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- PDB-6yww: MeCP2 is a microsatellite binding protein that protects CA repeat... -

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Basic information

Entry
Database: PDB / ID: 6yww
TitleMeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion
Components
  • DNA (5'-D(*AP*TP*AP*TP*AP*AP*TP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*CP*AP*G)-3')
  • DNA/RNA (5'-D(*TP*CP*TP*GP*CP*AP*CP*A)-R(P*(5HC))-D(P*AP*CP*AP*CP*AP*AP*TP*TP*AP*TP*A)-3')
  • Truncated methyl CpG binding protein 2 transcript 1
KeywordsDNA BINDING PROTEIN / Rett Syndrome / Microsatellite DNA
Function / homology
Function and homology information


DNA binding / nucleus
Similarity search - Function
Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Truncated methyl CpG binding protein 2 transcript 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsIbrahim, A. / Papin, C. / Mohideen-Abdul, K. / Gras, S.L. / Stoll, I. / Bronner, C. / Dimitrov, S. / Klaholz, B.P. / Hamiche, A.
CitationJournal: Science / Year: 2021
Title: MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion.
Authors: Ibrahim, A. / Papin, C. / Mohideen-Abdul, K. / Le Gras, S. / Stoll, I. / Bronner, C. / Dimitrov, S. / Klaholz, B.P. / Hamiche, A.
History
DepositionApr 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _citation_author.name
Revision 1.2Jul 28, 2021Group: Structure summary / Category: audit_author
Revision 1.3Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Truncated methyl CpG binding protein 2 transcript 1
B: DNA/RNA (5'-D(*TP*CP*TP*GP*CP*AP*CP*A)-R(P*(5HC))-D(P*AP*CP*AP*CP*AP*AP*TP*TP*AP*TP*A)-3')
C: DNA (5'-D(*AP*TP*AP*TP*AP*AP*TP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)23,7373
Polymers23,7373
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.377, 48.986, 66.187
Angle α, β, γ (deg.)90, 90.53, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

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Components

#1: Protein Truncated methyl CpG binding protein 2 transcript 1


Mass: 11441.876 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MECP2 / Production host: Escherichia coli (E. coli) / References: UniProt: D5L9I4
#2: DNA chain DNA/RNA (5'-D(*TP*CP*TP*GP*CP*AP*CP*A)-R(P*(5HC))-D(P*AP*CP*AP*CP*AP*AP*TP*TP*AP*TP*A)-3')


Mass: 6075.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*TP*AP*TP*AP*AP*TP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*CP*AP*G)-3')


Mass: 6219.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM HEPES 7.5, 300 mM NH4Cl, 30% PEG 2000, 1% Dioxane and 1 mM CaCl2

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→66.18 Å / Num. obs: 6178 / % possible obs: 87 % / Redundancy: 6.3 % / CC1/2: 0.991 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.35 Å / Num. unique obs: 310 / CC1/2: 0.311

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2I

3c2i


Resolution: 2.102→66.18 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.839 / SU R Cruickshank DPI: 1.238 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.338 / SU Rfree Cruickshank DPI: 0.328
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 312 -RANDOM
Rwork0.2205 ---
obs0.2225 6178 50.9 %-
Displacement parametersBiso mean: 47.19 Å2
Baniso -1Baniso -2Baniso -3
1-3.1316 Å20 Å2-5.0558 Å2
2--12.8112 Å20 Å2
3----15.9428 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.102→66.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms570 816 0 82 1468
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091498HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.992194HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d407SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes147HARMONIC5
X-RAY DIFFRACTIONt_it1498HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion191SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact668SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.11
X-RAY DIFFRACTIONt_other_torsion31.67
LS refinement shellResolution: 2.102→2.35 Å
RfactorNum. reflection% reflection
Rfree0.3838 18 -
Rwork0.2385 --
obs--12.31 %
Refinement TLS params.

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)
11.41592.35863.46085.92371.21115.6901-0.2980.4747-0.33240.47470.2286-0.1009-0.3324-0.10090.0694-0.22140.3059-0.14980.1133-0.21-0.1216-6.3544-15.787817.9823
20.34441.4778-3.206100.575715.35860.4618-0.12090.4819-0.12090.15240.35390.48190.3539-0.61420.02190.305-0.15460.0488-0.1129-0.3344-20.4003-12.579719.7662
30.44261.5015-2.88970.44323.160816.57850.5287-0.0571-0.2189-0.0571-0.12130.3247-0.21890.3247-0.40740.04550.2331-0.08960.147-0.0336-0.3925-20.5285-12.346123.4834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A92 - 162
2X-RAY DIFFRACTION2{ B|* }B1 - 20
3X-RAY DIFFRACTION3{ C|* }C21 - 40

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