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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mwk
TitleCrystal structure of MBD2 with DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*AP*(MC)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 / ventricular cardiac muscle tissue development / NuRD complex / maternal behavior / siRNA binding / methyl-CpG binding / C2H2 zinc finger domain binding / DNA methylation-dependent heterochromatin formation / cellular response to organic cyclic compound / positive regulation of Wnt signaling pathway ...satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / maternal behavior / siRNA binding / methyl-CpG binding / C2H2 zinc finger domain binding / DNA methylation-dependent heterochromatin formation / cellular response to organic cyclic compound / positive regulation of Wnt signaling pathway / embryonic organ development / heterochromatin / response to mechanical stimulus / 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 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: 2.453 Å
AuthorsLiu, K. / Dong, A. / 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. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionMay 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')
E: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)32,23610
Polymers32,2366
Non-polymers04
Water905
1
A: Methyl-CpG-binding domain protein 2
C: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,1183
Polymers16,1183
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-6 kcal/mol
Surface area7460 Å2
MethodPISA
2
B: Methyl-CpG-binding domain protein 2
E: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,1187
Polymers16,1183
Non-polymers04
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-5 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.521, 40.521, 202.097
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain F
21chain C
31chain D
41chain E
12(chain A and (resseq 148:159 or (resid 160 and (name...
22(chain B and (resseq 148:175 or (resid 176 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111DGDGDCDCchain FFF1 - 121 - 12
211DGDGDCDCchain CCC1 - 121 - 12
311DGDGDCDCchain DDD1 - 121 - 12
411DGDGDCDCchain EEE1 - 121 - 12
112LYSLYSTRPTRP(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 1597 - 18
122LYSLYSLYSLYS(chain A and (resseq 148:159 or (resid 160 and (name...AA16019
132LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
142LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
152LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
162LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
172LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
182LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
212LYSLYSSERSER(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 1757 - 34
222ASPASPASPASP(chain B and (resseq 148:175 or (resid 176 and (name...BB17635
232LYSLYSPROPRO(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 2157 - 74
242LYSLYSPROPRO(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 2157 - 74
252LYSLYSPROPRO(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 2157 - 74
262LYSLYSPROPRO(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 2157 - 74
272LYSLYSPROPRO(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 2157 - 74

NCS ensembles :
ID
1
2

-
Components

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


Mass: 8763.156 Da / Num. of mol.: 2 / 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*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')


Mass: 3677.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.97 Å3/Da / Density % sol: 58.61 % / Mosaicity: 0.18 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.45→34.575 Å / Num. obs: 27350 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 61.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.026 / Rrim(I) all: 0.062 / Net I/σ(I): 18.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.45-2.555.81.063919115780.5750.481.1671.8100
8.83-34.575.30.02615482930.9990.0120.02954.197.9

-
Processing

Software
NameVersionClassification
REFMAC1.10.1_2155refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6C2E

6c2e
PDB Unreleased entry


Resolution: 2.453→34.575 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 890 3.31 %
Rwork0.1915 --
obs0.1924 26856 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.9 Å2 / Biso mean: 63.2246 Å2 / Biso min: 38.04 Å2
Refinement stepCycle: final / Resolution: 2.453→34.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 976 4 5 2019
Biso mean--44.78 52.31 -
Num. residues----184
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11F412X-RAY DIFFRACTION6.977TORSIONAL
12C412X-RAY DIFFRACTION6.977TORSIONAL
13D412X-RAY DIFFRACTION6.977TORSIONAL
14E412X-RAY DIFFRACTION6.977TORSIONAL
21A594X-RAY DIFFRACTION6.977TORSIONAL
22B594X-RAY DIFFRACTION6.977TORSIONAL
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)
10.4284-0.41530.53711.51770.44781.03340.0922-0.0593-0.08760.0714-0.02360.29980.2027-0.3519-00.8336-0.02540.07660.47290.00530.383434.967720.8244-4.9456
21.0730.57490.01451.1244-0.73730.66190.3264-0.0201-0.21070.2133-0.33930.2042-0.0853-0.4786-0.01330.6570.0864-0.06190.5414-0.02950.451628.622810.2673-30.2582
30.1042-1.27810.3835-0.0424-0.25610.80580.16420.28440.1448-0.1952-0.2547-0.2011-0.01090.202401.01550.00070.10730.53250.01170.654249.037926.09710.9721
4-0.2410.0804-0.74120.4669-0.23060.8253-0.25950.32940.21670.6194-0.1057-0.3454-0.02780.059601.02230.01850.02240.51660.04280.594848.600126.04682.4765
51.53090.60340.83680.27440.3820.60380.50010.35330.2609-0.2044-0.7437-0.25790.11520.156-0.06660.80140.3971-0.01940.5635-0.0390.670739.919819.8663-37.4415
60.06940.8127-0.56340.8396-0.81881.6838-0.08230.17420.2550.34-0.2885-0.2796-0.09330.01860.00040.71180.2696-0.1430.4915-0.06710.667539.916820.397-35.8784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA148 - 215
2X-RAY DIFFRACTION2chain BB148 - 215
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://pdbjlc1.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