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- PDB-4edu: The MBT repeats of human SCML2 in a complex with histone H2A peptide -

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Basic information

Entry
Database: PDB / ID: 4edu
TitleThe MBT repeats of human SCML2 in a complex with histone H2A peptide
Components
  • Histone H2A.J peptide
  • Sex comb on midleg-like protein 2
KeywordsTRANSCRIPTION / MBT fold / Royal family / Histone PTM binding / Methylation
Function / homology
Function and homology information


PcG protein complex / anatomical structure morphogenesis / heterochromatin organization / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...PcG protein complex / anatomical structure morphogenesis / heterochromatin organization / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / extracellular exosome / nucleus
Similarity search - Function
Polycomb group protein, RNA binding region / RNA binding Region / : / SLED domain / SLED domain superfamily / SLED domain / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat ...Polycomb group protein, RNA binding region / RNA binding Region / : / SLED domain / SLED domain superfamily / SLED domain / 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) / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / SH3 type barrels. / Histone-fold / Roll / Mainly Beta
Similarity search - Domain/homology
Histone H2A.J / Sex comb on midleg-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsNady, N. / Amaya, M.F. / Tempel, W. / Ravichandran, M. / Arrowsmith, C.H.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Histone recognition by human malignant brain tumor domains.
Authors: Nady, N. / Krichevsky, L. / Zhong, N. / Duan, S. / Tempel, W. / Amaya, M.F. / Ravichandran, M. / Arrowsmith, C.H.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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 / 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: Sex comb on midleg-like protein 2
T: Histone H2A.J peptide


Theoretical massNumber of molelcules
Total (without water)25,9892
Polymers25,9892
Non-polymers00
Water84747
1
A: Sex comb on midleg-like protein 2
T: Histone H2A.J peptide

A: Sex comb on midleg-like protein 2
T: Histone H2A.J peptide


Theoretical massNumber of molelcules
Total (without water)51,9794
Polymers51,9794
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2260 Å2
ΔGint-26 kcal/mol
Surface area22430 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-7 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.949, 69.949, 169.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Sex comb on midleg-like protein 2


Mass: 24132.301 Da / Num. of mol.: 1 / Fragment: UNP residues 31-46 / Mutation: K147E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCML2 / Plasmid: pET28MHL / Production host: Escherichia coli (E. coli) / Strain (production host): C+ / References: UniProt: Q9UQR0
#2: Protein/peptide Histone H2A.J peptide / H2a/j


Mass: 1857.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BTM1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 4.2 Å3/Da / Density % sol: 70.6 %
Crystal growTemperature: 291 K / pH: 9.5
Details: 1.6M NH4PO4, 0.1M Tris/HCl, 1:5 molar ratio of protein:peptide, protein concentration 35 mg/ml, pH 9.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC Q315 / Detector: CCD / Date: Jul 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.58→43.97 Å / Num. obs: 15321 / % possible obs: 99.9 % / Redundancy: 7.71 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 15.5034
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) allNum. measured allNum. unique allRrim(I) all% possible all
2.58-2.727.920.980.771567019781.0599.95
2.72-2.887.980.581.311501818810.6299.89
2.88-3.087.960.342.221411917740.37100
3.08-3.337.910.23.771339316940.22100
3.33-3.657.790.126.211188615260.13100
3.65-4.087.630.089.481071914050.0899.96
4.08-4.717.630.0612.92968612690.06100
4.71-5.777.430.0513.18801010780.06100
5.77-8.167.070.0416.0961478700.05100
8.16-43.976.310.0323.6933485310.0398.95

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OI1

1oi1


Resolution: 2.58→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.099 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.245 692 4.962 %RANDOM
Rwork0.204 ---
obs0.206 13947 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.099 Å20 Å20 Å2
2--3.099 Å20 Å2
3----6.198 Å2
Refinement stepCycle: LAST / Resolution: 2.58→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 0 47 1750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021769
X-RAY DIFFRACTIONr_bond_other_d0.0020.021229
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9652403
X-RAY DIFFRACTIONr_angle_other_deg0.85632994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6065219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.74923.97478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62815283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5041511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02359
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
2.58-2.6470.391390.3778200.3788591000.342
2.647-2.7190.402360.2998100.30384799.8820.266
2.719-2.7970.302480.2837730.28382399.7570.242
2.797-2.8830.287430.2587410.2597841000.211
2.883-2.9770.29480.2267110.237591000.188
2.977-3.0810.272340.2427080.2447421000.211
3.081-3.1970.282340.2286910.2317251000.193
3.197-3.3260.233390.2166430.2176821000.186
3.326-3.4730.275330.2166100.226431000.186
3.473-3.6410.231260.1976010.1996271000.176
3.641-3.8360.253270.1935600.1955871000.17
3.836-4.0670.244280.175240.17455399.8190.145
4.067-4.3440.247210.1554990.1595201000.139
4.344-4.6880.197260.1444440.1464701000.127
4.688-5.1280.181220.1624110.1634331000.147
5.128-5.7220.254180.1773690.183871000.153
5.722-6.5840.203140.1873210.1883351000.167
6.584-8.010.221120.1932580.1942701000.173
8.01-11.1070.15170.181880.1782051000.173
11.107-400.3270.308850.3099695.8330.295
Refinement TLS params.Method: refined / Origin x: 18.8501 Å / Origin y: 6.2552 Å / Origin z: 57.4101 Å
111213212223313233
T0.0929 Å2-0.0517 Å2-0.027 Å2-0.0364 Å20.0119 Å2--0.0258 Å2
L0.3124 °20.0079 °20.2348 °2-1.8032 °22.4481 °2--5.4488 °2
S0.0249 Å °-0.0284 Å °0.0327 Å °-0.0077 Å °-0.0411 Å °-0.0205 Å °-0.0844 Å °0.0787 Å °0.0161 Å °

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