[English] 日本語
Yorodumi
- PDB-5bt2: MeCP2 MBD domain (A140V) in complex with methylated DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bt2
TitleMeCP2 MBD domain (A140V) in complex with methylated DNA
Components
  • DNA (5'-D(*AP*TP*AP*GP*AP*AP*GP*AP*AP*TP*TP*CP*(5CM)P*GP*TP*TP*CP*CP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*GP*GP*AP*AP*(5CM)P*GP*GP*AP*AP*TP*TP*CP*TP*TP*CP*TP*A)-3')
  • Methyl-CpG-binding protein 2MECP2
KeywordsDNA BINDING PROTEIN/DNA / A/T run / MeCP2 / hydration spine / methylated DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


trans-synaptic signaling by BDNF / regulation of action potential firing threshold / negative regulation of respiratory gaseous exchange / Loss of MECP2 binding ability to 5hmC-DNA / cellular response to isoquinoline alkaloid / positive regulation of anterograde dense core granule transport / positive regulation of retrograde dense core granule transport / positive regulation of branching morphogenesis of a nerve / catecholamine secretion / : ...trans-synaptic signaling by BDNF / regulation of action potential firing threshold / negative regulation of respiratory gaseous exchange / Loss of MECP2 binding ability to 5hmC-DNA / cellular response to isoquinoline alkaloid / positive regulation of anterograde dense core granule transport / positive regulation of retrograde dense core granule transport / positive regulation of branching morphogenesis of a nerve / catecholamine secretion / : / MECP2 regulates transcription of genes involved in GABA signaling / negative regulation of dendrite extension / biogenic amine metabolic process / principal sensory nucleus of trigeminal nerve development / cardiolipin metabolic process / negative regulation of locomotion involved in locomotory behavior / Loss of MECP2 binding ability to 5mC-DNA / nervous system process involved in regulation of systemic arterial blood pressure / proprioception / : / negative regulation of primary miRNA processing / negative regulation of smooth muscle cell differentiation / MECP2 regulates transcription of neuronal ligands / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of dendritic spine development / Transcriptional Regulation by MECP2 / inositol metabolic process / regulation of respiratory gaseous exchange by nervous system process / double-stranded methylated DNA binding / thalamus development / genomic imprinting / positive regulation of microtubule nucleation / glucocorticoid metabolic process / ventricular system development / cellular response to potassium ion / oligodendrocyte development / unmethylated CpG binding / positive regulation of synaptic plasticity / phosphatidylcholine metabolic process / respiratory gaseous exchange by respiratory system / olfactory bulb development / striatum development / positive regulation of dendrite extension / response to other organism / siRNA binding / neuron maturation / methyl-CpG binding / MECP2 regulates transcription factors / Loss of phosphorylation of MECP2 at T308 / response to ionizing radiation / lung alveolus development / regulation of synapse organization / spinal cord development / positive regulation of dendritic spine development / glutamine metabolic process / startle response / dendrite development / social behavior / negative regulation of blood vessel endothelial cell migration / Regulation of MECP2 expression and activity / negative regulation of astrocyte differentiation / behavioral fear response / glial cell proliferation / heterochromatin / Nuclear events stimulated by ALK signaling in cancer / long-term memory / heterochromatin formation / MECP2 regulates neuronal receptors and channels / four-way junction DNA binding / positive regulation of glial cell proliferation / Notch signaling pathway / sensory perception of pain / synapse assembly / excitatory postsynaptic potential / histone reader activity / cerebellum development / molecular condensate scaffold activity / adult locomotory behavior / negative regulation of angiogenesis / post-embryonic development / response to cocaine / long-term synaptic potentiation / promoter-specific chromatin binding / hippocampus development / response to lead ion / visual learning / protein localization / chromatin DNA binding / cerebral cortex development / histone deacetylase binding / transcription corepressor activity / response to estradiol / gene expression / heart development / postsynapse / negative regulation of neuron apoptotic process / nucleic acid binding / response to hypoxia / molecular adaptor activity / protein domain specific binding
Similarity search - Function
Methyl-CpG binding protein MeCP2 / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding protein MeCP2/MBD4 / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Methyl-CpG-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHo, K.L. / Chia, J.Y. / Tan, W.S. / Ng, C.L. / Hu, N.J. / Foo, H.L.
Funding support Malaysia, 2items
OrganizationGrant numberCountry
Ministry of Higher Education03-10-10-948FR Malaysia
Universiti Putra Malaysia04-02-12-1813RU Malaysia
CitationJournal: Sci Rep / Year: 2016
Title: A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence.
Authors: Chia, J.Y. / Tan, W.S. / Ng, C.L. / Hu, N.J. / Foo, H.L. / Ho, K.L.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyl-CpG-binding protein 2
B: DNA (5'-D(*TP*CP*TP*GP*GP*AP*AP*(5CM)P*GP*GP*AP*AP*TP*TP*CP*TP*TP*CP*TP*A)-3')
C: DNA (5'-D(*AP*TP*AP*GP*AP*AP*GP*AP*AP*TP*TP*CP*(5CM)P*GP*TP*TP*CP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)23,4503
Polymers23,4503
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-14 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.660, 53.490, 65.780
Angle α, β, γ (deg.)90.000, 132.470, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Methyl-CpG-binding protein 2 / MECP2 / MeCp2


Mass: 11155.526 Da / Num. of mol.: 1 / Fragment: MBD domain, UNP residues 77-167 / Mutation: A140V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MECP2 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys / References: UniProt: P51608
#2: DNA chain DNA (5'-D(*TP*CP*TP*GP*GP*AP*AP*(5CM)P*GP*GP*AP*AP*TP*TP*CP*TP*TP*CP*TP*A)-3')


Mass: 6138.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*TP*AP*GP*AP*AP*GP*AP*AP*TP*TP*CP*(5CM)P*GP*TP*TP*CP*CP*AP*G)-3')


Mass: 6156.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 2000, 200 mM ammonium acetate, 10 mM magnesium acetate, 50 mM sodium cacodylate
PH range: 6.0-6.7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→48.5 Å / Num. obs: 10482 / % possible obs: 98.9 % / Redundancy: 3.8 % / Net I/σ(I): 9.2

-
Processing

Software
NameVersionClassification
MOSFLMdata collection
SCALAdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SCALAdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2I

3c2i


Resolution: 2.2→48.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 13.84 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 525 5 %RANDOM
Rwork0.1746 ---
obs0.1773 9955 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.62 Å2 / Biso mean: 73.464 Å2 / Biso min: 39.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å21.92 Å2
2---3.4 Å20 Å2
3----1.21 Å2
Refinement stepCycle: final / Resolution: 2.2→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms572 816 0 141 1529
Biso mean---69.46 -
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0141500
X-RAY DIFFRACTIONr_bond_other_d0.0030.021011
X-RAY DIFFRACTIONr_angle_refined_deg1.831.5132198
X-RAY DIFFRACTIONr_angle_other_deg1.37232365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.441570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28723.21428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.8515102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.745155
X-RAY DIFFRACTIONr_chiral_restr0.0920.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02323
X-RAY DIFFRACTIONr_mcbond_it3.3994.784283
X-RAY DIFFRACTIONr_mcbond_other3.3994.773282
X-RAY DIFFRACTIONr_mcangle_it4.7097.152352
LS refinement shellResolution: 2.182→2.239 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 44 -
Rwork0.284 734 -
all-778 -
obs--98.86 %
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)
12.92860.315-0.18097.95460.70722.9093-0.0596-0.3707-0.30380.99270.1367-0.82570.14150.2197-0.07710.20540.0437-0.1860.06390.00630.229.222-1.429-17.755
25.1673-0.404-2.92580.60680.26124.1612-0.15340.14120.2714-0.08330.27220.18220.39040.1195-0.11880.0634-0.046-0.0190.21520.03560.16981.6860.63-30.22
34.32010.1296-2.27150.4598-0.5394.2976-0.450.48730.08510.03050.2233-0.01440.5495-0.08590.22670.1359-0.02020.05360.24980.00330.11014.7680.483-33.654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A92 - 162
2X-RAY DIFFRACTION2B1 - 20
3X-RAY DIFFRACTION3C21 - 40

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more