[English] 日本語
Yorodumi
- PDB-8q9q: Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q9q
TitleCrystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC7 deacetylase binding motif
Components
  • HDAC7 (histone deacetylase 7) binding motif peptide: GLY-VAL-VAL-LYS-GLN-LYS-LEU-ALA-GLU-VAL-ILE-LEU-LYS-LYS-GLN
  • MADS box dsDNA: AACTATTTATAAGA
  • MADS box dsDNA: TCTTATAAATAGTT
  • MEF2D protein
KeywordsTRANSCRIPTION / transcriptional repressor
Function / homology
Function and homology information


animal organ development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nervous system development / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS
Similarity search - Domain/homology
DNA / DNA (> 10) / MEF2D protein
Similarity search - Component
Biological speciesHomo sapiens (human)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsChinellato, M. / Carli, A. / Perin, S. / Mazzocato, Y. / Biondi, B. / Di Giorgio, E. / Brancolini, C. / Angelini, A. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationC94I19001550001 Italy
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Folding of Class IIa HDAC Derived Peptides into alpha-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA.
Authors: Chinellato, M. / Perin, S. / Carli, A. / Lastella, L. / Biondi, B. / Borsato, G. / Di Giorgio, E. / Brancolini, C. / Cendron, L. / Angelini, A.
History
DepositionAug 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: HDAC7 (histone deacetylase 7) binding motif peptide: GLY-VAL-VAL-LYS-GLN-LYS-LEU-ALA-GLU-VAL-ILE-LEU-LYS-LYS-GLN
A: MEF2D protein
B: MEF2D protein
K: MADS box dsDNA: AACTATTTATAAGA
L: MADS box dsDNA: TCTTATAAATAGTT


Theoretical massNumber of molelcules
Total (without water)32,7495
Polymers32,7495
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, EMSA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-73 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.883, 59.361, 76.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide HDAC7 (histone deacetylase 7) binding motif peptide: GLY-VAL-VAL-LYS-GLN-LYS-LEU-ALA-GLU-VAL-ILE-LEU-LYS-LYS-GLN


Mass: 1685.101 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#2: Protein MEF2D protein / Myocyte enhancer factor 2D


Mass: 11254.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Missing residues are not visible in the electron density maps
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05BX2
#3: DNA chain MADS box dsDNA: AACTATTTATAAGA


Mass: 4286.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: synthetic construct (others)
#4: DNA chain MADS box dsDNA: TCTTATAAATAGTT


Mass: 4268.813 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: synthetic construct (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium acetate trihydrate, 100 mM Bis-Tris propane pH 6.5 and 20% w/v polyethylene glycol 3350 (PEG 3350)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.11→76.5 Å / Num. obs: 14910 / % possible obs: 96 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.732 / Num. unique obs: 1222 / CC1/2: 0.882 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→46.94 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.563 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28489 692 4.7 %RANDOM
Rwork0.26532 ---
obs0.26635 14174 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å20 Å2
2--3.11 Å20 Å2
3----1.38 Å2
Refinement stepCycle: 1 / Resolution: 2.11→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 574 0 46 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122305
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.6963204
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1485195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.82621.70294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.49615353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6721514
X-RAY DIFFRACTIONr_chiral_restr0.1280.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021486
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5954.884789
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.4187.292981
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6425.2011516
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.68888.5749044
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2654 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.11→2.163 Å
RfactorNum. reflection% reflection
Rfree0.381 48 -
Rwork0.346 1043 -
obs--98.82 %

+
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