[English] 日本語
Yorodumi
- PDB-8c5l: NR2F6 ligand binding domain in complex with NSD1 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8c5l
TitleNR2F6 ligand binding domain in complex with NSD1 peptide
Components
  • Histone-lysine N-methyltransferase, H3 lysine-36 specific
  • Maltose/maltodextrin-binding periplasmic protein,Nuclear receptor subfamily 2 group F member 6
KeywordsTRANSCRIPTION / NR2F6 / NSD1 / Nuclear receptor / EAR-2 / coregulator
Function / homology
Function and homology information


regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of peptidyl-serine phosphorylation / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / histone H3K36 dimethyltransferase activity / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / nuclear thyroid hormone receptor binding / histone H3 methyltransferase activity / nuclear androgen receptor binding ...regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of peptidyl-serine phosphorylation / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / histone H3K36 dimethyltransferase activity / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / nuclear thyroid hormone receptor binding / histone H3 methyltransferase activity / nuclear androgen receptor binding / entrainment of circadian clock by photoperiod / detection of maltose stimulus / maltose transport complex / carbohydrate transport / detection of temperature stimulus involved in sensory perception of pain / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / neuron development / nuclear retinoid X receptor binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / nuclear estrogen receptor binding / cell chemotaxis / transcription coregulator activity / PKMTs methylate histone lysines / Nuclear Receptor transcription pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear receptor activity / transcription corepressor activity / sequence-specific double-stranded DNA binding / outer membrane-bounded periplasmic space / methylation / sequence-specific DNA binding / cell differentiation / periplasmic space / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA damage response / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
: / : / : / : / : / : / : / NSD, Cys-His rich domain / : / : ...: / : / : / : / : / : / : / NSD, Cys-His rich domain / : / : / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / : / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / : / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Zinc finger, PHD-type, conserved site / PHD-finger / Bacterial extracellular solute-binding protein / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Nuclear receptor subfamily 2 group F member 6 / Histone-lysine N-methyltransferase, H3 lysine-36 specific
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOerlemans, G.J.M. / van den Oetelaar, M.C.M. / Brunsveld, L.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)024.001.035 Netherlands
CitationJournal: To Be Published
Title: Structural insights into coregulator recruitment to the autorepressed NR2F6 nuclear receptor
Authors: Oerlemans, G.J.M. / van den Oetelaar, M.C.M. / Brunsveld, L.
History
DepositionJan 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Nuclear receptor subfamily 2 group F member 6
B: Maltose/maltodextrin-binding periplasmic protein,Nuclear receptor subfamily 2 group F member 6
C: Histone-lysine N-methyltransferase, H3 lysine-36 specific
D: Histone-lysine N-methyltransferase, H3 lysine-36 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0376
Polymers128,3534
Non-polymers6852
Water1,00956
1
A: Maltose/maltodextrin-binding periplasmic protein,Nuclear receptor subfamily 2 group F member 6
C: Histone-lysine N-methyltransferase, H3 lysine-36 specific
hetero molecules

B: Maltose/maltodextrin-binding periplasmic protein,Nuclear receptor subfamily 2 group F member 6
D: Histone-lysine N-methyltransferase, H3 lysine-36 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0376
Polymers128,3534
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)170.383, 170.383, 83.667
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Nuclear receptor subfamily 2 group F member 6 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / V-erbA-related protein 2 / EAR-2


Mass: 61867.578 Da / Num. of mol.: 2
Mutation: D108A,K109A,E198A,N199A,K265A,E385A,K388A,D389A in Maltose/maltodextrin-binding periplasmic protein (Uniprot ID P0AEX9)
Source method: isolated from a genetically manipulated source
Details: This applies to the NR2F6 part of the protein. Maltose/maltodextrin-binding periplasmic protein originates from E.coli.
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K-12 / Gene: malE, b4034, JW3994, NR2F6, EAR2, ERBAL2 / Plasmid: pET-28a (+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9, UniProt: P10588
#2: Protein/peptide Histone-lysine N-methyltransferase, H3 lysine-36 specific / Androgen receptor coactivator 267 kDa protein / Androgen receptor-associated protein of 267 kDa / ...Androgen receptor coactivator 267 kDa protein / Androgen receptor-associated protein of 267 kDa / H3-K36-HMTase / Lysine N-methyltransferase 3B / Nuclear receptor-binding SET domain-containing protein 1 / NR-binding SET domain-containing protein


Mass: 2308.737 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96L73, [histone H3]-lysine36 N-dimethyltransferase
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 90 mM SPG pH 8.0, 22.5% w/v PEG1500, 100 mM potassium chloride
Temp details: Room Temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972425 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972425 Å / Relative weight: 1
ReflectionResolution: 2.6→147.56 Å / Num. obs: 42757 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 76.1 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 10.1 % / Num. unique obs: 4485 / CC1/2: 0.376 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0.352refinement
PDB-REDOrefinement
PHENIX1.19.1_4122refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→55.34 Å / SU ML: 0.442 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1793
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2328 2212 5.18 %
Rwork0.2003 40516 -
obs0.202 42728 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.65 Å2
Refinement stepCycle: LAST / Resolution: 2.6→55.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8642 0 46 56 8744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00628904
X-RAY DIFFRACTIONf_angle_d0.895312158
X-RAY DIFFRACTIONf_chiral_restr0.05251393
X-RAY DIFFRACTIONf_plane_restr0.00791577
X-RAY DIFFRACTIONf_dihedral_angle_d14.77073138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.45111290.37942511X-RAY DIFFRACTION100
2.66-2.720.34611220.32932548X-RAY DIFFRACTION99.96
2.72-2.790.33971520.31322512X-RAY DIFFRACTION100
2.79-2.860.38251360.29422490X-RAY DIFFRACTION100
2.86-2.950.32041490.28672511X-RAY DIFFRACTION100
2.95-3.040.32581440.25882516X-RAY DIFFRACTION100
3.04-3.150.31191570.27642492X-RAY DIFFRACTION100
3.15-3.280.33431230.26822550X-RAY DIFFRACTION99.96
3.28-3.420.31521550.24882496X-RAY DIFFRACTION100
3.43-3.60.25211450.20342532X-RAY DIFFRACTION99.96
3.61-3.830.21191400.19342528X-RAY DIFFRACTION100
3.83-4.130.23361180.18282570X-RAY DIFFRACTION100
4.13-4.540.22061570.16882493X-RAY DIFFRACTION100
4.54-5.20.19321290.16912567X-RAY DIFFRACTION99.96
5.2-6.550.23151120.20552600X-RAY DIFFRACTION99.89
6.55-55.340.15761440.15082600X-RAY DIFFRACTION99.78

+
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