 - 383200 - 213

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