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- PDB-9o15: Crystal Structure of BCL-2 (G101V) mutant in complex with a stapl... -

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基本情報

登録情報
データベース: PDB / ID: 9o15
タイトルCrystal Structure of BCL-2 (G101V) mutant in complex with a stapled BAD BH3 peptide BAD SAHB 4.2
要素
  • Apoptosis regulator Bcl-2,Bcl-2-like protein 1
  • stapled BAD BH3 peptide BAD SAHB 4.2
キーワードAPOPTOSIS / Apoptosis regulator / stapled peptide
機能・相同性
機能・相同性情報


: / negative regulation of retinal cell programmed cell death / pigment granule organization / BCL-2 complex / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / melanin metabolic process ...: / negative regulation of retinal cell programmed cell death / pigment granule organization / BCL-2 complex / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / melanin metabolic process / positive regulation of neuron maturation / channel inhibitor activity / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / stem cell development / apoptotic process in bone marrow cell / gland morphogenesis / dendritic cell apoptotic process / renal system process / regulation of cell-matrix adhesion / dendritic cell proliferation / The NLRP1 inflammasome / ear development / positive regulation of mononuclear cell proliferation / negative regulation of calcium ion transport into cytosol / SARS-CoV-1-mediated effects on programmed cell death / T cell apoptotic process / negative regulation of myeloid cell apoptotic process / lymphoid progenitor cell differentiation / melanocyte differentiation / negative regulation of epithelial cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / regulation of nitrogen utilization / negative regulation of dendritic cell apoptotic process / focal adhesion assembly / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of T cell apoptotic process / B cell apoptotic process / glomerulus development / metanephros development / neuron maturation / negative regulation of motor neuron apoptotic process / regulation of viral genome replication / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of multicellular organism growth / negative regulation of execution phase of apoptosis / calcium ion transport into cytosol / oocyte development / fertilization / regulation of mitochondrial membrane permeability / epithelial cell apoptotic process / regulation of growth / negative regulation of ossification / response to UV-B / response to iron ion / Bcl-2 family protein complex / motor neuron apoptotic process / axon regeneration / organ growth / negative regulation of mitochondrial depolarization / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of B cell apoptotic process / hair follicle morphogenesis / positive regulation of smooth muscle cell migration / branching involved in ureteric bud morphogenesis / response to cycloheximide / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / STAT5 activation downstream of FLT3 ITD mutants / digestive tract morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / B cell lineage commitment / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / hepatocyte apoptotic process / pore complex / regulation of calcium ion transport / negative regulation of intrinsic apoptotic signaling pathway / germ cell development / B cell homeostasis / T cell homeostasis / apoptotic mitochondrial changes / negative regulation of reproductive process / negative regulation of developmental process / humoral immune response / B cell proliferation / negative regulation of anoikis / BH3 domain binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling
類似検索 - 分子機能
Apoptosis regulator, Bcl-2 / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site ...Apoptosis regulator, Bcl-2 / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
類似検索 - ドメイン・相同性
Apoptosis regulator Bcl-2 / Bcl-2-like protein 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: 1.99 Å
データ登録者Seo, H.-S. / DeAngelo, T.M. / Bird, G.H. / Walensky, L.D. / Dhe-Paganon, S.
資金援助 米国, 1件
組織認可番号国
Other private 米国
引用ジャーナル: Nat Commun / 年: 2025
タイトル: Structural insights into chemoresistance mutants of BCL-2 and their targeting by stapled BAD BH3 helices.
著者: DeAngelo, T.M. / Adhikary, U. / Korshavn, K.J. / Seo, H.S. / Brotzen-Smith, C.R. / Camara, C.M. / Dhe-Paganon, S. / Bird, G.H. / Wales, T.E. / Walensky, L.D.
履歴
登録2025年4月3日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年10月8日Provider: repository / タイプ: Initial release
改定 1.12025年10月15日Group: Database references / カテゴリ: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
B: stapled BAD BH3 peptide BAD SAHB 4.2
C: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
D: stapled BAD BH3 peptide BAD SAHB 4.2
E: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
F: stapled BAD BH3 peptide BAD SAHB 4.2
G: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
H: stapled BAD BH3 peptide BAD SAHB 4.2
I: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
J: stapled BAD BH3 peptide BAD SAHB 4.2
K: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
L: stapled BAD BH3 peptide BAD SAHB 4.2
M: stapled BAD BH3 peptide BAD SAHB 4.2
N: stapled BAD BH3 peptide BAD SAHB 4.2


分子量 (理論値)分子数
合計 (水以外)138,64714
ポリマ－138,64714
非ポリマー00
水8,521473
1
A: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
B: stapled BAD BH3 peptide BAD SAHB 4.2


分子量 (理論値)分子数
合計 (水以外)22,1812
ポリマ－22,1812
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-16 kcal/mol
Surface area8370 Å2
手法PISA
2
C: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
D: stapled BAD BH3 peptide BAD SAHB 4.2


分子量 (理論値)分子数
合計 (水以外)22,1812
ポリマ－22,1812
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-12 kcal/mol
Surface area8870 Å2
手法PISA
3
E: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
F: stapled BAD BH3 peptide BAD SAHB 4.2


分子量 (理論値)分子数
合計 (水以外)22,1812
ポリマ－22,1812
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-14 kcal/mol
Surface area8500 Å2
手法PISA
4
G: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
H: stapled BAD BH3 peptide BAD SAHB 4.2


分子量 (理論値)分子数
合計 (水以外)22,1812
ポリマ－22,1812
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-12 kcal/mol
Surface area8320 Å2
手法PISA
5
I: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
J: stapled BAD BH3 peptide BAD SAHB 4.2


分子量 (理論値)分子数
合計 (水以外)22,1812
ポリマ－22,1812
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-11 kcal/mol
Surface area8570 Å2
手法PISA
6
K: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
L: stapled BAD BH3 peptide BAD SAHB 4.2


分子量 (理論値)分子数
合計 (水以外)22,1812
ポリマ－22,1812
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-14 kcal/mol
Surface area8240 Å2
手法PISA
7
M: stapled BAD BH3 peptide BAD SAHB 4.2


分子量 (理論値)分子数
合計 (水以外)2,7811
ポリマ－2,7811
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-1 kcal/mol
Surface area1120 Å2
手法PISA
8
N: stapled BAD BH3 peptide BAD SAHB 4.2


分子量 (理論値)分子数
合計 (水以外)2,7811
ポリマ－2,7811
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-1 kcal/mol
Surface area1180 Å2
手法PISA
単位格子
Length a, b, c (Å)68.200, 111.770, 147.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質
Apoptosis regulator Bcl-2,Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X


分子量: 19399.637 Da / 分子数: 6 / 変異: G101V / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BCL2, BCL2L1, BCL2L, BCLX / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P10415, UniProt: Q07817
#2: タンパク質・ペプチド
stapled BAD BH3 peptide BAD SAHB 4.2


分子量: 2781.196 Da / 分子数: 8 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 473 / 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N
Has protein modificationY

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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: 2.02 Å3/Da / 溶媒含有率: 39.23 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 30% Tacsimate, pH 7.0

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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: NSLS-II / ビームライン: 17-ID-2 / 波長: 0.9793 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2024年2月2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: 0.9793 Å / 相対比: 1
反射解像度: 1.99→43.23 Å / Num. obs: 76944 / % possible obs: 98.7 % / 冗長度: 7.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.061 / Rrim(I) all: 0.172 / Net I/σ(I): 8.7 / Num. measured all: 589974
反射 シェル解像度: 1.99→2.02 Å / % possible obs: 97.8 % / 冗長度: 8 % / Rmerge(I) obs: 2.087 / Num. measured all: 29745 / Num. unique obs: 3737 / CC1/2: 0.349 / Rpim(I) all: 0.781 / Rrim(I) all: 2.23 / Net I/σ(I) obs: 0.9

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.21_5207: ???)精密化
xia2データスケーリング
xia2データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 1.99→43.23 Å / SU ML: 0.24 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 22.54 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.223 3874 5.04 %
Rwork0.191 --
obs0.192 76895 98.6 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 1.99→43.23 Å
タンパク質核酸リガンド溶媒全体
原子数8371 0 0 473 8844
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0078573
X-RAY DIFFRACTIONf_angle_d0.93711560
X-RAY DIFFRACTIONf_dihedral_angle_d17.2783092
X-RAY DIFFRACTIONf_chiral_restr0.0561149
X-RAY DIFFRACTIONf_plane_restr0.0091486
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.010.30061350.28342576X-RAY DIFFRACTION98
2.01-2.040.32181390.28342496X-RAY DIFFRACTION98
2.04-2.070.31611290.28662610X-RAY DIFFRACTION98
2.07-2.090.32811350.27972521X-RAY DIFFRACTION98
2.09-2.120.31311590.25592573X-RAY DIFFRACTION98
2.12-2.160.28331180.2452554X-RAY DIFFRACTION98
2.16-2.190.25711300.23932599X-RAY DIFFRACTION98
2.19-2.230.31051460.23462551X-RAY DIFFRACTION98
2.23-2.260.27161440.23052564X-RAY DIFFRACTION98
2.26-2.310.29081260.22022570X-RAY DIFFRACTION98
2.31-2.350.25471260.21442624X-RAY DIFFRACTION98
2.35-2.40.23671280.20792545X-RAY DIFFRACTION98
2.4-2.450.27161410.21222593X-RAY DIFFRACTION98
2.45-2.510.24721260.19742611X-RAY DIFFRACTION99
2.51-2.570.2291530.19192568X-RAY DIFFRACTION99
2.57-2.640.22911440.19022599X-RAY DIFFRACTION99
2.64-2.720.24111300.19972623X-RAY DIFFRACTION99
2.72-2.80.26751250.19182609X-RAY DIFFRACTION99
2.8-2.90.20521320.17692620X-RAY DIFFRACTION99
2.9-3.020.2111380.1832603X-RAY DIFFRACTION99
3.02-3.160.25481260.18242643X-RAY DIFFRACTION99
3.16-3.330.19741600.17812622X-RAY DIFFRACTION99
3.33-3.530.20651470.16032630X-RAY DIFFRACTION99
3.53-3.810.19871550.1542618X-RAY DIFFRACTION99
3.81-4.190.17781430.1572680X-RAY DIFFRACTION99
4.19-4.790.18131370.15762670X-RAY DIFFRACTION99
4.79-6.040.21871490.19062709X-RAY DIFFRACTION99
6.04-43.230.20011530.20622840X-RAY DIFFRACTION99
精密化 TLS

手法: 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)
15.6207-0.5694-2.20445.214-2.42327.4649-0.0189-0.77350.87590.3660.1041-0.6742-0.8040.60990.11980.2732-0.0186-0.04210.2474-0.01720.2937-7.685-17.40533.549
22.3549-1.23690.9072.2599-0.70393.75140.10010.7320.0467-0.2192-0.21430.12960.01420.52060.10910.22790.00690.0550.3070.04970.2745-11.502-24.72223.017
33.15012.672-0.09663.0437-1.48332.5421-0.1492-0.11250.502-0.09020.3031.1331-0.0311-0.3513-0.12890.22920.02780.02570.32120.08810.3045-24.686-14.15123.585
42.3606-0.1223-0.49125.5374-0.56252.74-0.04260.22470.00360.04470.0652-0.09740.067-0.08560.01240.13710.01150.00540.169-0.0010.1531-18.24-21.51231.498
55.9936-4.30041.58077.2568-2.72565.38540.0082-0.3523-0.8901-0.40450.51620.70430.6412-0.4446-0.39390.23380.0025-0.00730.30530.00270.2837-22.668-28.60220.152
67.7133-1.4199-1.34151.85871.18463.18810.54080.3121-0.3265-0.4275-0.6764-0.57250.12750.03030.39160.520.0098-0.07770.65750.00830.466713.182-34.77948.615
76.22011.0039-0.24966.12655.83877.0894-0.0769-0.0272-0.34270.4331-0.33980.37820.612-0.37080.29050.25670.00910.00350.2993-0.0060.28914.611-42.97734.047
83.1882-1.0792-1.82252.60630.76233.6408-0.03960.3328-0.1697-0.3081-0.01980.0393-0.0082-0.02170.10310.20990.0147-0.04280.2617-0.03360.21947.566-34.33424.303
92.47020.2135-0.50753.69841.66514.12710.01150.2201-0.15080.58110.0129-1.2080.21811.01550.07640.2660.0705-0.04190.5368-0.05040.35822.856-41.17225.858
101.7672-0.4352-0.38135.04830.74882.376-0.0321-0.14260.08950.2008-0.0187-0.2182-0.1470.31430.06720.16770.0204-0.03390.3157-0.00930.184415.823-37.18732.368
119.6669-1.84280.28084.9116-1.94224.3770.1225-0.15911.2780.9196-0.2642-0.245-0.4806-0.21610.09510.3190.04820.04050.2973-0.08530.29855.304-23.34538.798
127.0112-4.8711-3.66418.9433.2824.92390.0107-0.28640.7574-0.00090.1609-0.1722-0.48790.4776-0.19740.2857-0.0638-0.01190.3830.00550.29817.707-27.67821.607
134.24830.7893-2.84685.7135-1.0062.0961-0.1167-0.6969-0.0588-0.2326-0.10010.21060.897-0.56551.00770.725-0.12180.10850.73730.02740.5499-3.523-51.33522.416
143.1740.4475-1.26965.36983.273.6523-0.1875-0.0184-0.66290.5033-0.062-0.11121.133-0.59580.21450.3193-0.0610.0430.2765-0.00480.3664-2.123-58.6446.768
153.83431.7942-1.89433.9789-1.60651.6589-0.41510.6674-0.3795-0.51350.34870.14330.5827-1.17560.00930.2389-0.08540.03030.3349-0.0740.3094-11.993-51.0324.921
161.6813-1.6768-1.78573.19120.0714.8089-0.17480.3511-0.2863-1.18540.16910.450.14-0.53870.02210.4463-0.107-0.01370.4114-0.07350.4562-3.505-46.495-10.024
177.1256-5.9268-1.22976.38250.16531.8049-0.0199-0.23790.3109-0.50410.1253-0.50490.03710.1732-0.11670.2637-0.05120.03170.27-0.02770.30479.666-45.427-1.334
182.2156-0.6472-1.07871.0561.62313.16740.02550.20310.2652-0.2650.0882-0.0417-0.1606-0.2683-0.18880.2262-0.01210.01320.2022-0.00860.2296-0.788-45.1972.442
193.7377-0.748-0.74232.51020.81823.7637-0.184-0.1661-0.12290.13690.14360.01720.12530.10380.04270.1534-0.0102-0.00080.12330.01420.1375-1.017-47.12810.542
207.0453-1.0072-5.88711.38661.37165.9640.48440.09790.6687-0.2367-0.07720.0031-0.7836-0.1859-0.28760.24980.0007-0.04320.25710.02980.2711-4.176-37.32-2.602
216.85410.05290.84874.0565-2.57496.819-0.1890.05420.72310.5995-0.1872-0.4164-1.5070.35060.38080.4803-0.1024-0.06620.3407-0.00760.38114.285-3.2287.089
222.9238-0.31030.173.36011.12711.77510.00950.01570.68050.1278-0.0729-0.6796-0.02160.7864-0.04310.3111-0.02320.00670.5020.06890.544311.423-12.2132.547
235.939-3.05323.85364.4986-2.18995.1609-0.43850.925-0.2589-0.52080.60430.2868-0.1675-0.5564-0.17950.4589-0.0648-0.00510.70.12710.4332.627-12.65-11.857
248.2424-5.23-1.05435.42232.08261.59090.05740.6815-0.0984-0.5634-0.04450.7283-0.2469-0.0944-0.10580.2559-0.0253-0.03490.33440.05320.2926-10.723-11.567-2.902
252.54060.1219-0.21182.9543-1.68712.5031-0.0135-0.1382-0.0110.07680.02410.0089-0.07510.1476-0.05550.1863-0.0069-0.00070.26530.0270.1938-0.372-13.9065.713
268.2084-0.63032.56035.6735-1.00814.3487-0.03540.0633-0.7173-0.41670.0347-0.79330.92210.0362-0.09940.2848-0.05420.07990.2832-0.02150.31681.337-22.566-5.27
279.633-2.951-7.18845.19690.42158.1867-0.3614-0.6908-0.22340.4371-0.0786-0.07680.58180.66290.61930.4812-0.0302-0.01570.31340.02060.3911-25.413-17.10358.299
281.0007-0.2472-1.13613.1986-1.20241.9940.0303-0.1908-0.14140.1648-0.1047-0.3790.13580.32760.10650.57870.0090.03610.28510.01040.4074-28.287-21.855.391
296.44633.5684-2.3295.4021-1.32535.6393-0.25420.1679-0.6663-0.3399-0.07630.51740.74480.18820.2910.53490.1024-0.00110.4366-0.0440.55-33.846-15.12539.287
302.09211.6039-1.57564.5847-0.6693.66320.11630.5230.7224-0.12040.16490.5933-0.4181-0.5486-0.37370.38590.0389-0.01870.3044-0.0140.4095-35.275-3.81548.864
313.05771.4703-0.33942.817-1.3552.2775-0.0279-0.01310.10190.2898-0.03180.1642-0.258-0.17940.09650.3334-0.0027-0.00850.1993-0.01890.3023-31.533-9.74755.347
326.44361.4925-0.25817.45643.18035.32770.4807-0.33950.42250.36090.20151.98410.1493-0.5338-0.21050.47590.02310.10490.40830.12880.6335-39.349-24.00963.669
336.73333.339-3.07092.0567-2.37446.4017-0.05540.4217-0.7936-0.16450.00630.10870.1713-0.51350.09160.36320.01570.01010.3682-0.04740.4977-42.922-12.52945.428
345.89350.13012.69555.5345-0.07553.1627-0.1165-0.46520.04720.65030.02270.2948-0.4677-0.5759-0.08640.4967-0.02740.01940.31830.0050.3553-39.228-39.08859.005
352.6141-0.5935-0.38954.91241.91294.32590.16420.22130.0539-0.4234-0.2531-0.0876-0.3192-0.46710.05620.4407-0.059-0.02480.31150.03980.4136-29.97-38.5949.86
363.05952.48861.09662.9880.90222.64660.1040.6307-1.0502-0.0074-0.0779-0.17410.5454-0.0692-0.04890.4747-0.042-0.05940.3097-0.03620.3548-36.611-56.02747.935
377.35580.98631.13382.40980.02583.41690.05310.0737-0.2207-0.0524-0.0597-0.11750.05830.3205-0.02220.3549-0.0167-0.01530.2270.02630.2953-31.049-47.3656.594
384.23312.00121.00026.94930.80924.4620.06530.313-0.33880.05210.0512-1.41990.1440.73110.01310.43440.0696-0.02230.39330.06540.4248-22.88-49.12645.299
396.14821.0476-0.01384.01052.65071.8403-0.4281.48070.7782-1.60470.43830.59770.8913-0.1329-0.31550.99240.0937-0.18651.06720.24310.943714.948-57.36114.551
406.0684-0.2290.05996.821.83351.84411.31550.1250.34290.6632-1.36720.3371-0.2001-0.4210.13741.06380.164-0.02730.9191-0.02750.781215.608-57.18737.883
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:90 )A8 - 90
2X-RAY DIFFRACTION2( CHAIN A AND RESID 91:122 )A91 - 122
3X-RAY DIFFRACTION3( CHAIN A AND RESID 123:137 )A123 - 137
4X-RAY DIFFRACTION4( CHAIN A AND RESID 138:203 )A138 - 203
5X-RAY DIFFRACTION5( CHAIN B AND RESID 303:323 )B303 - 323
6X-RAY DIFFRACTION6( CHAIN C AND RESID 4:10 )C4 - 10
7X-RAY DIFFRACTION7( CHAIN C AND RESID 11:90 )C11 - 90
8X-RAY DIFFRACTION8( CHAIN C AND RESID 91:122 )C91 - 122
9X-RAY DIFFRACTION9( CHAIN C AND RESID 123:137 )C123 - 137
10X-RAY DIFFRACTION10( CHAIN C AND RESID 138:193 )C138 - 193
11X-RAY DIFFRACTION11( CHAIN C AND RESID 194:206 )C194 - 206
12X-RAY DIFFRACTION12( CHAIN D AND RESID 303:323 )D303 - 323
13X-RAY DIFFRACTION13( CHAIN E AND RESID 6:10 )E6 - 10
14X-RAY DIFFRACTION14( CHAIN E AND RESID 11:90 )E11 - 90
15X-RAY DIFFRACTION15( CHAIN E AND RESID 91:107 )E91 - 107
16X-RAY DIFFRACTION16( CHAIN E AND RESID 108:118 )E108 - 118
17X-RAY DIFFRACTION17( CHAIN E AND RESID 119:137 )E119 - 137
18X-RAY DIFFRACTION18( CHAIN E AND RESID 138:163 )E138 - 163
19X-RAY DIFFRACTION19( CHAIN E AND RESID 164:205 )E164 - 205
20X-RAY DIFFRACTION20( CHAIN F AND RESID 303:324 )F303 - 324
21X-RAY DIFFRACTION21( CHAIN G AND RESID 9:91 )G9 - 91
22X-RAY DIFFRACTION22( CHAIN G AND RESID 92:107 )G92 - 107
23X-RAY DIFFRACTION23( CHAIN G AND RESID 108:118 )G108 - 118
24X-RAY DIFFRACTION24( CHAIN G AND RESID 119:137 )G119 - 137
25X-RAY DIFFRACTION25( CHAIN G AND RESID 138:204 )G138 - 204
26X-RAY DIFFRACTION26( CHAIN H AND RESID 303:324 )H303 - 324
27X-RAY DIFFRACTION27( CHAIN I AND RESID 9:26 )I9 - 26
28X-RAY DIFFRACTION28( CHAIN I AND RESID 27:107 )I27 - 107
29X-RAY DIFFRACTION29( CHAIN I AND RESID 108:119 )I108 - 119
30X-RAY DIFFRACTION30( CHAIN I AND RESID 120:143 )I120 - 143
31X-RAY DIFFRACTION31( CHAIN I AND RESID 144:193 )I144 - 193
32X-RAY DIFFRACTION32( CHAIN I AND RESID 194:204 )I194 - 204
33X-RAY DIFFRACTION33( CHAIN J AND RESID 303:323 )J303 - 323
34X-RAY DIFFRACTION34( CHAIN K AND RESID 9:88 )K9 - 88
35X-RAY DIFFRACTION35( CHAIN K AND RESID 89:118 )K89 - 118
36X-RAY DIFFRACTION36( CHAIN K AND RESID 119:137 )K119 - 137
37X-RAY DIFFRACTION37( CHAIN K AND RESID 138:202 )K138 - 202
38X-RAY DIFFRACTION38( CHAIN L AND RESID 303:323 )L303 - 323
39X-RAY DIFFRACTION39( CHAIN M AND RESID 303:310 )M303 - 310
40X-RAY DIFFRACTION40( CHAIN N AND RESID 303:311 )N303 - 311

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る