[English] 日本語
Yorodumi
- PDB-7ray: Crystal structure of MBD2 with DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ray
TitleCrystal structure of MBD2 with DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')
  • Methyl-CpG-binding domain protein 2
KeywordsDNA BINDING PROTEIN/DNA / DNA binding protein-DNA complex / MBD / TAM / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


satellite DNA binding / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / C2H2 zinc finger domain binding / RNA Polymerase I Promoter Opening / NoRC negatively regulates rRNA expression / molecular adaptor activity / chromatin remodeling / protein domain specific binding ...satellite DNA binding / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / C2H2 zinc finger domain binding / RNA Polymerase I Promoter Opening / NoRC negatively regulates rRNA expression / molecular adaptor activity / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / 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 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) / Methyl-CpG-binding domain protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsLiu, K. / Dong, A. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of MBD2 with DNA
Authors: Liu, K. / Dong, A. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionJul 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 domain protein 2
B: DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,1605
Polymers16,1603
Non-polymers02
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-3 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.599, 71.992, 126.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 8805.196 Da / Num. of mol.: 1 / Fragment: UNP 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) / References: UniProt: Q9UBB5
#2: DNA chain DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')


Mass: 3677.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M disodium tartrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.78→42.04 Å / Num. obs: 33442 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Net I/σ(I): 28.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.78-1.827.30.47149380.9710.1850.50698.5
9.08-42.045.60.0321550.9980.0150.03698.9

-
Processing

Software
NameVersionClassification
PHENIXdev_1439refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6C2Z

6c2z


Resolution: 1.78→36 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.43 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 1587 5.05 %
Rwork0.2092 29843 -
obs0.2113 31430 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.66 Å2 / Biso mean: 34.74 Å2 / Biso min: 16.85 Å2
Refinement stepCycle: final / Resolution: 1.78→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms557 488 2 72 1119
Biso mean--35.65 34.58 -
Num. residues----98
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071140
X-RAY DIFFRACTIONf_angle_d1.2171645
X-RAY DIFFRACTIONf_chiral_restr0.051173
X-RAY DIFFRACTIONf_plane_restr0.008131
X-RAY DIFFRACTIONf_dihedral_angle_d27.22459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7801-1.83750.32071600.3001270898
1.8375-1.90320.34431640.305264898
1.9032-1.97940.31771760.2737267299
1.9794-2.06950.33571240.2641273499
2.0695-2.17860.29271550.2638267499
2.1786-2.3150.34431450.25352730100
2.315-2.49370.2591190.2415276299
2.4937-2.74460.28581470.25362725100
2.7446-3.14160.24071260.2297274899
3.1416-3.95730.2341330.1859269899
3.9573-35.9960.1831380.1432744100
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)
14.2328-0.7239-0.07950.5108-0.84021.8566-0.3644-0.6817-0.0560.18080.2657-0.1522-0.2598-0.1150.03070.25060.1169-0.01660.29440.00950.154-27.91319.376710.5959
20.0170.18870.89220.97590.46031.0392-0.1593-0.0875-0.10430.28930.01560.14810.2203-0.0837-0.00030.27490.0480.07280.22940.05190.3001-41.370614.043917.9895
31.0537-1.20360.7841.17740.98020.5201-0.1474-0.0265-0.16670.50150.02610.3246-0.0537-0.0901-0.01290.24580.08230.08690.24480.02520.2589-41.704714.105416.6324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA142 - 215
2X-RAY DIFFRACTION2chain BB1 - 12
3X-RAY DIFFRACTION3chain CC1 - 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