[English] 日本語
Yorodumi
- PDB-6cnp: Crystal structure of MBD2 complex with methylated CpG island -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cnp
TitleCrystal structure of MBD2 complex with methylated CpG island
Components
  • DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
  • Methyl-CpG-binding domain protein 2
KeywordsTRANSCRIPTION/DNA / Structural Genomics Consortium / SGC / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / siRNA binding / maternal behavior / C2H2 zinc finger domain binding / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / embryonic organ development / positive regulation of Wnt signaling pathway ...satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / siRNA binding / maternal behavior / C2H2 zinc finger domain binding / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / embryonic organ development / positive regulation of Wnt signaling pathway / response to mechanical stimulus / heterochromatin / RNA Polymerase I Promoter Opening / response to nutrient levels / NoRC negatively regulates rRNA expression / Wnt signaling pathway / response to estradiol / regulation of cell population proliferation / protein-containing complex assembly / molecular adaptor activity / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Methyl-CpG binding protein 2/3, C-terminal domain / Methyl-CpG-binding domain protein 2/3, p55-binding region / C-terminal domain of methyl-CpG binding protein 2 and 3 / p55-binding region of Methyl-CpG-binding domain proteins MBD / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. ...Methyl-CpG binding protein 2/3, C-terminal domain / Methyl-CpG-binding domain protein 2/3, p55-binding region / C-terminal domain of methyl-CpG binding protein 2 and 3 / p55-binding region of Methyl-CpG-binding domain proteins MBD / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / 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 domain protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXu, C. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA.
Authors: Liu, K. / Xu, C. / Lei, M. / Yang, A. / Loppnau, P. / Hughes, T.R. / Min, J.
History
DepositionMar 8, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMar 28, 2018ID: 6C2K
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,62318
Polymers36,5836
Non-polymers4012
Water61334
1
A: Methyl-CpG-binding domain protein 2
C: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,33111
Polymers18,2913
Non-polymers408
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-13 kcal/mol
Surface area7440 Å2
MethodPISA
2
B: Methyl-CpG-binding domain protein 2
E: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)18,2917
Polymers18,2913
Non-polymers04
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-5 kcal/mol
Surface area7120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.960, 41.320, 58.670
Angle α, β, γ (deg.)101.570, 99.460, 100.540
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Methyl-CpG-binding domain protein 2 / Demethylase / DMTase / Methyl-CpG-binding protein MBD2


Mass: 10934.497 Da / Num. of mol.: 2 / Fragment: residues 143-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD2 / Plasmid: pET28-mhl / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9UBB5
#2: DNA chain
DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')


Mass: 3678.407 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.2 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 8% PEG550MME, 8% PEG20000, 0.2M calcium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.1→39.46 Å / Num. obs: 20704 / % possible obs: 97.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 50.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.026 / Rrim(I) all: 0.051 / Net I/σ(I): 15.3 / Num. measured all: 80533 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.163.90.9716970.6850.5631.12297.2
8.91-39.463.50.0320.9970.020.03895

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2KY8, 3QMG

2ky8

3qmg


Resolution: 2.1→39.457 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.66
Details: Prior to molecular replacement, protein coordinates of the NMR model ensemble of pdb entry 2KY8 were averaged using a program written by Aiping Dong. refmac was used during intermediate ...Details: Prior to molecular replacement, protein coordinates of the NMR model ensemble of pdb entry 2KY8 were averaged using a program written by Aiping Dong. refmac was used during intermediate refinement steps. coot was used for interactive model building. Model geometry was assessed with molprobity.
RfactorNum. reflection% reflection
Rfree0.2177 2109 5.15 %
Rwork0.189 --
obs0.1906 40927 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.94 Å2 / Biso mean: 61.2521 Å2 / Biso min: 33.42 Å2
Refinement stepCycle: final / Resolution: 2.1→39.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 976 12 34 1968
Biso mean--52.69 54.33 -
Num. residues----174
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.24771320.27622623275597
2.1489-2.20260.36461230.28282576269997
2.2026-2.26210.31391470.27062576272396
2.2621-2.32870.31151490.26022549269897
2.3287-2.40390.31711160.25692661277797
2.4039-2.48980.32971380.25352600273897
2.4898-2.58940.2611280.25412604273298
2.5894-2.70730.24421020.23412653275597
2.7073-2.84990.34621520.25912591274398
2.8499-3.02840.25891550.23582589274498
3.0284-3.26220.22121680.20612585275397
3.2622-3.59030.20071360.18512411254791
3.5903-4.10930.20891550.16272644279997
4.1093-5.17540.16531360.1442590272698
5.1754-39.46430.18591720.15692566273897
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)
13.1128-0.05950.93013.91670.27071.4034-0.12430.37920.4865-0.9275-0.20150.6459-0.6114-0.26510.22320.43380.03-0.0550.4110.03510.4468-6.985-14.964413.5895
20.8172-1.0945-0.09122.88880.77361.8160.1387-0.71390.17420.886-0.05670.11350.5603-0.3634-0.12030.6498-0.0461-0.0080.5171-0.05590.38528.2251-12.325147.3323
33.1008-0.7214-0.22741.07320.44432.6678-0.0435-0.7379-0.1887-0.13770.12960.014-0.0440.17110.0290.3285-0.0451-0.00830.6060.00740.481-5.8193-30.883215.0722
43.45290.6502-0.4480.70370.48052.2768-0.09720.2274-0.58960.00360.0212-0.03850.09170.02870.10770.3504-0.03410.0030.52630.01960.5702-5.6665-31.380413.7199
52.22451.11370.59224.4768-0.1072.00680.10650.21890.3720.7312-0.646-0.8608-0.2195-0.07730.50330.71620.0072-0.10680.43580.05130.533611.0376-11.081733.3484
62.6358-1.55040.01684.74761.66491.87240.51890.17120.0261-0.4307-0.6190.35910.03420.08450.1570.7163-0.0126-0.02380.4237-0.01740.48949.6715-10.888732.7005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA148 - 215
2X-RAY DIFFRACTION2chain BB153 - 210
3X-RAY DIFFRACTION3chain CC1 - 12
4X-RAY DIFFRACTION4chain DD1 - 12
5X-RAY DIFFRACTION5chain EE1 - 12
6X-RAY DIFFRACTION6chain FF1 - 12

+
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