[English] 日本語
Yorodumi
- PDB-2y48: Crystal structure of LSD1-CoREST in complex with a N-terminal SNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y48
TitleCrystal structure of LSD1-CoREST in complex with a N-terminal SNAIL peptide
Components
  • LYSINE-SPECIFIC DEMETHYLASE 1A
  • REST COREPRESSOR 1
  • ZINC FINGER PROTEIN SNAI1
KeywordsOXIDOREDUCTASE / FLAVIN / HISTONE / REPRESSOR / TRANSCRIPTION REGULATION / CHROMATIN / NUCLEAR PROTEIN
Function / homology
Function and homology information


negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / Regulation of CDH11 gene transcription / negative regulation of vitamin D biosynthetic process / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / trophoblast giant cell differentiation / heterochromatin organization / positive regulation of megakaryocyte differentiation ...negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / Regulation of CDH11 gene transcription / negative regulation of vitamin D biosynthetic process / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / trophoblast giant cell differentiation / heterochromatin organization / positive regulation of megakaryocyte differentiation / guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / Epithelial-Mesenchymal Transition (EMT) during gastrulation / protein demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / neuron maturation / muscle cell development / positive regulation of neural precursor cell proliferation / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MRF binding / regulation of androgen receptor signaling pathway / DNA repair complex / aortic valve morphogenesis / regulation of bicellular tight junction assembly / hair follicle morphogenesis / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of neuroblast proliferation / DNA repair-dependent chromatin remodeling / positive regulation of stem cell proliferation / histone H3K9 demethylase activity / histone deacetylase complex / negative regulation of DNA damage response, signal transduction by p53 class mediator / E-box binding / histone methyltransferase complex / roof of mouth development / mesoderm formation / histone demethylase activity / epithelial to mesenchymal transition / positive regulation of cell size / canonical Wnt signaling pathway / positive regulation of epithelial to mesenchymal transition / pericentric heterochromatin / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Notch signaling pathway / transcription repressor complex / epigenetic regulation of gene expression / cellular response to cAMP / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / HDACs deacetylate histones / promoter-specific chromatin binding / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / positive regulation of neuron projection development / HDMs demethylate histones / cerebral cortex development / protein modification process / DNA-binding transcription repressor activity, RNA polymerase II-specific / kinase binding / fibrillar center / sequence-specific double-stranded DNA binding / osteoblast differentiation / p53 binding / cellular response to UV / transcription corepressor activity / flavin adenine dinucleotide binding / regulation of protein localization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / chromatin organization / transcription regulator complex / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / oxidoreductase activity / chromosome, telomeric region / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II
Similarity search - Function
: / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / C2H2-type zinc finger / : / Helical region in REST corepressor / : / Histone lysine-specific demethylase / ELM2 domain / ELM2 domain / ELM2 domain profile. ...: / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / C2H2-type zinc finger / : / Helical region in REST corepressor / : / Histone lysine-specific demethylase / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / ATP synthase, gamma subunit, helix hairpin domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / : / SANT domain profile. / Amine oxidase / Flavin containing amine oxidoreductase / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Zinc finger, C2H2 type / SANT/Myb domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Zinc finger C2H2-type / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Lysine-specific histone demethylase 1A / Zinc finger protein SNAI1 / REST corepressor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBaron, R. / Binda, C. / Tortorici, M. / McCammon, J.A. / Mattevi, A.
CitationJournal: Structure / Year: 2011
Title: Molecular Mimicry and Ligand Recognition in Binding and Catalysis by the Histone Demethylase Lsd1-Corest Complex.
Authors: Baron, R. / Binda, C. / Tortorici, M. / Mccammon, J.A. / Mattevi, A.
History
DepositionJan 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LYSINE-SPECIFIC DEMETHYLASE 1A
B: REST COREPRESSOR 1
C: ZINC FINGER PROTEIN SNAI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7034
Polymers103,9173
Non-polymers7861
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-52.3 kcal/mol
Surface area38140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.170, 181.460, 234.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 1A / LYSINE-SPECIFIC DEMETHYLASE 1 / BRAF35-HDAC COMPLEX PROTEIN BHC110 / FLAVIN-CONTAINING AMINE ...LYSINE-SPECIFIC DEMETHYLASE 1 / BRAF35-HDAC COMPLEX PROTEIN BHC110 / FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2


Mass: 81279.438 Da / Num. of mol.: 1 / Fragment: RESIDUES 123-852
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60341, Oxidoreductases
#2: Protein REST COREPRESSOR 1 / COREPRESSOR COREST / PROTEIN COREST


Mass: 20244.824 Da / Num. of mol.: 1 / Fragment: RESIDUES 305-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9UKL0
#3: Protein/peptide ZINC FINGER PROTEIN SNAI1 / TRANSCRIPTION FACTOR SNAIL / PROTEIN SNAIL HOMOLOG 1 / PROTEIN SNA


Mass: 2392.692 Da / Num. of mol.: 1 / Fragment: N-TERMINAL 20 AMINO ACIDS TAIL, RESIUDES 2-21 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O95863
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 7 Å3/Da / Density % sol: 80 % / Description: NONE
Crystal growDetails: 1.2 M SODIUM/POTASSIUM TARTRATE, 100 MM ADA BUFFER PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→70 Å / Num. obs: 50937 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V1D

2v1d


Resolution: 3→71.77 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.871 / SU B: 12.084 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24559 992 1.9 %RANDOM
Rwork0.21227 ---
obs0.21296 49943 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.004 Å2
Baniso -1Baniso -2Baniso -3
1-4.75 Å20 Å20 Å2
2---3.24 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 3→71.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6363 0 53 0 6416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9738885
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03824.362298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.126151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.581544
X-RAY DIFFRACTIONr_chiral_restr0.0970.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214924
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_it0.7851.54024
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5226502
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.77532527
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2134.52383
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 74 -
Rwork0.338 3666 -
obs--99.87 %

+
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