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- PDB-8d8i: Crystal structure of Reverb alpha in complex with synthetic agonist -

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基本情報

登録情報
データベース: PDB / ID: 8d8i
タイトルCrystal structure of Reverb alpha in complex with synthetic agonist
要素
  • Nuclear receptor corepressor 1
  • Nuclear receptor subfamily 1 group D member 1
キーワードTRANSCRIPTION / REV-ERB / Nuclear receptor / Agonist
機能・相同性
機能・相同性情報


regulation of circadian sleep/wake cycle / positive regulation of bile acid biosynthetic process / : / circadian temperature homeostasis / regulation of type B pancreatic cell proliferation / negative regulation of astrocyte activation / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of microglial cell activation / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of neuroinflammatory response ...regulation of circadian sleep/wake cycle / positive regulation of bile acid biosynthetic process / : / circadian temperature homeostasis / regulation of type B pancreatic cell proliferation / negative regulation of astrocyte activation / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of microglial cell activation / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of neuroinflammatory response / response to leptin / negative regulation of androgen receptor signaling pathway / regulation of insulin secretion involved in cellular response to glucose stimulus / glycogen biosynthetic process / negative regulation of JNK cascade / negative regulation of glycolytic process / regulation of fat cell differentiation / nuclear thyroid hormone receptor binding / negative regulation of cold-induced thermogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear steroid receptor activity / negative regulation of fatty acid metabolic process / Notch-HLH transcription pathway / E-box binding / intracellular glucose homeostasis / locomotor rhythm / regulation of lipid metabolic process / histone deacetylase complex / Regulation of MECP2 expression and activity / cellular response to interleukin-1 / proteasomal protein catabolic process / Nuclear signaling by ERBB4 / spindle assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / hormone-mediated signaling pathway / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / negative regulation of miRNA transcription / cholesterol homeostasis / transcription corepressor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / protein destabilization / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / nuclear receptor activity / HCMV Early Events / transcription corepressor activity / sequence-specific double-stranded DNA binding / mitotic spindle / : / cellular response to tumor necrosis factor / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / cellular response to lipopolysaccharide / dendritic spine / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / heme binding / dendrite / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
類似検索 - 分子機能
N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / : ...N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / : / Homeobox-like domain superfamily / 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
類似検索 - ドメイン・相同性
Chem-QFX / Nuclear receptor corepressor 1 / Nuclear receptor subfamily 1 group D member 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.504 Å
データ登録者Ronin, C. / Ciesielski, F. / Hegazy, L. / Burris, P.T.
資金援助1件
組織認可番号国
Not fundedW81XWH-19-1-0632
引用ジャーナル: Nat Commun / 年: 2022
タイトル: Structural basis of synthetic agonist activation of the nuclear receptor REV-ERB.
著者: Murray, M.H. / Valfort, A.C. / Koelblen, T. / Ronin, C. / Ciesielski, F. / Chatterjee, A. / Veerakanellore, G.B. / Elgendy, B. / Walker, J.K. / Hegazy, L. / Burris, T.P.
履歴
登録2022年6月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年12月14日Provider: repository / タイプ: Initial release
改定 1.12024年4月3日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Nuclear receptor subfamily 1 group D member 1
B: Nuclear receptor corepressor 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,0943
ポリマ－28,7712
非ポリマー3231
水46826
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: mass spectrometry
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-18 kcal/mol
Surface area10520 Å2
手法PISA
単位格子
Length a, b, c (Å)115.073, 115.073, 107.32
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32

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要素

#1: タンパク質 Nuclear receptor subfamily 1 group D member 1 / Rev-erbA-alpha / V-erbA-related protein 1 / EAR-1


分子量: 26490.156 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NR1D1, EAR1, HREV, THRAL / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P20393
#2: タンパク質・ペプチド Nuclear receptor corepressor 1 / N-CoR / N-CoR1


分子量: 2280.601 Da / 分子数: 1 / Mutation: C2056A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NCOR1, KIAA1047 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O75376
#3: 化合物 ChemComp-QFX / (4S)-6-[([1,1'-biphenyl]-2-yl)oxy]-3-chloro[1,2,4]triazolo[4,3-b]pyridazine


分子量: 322.748 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C17H11ClN4O / タイプ: SUBJECT OF INVESTIGATION
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 26 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.38 Å3/Da / 溶媒含有率: 48.24 %
結晶化温度: 295.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: 80mM Na Hepes pH7.5, 200mM proline, 8% glycerol and 18% PEG3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.9786 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年3月15日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9786 Å / 相対比: 1
反射解像度: 2.504→73.027 Å / Num. obs: 7248 / % possible obs: 85.5 % / 冗長度: 8.11 %
詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.999 / CC1/2 anomalous: -0.069 / Rmerge(I) obs: 0.0691 / Rpim(I) all: 0.0258 / Rrim(I) all: 0.0741 / AbsDiff over sigma anomalous: 0.779 / Baniso tensor eigenvalue 1: 86.5 Å2 / Baniso tensor eigenvalue 2: 86.5 Å2 / Baniso tensor eigenvalue 3: 68.8 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 2.704 Å / Aniso diffraction limit 2: 2.704 Å / Aniso diffraction limit 3: 2.413 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 18.44 / Num. measured all: 58812 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 83.2 / % possible ellipsoidal: 85.5 / % possible ellipsoidal anomalous: 83.2 / % possible spherical: 75.7 / % possible spherical anomalous: 73.2 / Redundancy anomalous: 4.33 / Signal type: local
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
7.458-73.0276.970.028551.19268226823853850.999-0.1130.0110.03070.72591969196914.0996
5.93-7.4587.70.039740.14287328733733730.9990.0560.01480.04260.75595.999.295.999.295.94.2699.2
5.167-5.937.720.046237.4288828883743740.998-0.040.01740.04960.81697.210097.210097.24.2100
4.696-5.1678.120.044539.48299029903683680.999-0.040.01650.04770.72697.599.797.599.797.54.3899.7
4.358-4.6967.940.048435.58289028903643640.9990.1050.01820.0520.77897.510097.510097.54.25100
4.103-4.3588.030.055933.1296329633693690.998-0.1230.02090.05990.78497.610097.610097.64.28100
3.894-4.1037.720.07526.84284928493693690.997-0.0330.02920.08090.81297.610097.610097.64.14100
3.724-3.8948.120.091823.02291629163593590.995-0.0280.03450.09840.83198.210098.210098.24.27100
3.578-3.7248.120.131818.79293329333613610.989-0.1340.04940.14140.7998.210098.210098.24.28100
3.363-3.5787.840.180913.41291729173723720.9890.0570.06830.19420.77253.754.953.754.953.74.1954.9
3.264-3.3637.930.2549.56288028803633630.9780.0250.09540.27220.8699799.79799.7974.299.7
3.18-3.2648.160.32747.36293829383603600.961-0.0570.1210.35020.76896.199.796.199.796.14.3499.7
3.1-3.188.290.4026.25298429843603600.9640.0530.14740.42940.7759799.79799.7974.3899.7
3.028-3.17.660.45544.95277427743623620.933-0.060.17310.48870.77996.710096.710096.74.07100
2.965-3.0288.080.59883.68286028603543540.901-0.0580.22060.63990.78697.510097.510097.54.28100
2.905-2.9658.270.77172.82295129513573570.833-0.0270.28180.82410.799710097100974.33100
2.851-2.9058.370.8742.52296329633543540.801-0.0290.31590.93150.73496.197.896.197.896.14.3997.8
2.793-2.8518.690.98442.24302430243483480.7680.0880.34881.04680.7887.888.887.888.887.84.5288.8
2.734-2.7939.431.08272.13326332633463460.6980.030.36811.14490.79175.374.975.374.975.34.8574.9
2.504-2.7349.351.51371.42327432743503500.559-0.110.51691.6020.70431.532.631.516.115.24.9932.6

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解析

ソフトウェア
名称バージョン分類
BUSTER2.11.8精密化
autoPROCdata processing
XDSjan 10, 2022データ削減
STARANISO2.3.77データスケーリング
PHASER2.8.3位相決定
精密化構造決定の手法: 分子置換
開始モデル: In house structure

解像度: 2.504→73.03 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / 交差検証法: THROUGHOUT / SU R Blow DPI: 3.057 / SU Rfree Blow DPI: 0.321
Rfactor反射数%反射Selection details
Rfree0.2395 363 -RANDOM
Rwork0.2052 ---
obs0.2069 7248 75.8 %-
原子変位パラメータBiso mean: 77.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.7349 Å20 Å20 Å2
2--0.7349 Å20 Å2
3----1.4697 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
精密化ステップサイクル: LAST / 解像度: 2.504→73.03 Å
タンパク質核酸リガンド溶媒全体
原子数1761 0 23 26 1810
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081824HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.932469HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d648SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes341HARMONIC5
X-RAY DIFFRACTIONt_it1813HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion240SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1471SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion20.42
LS精密化 シェル解像度: 2.504→2.74 Å
Rfactor反射数%反射
Rfree0.2015 18 -
Rwork0.2832 --
obs--17.95 %

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