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基本情報

登録情報
データベース: PDB / ID: 7xge
タイトルCrystal structure of MCL-1 in complex with computationally designed inhibitor protein
要素
  • BCL-xL and MCL-1 dual binder 2
  • Induced myeloid leukemia cell differentiation protein Mcl-1
キーワードAPOTOSIS / DE NOVO PROTEIN / computational design
機能・相同性
機能・相同性情報


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / negative regulation of autophagy / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / positive regulation of neuron apoptotic process / channel activity / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
類似検索 - 分子機能
Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / 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 ...Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / 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 / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Induced myeloid leukemia cell differentiation protein Mcl-1
類似検索 - 構成要素
生物種synthetic construct (人工物)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.38 Å
データ登録者Oh, B.-H. / Kim, S.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Comput Struct Biotechnol J / 年: 2022
タイトル: Computational design of an apoptogenic protein that binds BCL-xL and MCL-1 simultaneously and potently.
著者: Kim, S. / Park, H.S. / Oh, B.H.
履歴
登録2022年4月4日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年7月20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

ダウンロードとリンク

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集合体

登録構造単位
A: BCL-xL and MCL-1 dual binder 2
B: Induced myeloid leukemia cell differentiation protein Mcl-1
C: BCL-xL and MCL-1 dual binder 2
D: Induced myeloid leukemia cell differentiation protein Mcl-1
E: BCL-xL and MCL-1 dual binder 2
F: Induced myeloid leukemia cell differentiation protein Mcl-1
G: BCL-xL and MCL-1 dual binder 2
H: Induced myeloid leukemia cell differentiation protein Mcl-1


分子量 (理論値)分子数
合計 (水以外)148,0678
ポリマ－148,0678
非ポリマー00
水3,369187
1
A: BCL-xL and MCL-1 dual binder 2
B: Induced myeloid leukemia cell differentiation protein Mcl-1


分子量 (理論値)分子数
合計 (水以外)37,0172
ポリマ－37,0172
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-14 kcal/mol
Surface area15600 Å2
手法PISA
2
C: BCL-xL and MCL-1 dual binder 2
D: Induced myeloid leukemia cell differentiation protein Mcl-1


分子量 (理論値)分子数
合計 (水以外)37,0172
ポリマ－37,0172
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-10 kcal/mol
Surface area14690 Å2
手法PISA
3
E: BCL-xL and MCL-1 dual binder 2
F: Induced myeloid leukemia cell differentiation protein Mcl-1


分子量 (理論値)分子数
合計 (水以外)37,0172
ポリマ－37,0172
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-13 kcal/mol
Surface area14230 Å2
手法PISA
4
G: BCL-xL and MCL-1 dual binder 2
H: Induced myeloid leukemia cell differentiation protein Mcl-1


分子量 (理論値)分子数
合計 (水以外)37,0172
ポリマ－37,0172
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-11 kcal/mol
Surface area14500 Å2
手法PISA
単位格子
Length a, b, c (Å)67.990, 74.770, 92.160
Angle α, β, γ (deg.)70.830, 89.590, 67.580
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 4 through 5 or resid 8...
21(chain C and (resid 4 through 5 or resid 8...
31(chain E and (resid 4 through 5 or resid 8...
41(chain G and (resid 4 through 5 or resid 8...
12(chain B and (resid 4 through 25 or resid 36...
22(chain D and (resid 4 through 25 or resid 36...
32(chain F and (resid 4 through 25 or resid 36...
42(chain H and (resid 4 through 38 or resid 40...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 5 or resid 8...A4 - 5
121(chain A and (resid 4 through 5 or resid 8...A8 - 9
131(chain A and (resid 4 through 5 or resid 8...A0
141(chain A and (resid 4 through 5 or resid 8...A40
151(chain A and (resid 4 through 5 or resid 8...A47 - 71
161(chain A and (resid 4 through 5 or resid 8...A73
171(chain A and (resid 4 through 5 or resid 8...A73
181(chain A and (resid 4 through 5 or resid 8...A75 - 98
191(chain A and (resid 4 through 5 or resid 8...A104 - 10113
1101(chain A and (resid 4 through 5 or resid 8...A117
1111(chain A and (resid 4 through 5 or resid 8...A4 - 171
1121(chain A and (resid 4 through 5 or resid 8...A129 - 130
1131(chain A and (resid 4 through 5 or resid 8...A4 - 171
1141(chain A and (resid 4 through 5 or resid 8...A136 - 1
1151(chain A and (resid 4 through 5 or resid 8...A157 - 15
1161(chain A and (resid 4 through 5 or resid 8...A161 - 164
211(chain C and (resid 4 through 5 or resid 8...C4 - 5
221(chain C and (resid 4 through 5 or resid 8...C8 - 9
231(chain C and (resid 4 through 5 or resid 8...C11 - 17
241(chain C and (resid 4 through 5 or resid 8...C19 - 35
251(chain C and (resid 4 through 5 or resid 8...C43 - 44
261(chain C and (resid 4 through 5 or resid 8...C7 - 71
271(chain C and (resid 4 through 5 or resid 8...C4 - 164
281(chain C and (resid 4 through 5 or resid 8...C75 - 98
291(chain C and (resid 4 through 5 or resid 8...C0
2101(chain C and (resid 4 through 5 or resid 8...C4 - 164
2111(chain C and (resid 4 through 5 or resid 8...C115
2121(chain C and (resid 4 through 5 or resid 8...C115
2131(chain C and (resid 4 through 5 or resid 8...C117
2141(chain C and (resid 4 through 5 or resid 8...C132 - 133
2151(chain C and (resid 4 through 5 or resid 8...C142 - 155
2161(chain C and (resid 4 through 5 or resid 8...C157 - 15
2171(chain C and (resid 4 through 5 or resid 8...C161 - 164
311(chain E and (resid 4 through 5 or resid 8...E4 - 5
321(chain E and (resid 4 through 5 or resid 8...E8 - 9
331(chain E and (resid 4 through 5 or resid 8...E11 - 17
341(chain E and (resid 4 through 5 or resid 8...E19 - 35
351(chain E and (resid 4 through 5 or resid 8...E43 - 44
361(chain E and (resid 4 through 5 or resid 8...E7 - 71
371(chain E and (resid 4 through 5 or resid 8...E4 - 164
381(chain E and (resid 4 through 5 or resid 8...E75 - 98
391(chain E and (resid 4 through 5 or resid 8...E0
3101(chain E and (resid 4 through 5 or resid 8...E4 - 164
3111(chain E and (resid 4 through 5 or resid 8...E115
3121(chain E and (resid 4 through 5 or resid 8...E115
3131(chain E and (resid 4 through 5 or resid 8...E117
3141(chain E and (resid 4 through 5 or resid 8...E132 - 133
3151(chain E and (resid 4 through 5 or resid 8...E142 - 155
3161(chain E and (resid 4 through 5 or resid 8...E157 - 15
3171(chain E and (resid 4 through 5 or resid 8...E161 - 164
411(chain G and (resid 4 through 5 or resid 8...G4 - 5
421(chain G and (resid 4 through 5 or resid 8...G8 - 9
431(chain G and (resid 4 through 5 or resid 8...G11 - 17
441(chain G and (resid 4 through 5 or resid 8...G43 - 44
451(chain G and (resid 4 through 5 or resid 8...G47 - 71
461(chain G and (resid 4 through 5 or resid 8...G7 - 71
471(chain G and (resid 4 through 5 or resid 8...G73
481(chain G and (resid 4 through 5 or resid 8...G700 - 102
491(chain G and (resid 4 through 5 or resid 8...G4 - 1091
4101(chain G and (resid 4 through 5 or resid 8...G4 - 167
4111(chain G and (resid 4 through 5 or resid 8...G115
4121(chain G and (resid 4 through 5 or resid 8...G4 - 167
4131(chain G and (resid 4 through 5 or resid 8...G129 - 130
4141(chain G and (resid 4 through 5 or resid 8...G133
4151(chain G and (resid 4 through 5 or resid 8...G4 - 167
4161(chain G and (resid 4 through 5 or resid 8...G142 - 155
4171(chain G and (resid 4 through 5 or resid 8...G157 - 159
4181(chain G and (resid 4 through 5 or resid 8...G161 - 164
112(chain B and (resid 4 through 25 or resid 36...B4 - 25
122(chain B and (resid 4 through 25 or resid 36...B36 - 38
132(chain B and (resid 4 through 25 or resid 36...B40 - 42
142(chain B and (resid 4 through 25 or resid 36...B44 - 75
152(chain B and (resid 4 through 25 or resid 36...B4 - 153
162(chain B and (resid 4 through 25 or resid 36...B112 - 115
172(chain B and (resid 4 through 25 or resid 36...B117 - 152
212(chain D and (resid 4 through 25 or resid 36...D4 - 25
222(chain D and (resid 4 through 25 or resid 36...D36 - 38
232(chain D and (resid 4 through 25 or resid 36...D4 - 154
242(chain D and (resid 4 through 25 or resid 36...D4 - 154
252(chain D and (resid 4 through 25 or resid 36...D112 - 1
262(chain D and (resid 4 through 25 or resid 36...D11715
272(chain D and (resid 4 through 25 or resid 36...D117 - 152
312(chain F and (resid 4 through 25 or resid 36...F4 - 25
322(chain F and (resid 4 through 25 or resid 36...F36 - 38
332(chain F and (resid 4 through 25 or resid 36...F40 - 42
342(chain F and (resid 4 through 25 or resid 36...F112 - 115
352(chain F and (resid 4 through 25 or resid 36...F4 - 154
362(chain F and (resid 4 through 25 or resid 36...F112 - 115
372(chain F and (resid 4 through 25 or resid 36...F117 - 152
412(chain H and (resid 4 through 38 or resid 40...H4 - 38
422(chain H and (resid 4 through 38 or resid 40...H40 - 42
432(chain H and (resid 4 through 38 or resid 40...H44 - 75
442(chain H and (resid 4 through 38 or resid 40...H77 - 110
452(chain H and (resid 4 through 38 or resid 40...H112 - 115
462(chain H and (resid 4 through 38 or resid 40...H117 - 152

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
BCL-xL and MCL-1 dual binder 2


分子量: 19149.291 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3)
#2: タンパク質
Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


分子量: 17867.512 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MCL1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q07820
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 187 / 由来タイプ: 天然 / 式: H2O

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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: 2.74 Å3/Da / 溶媒含有率: 55.09 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 12% PEG 6,000 (w/v), 0.1M Magnesium chloride, 0.1M ADA (pH 6.5)

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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: PAL/PLS / ビームライン: 5C (4A) / 波長: 0.97959 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2021年3月3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: 0.97959 Å / 相対比: 1
反射解像度: 2.38→29.46 Å / Num. obs: 61301 / % possible obs: 97.36 % / 冗長度: 3.6 % / CC1/2: 0.99 / Net I/σ(I): 14
反射 シェル解像度: 2.38→2.47 Å / Num. unique obs: 6115 / CC1/2: 0.721

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: design model

解像度: 2.38→29.46 Å / SU ML: 0.3 / 交差検証法: THROUGHOUT / σ(F): 1.98 / 位相誤差: 26.79 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2403 3064 5 %
Rwork0.2024 58223 -
obs0.2042 61287 97.34 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 165.94 Å2 / Biso mean: 70.892 Å2 / Biso min: 32.82 Å2
精密化ステップサイクル: final / 解像度: 2.38→29.46 Å
タンパク質核酸リガンド溶媒全体
原子数9769 0 0 187 9956
Biso mean---57.69 -
残基数----1219
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A1300X-RAY DIFFRACTION4.979TORSIONAL
12C1300X-RAY DIFFRACTION4.979TORSIONAL
13E1300X-RAY DIFFRACTION4.979TORSIONAL
14G1300X-RAY DIFFRACTION4.979TORSIONAL
21B1572X-RAY DIFFRACTION4.979TORSIONAL
22D1572X-RAY DIFFRACTION4.979TORSIONAL
23F1572X-RAY DIFFRACTION4.979TORSIONAL
24H1572X-RAY DIFFRACTION4.979TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.38-2.420.3181400.2922673281397
2.42-2.460.30281370.27152596273397
2.46-2.50.28271400.26282666280697
2.5-2.540.28521380.25332612275097
2.54-2.590.2941380.25162619275797
2.59-2.650.27751390.24582647278697
2.65-2.70.27861380.24192629276797
2.7-2.770.3121400.24832663280397
2.77-2.840.30541400.2452662280297
2.84-2.910.3011380.26082632277098
2.91-30.3131390.23712641278098
3-3.090.27061420.23772684282698
3.09-3.210.28991380.23622633277198
3.21-3.330.27451380.23572627276597
3.33-3.480.24931400.22872661280197
3.49-3.670.27621390.20472632277197
3.67-3.90.23041390.1922643278298
3.9-4.20.18011410.17552680282197
4.2-4.620.20661380.16212627276597
4.62-5.280.23431390.17582641278097
5.28-6.640.21551410.20882663280498
6.65-29.460.18861420.15452692283499
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)
14.03932.0204-0.29352.0655-0.27741.8250.11550.35330.31970.03740.10250.040.07480.0489-0.21230.39750.0342-0.0120.35870.03390.4092-20.792335.327532.6189
24.42-0.0266-0.66842.06640.54632.8652-0.20180.1114-0.73040.30990.0964-0.19460.56490.1335-0.07250.47680.0207-0.04570.34060.0330.4724-25.424325.756737.0727
34.6761-0.40772.99920.30690.18712.59921.12773.07650.586-1.2267-0.9705-1.0934-0.173.0780.56650.98610.32040.10991.5325-0.05611.1294-0.330227.298215.2801
41.3804-0.1239-0.00041.54560.51942.51760.12650.8406-0.25060.10990.0808-0.08480.1206-0.2728-0.14570.52510.01-0.06980.4624-0.02610.5256-29.957223.410228.4191
52.0334-1.3311-0.24884.38590.73761.92070.0528-0.8487-0.3011.8589-0.1713-0.91560.40250.5050.01090.80070.0261-0.17310.73110.10050.5496-9.892739.619156.4338
61.3020.4048-0.13230.7216-0.24810.25170.9664-0.5017-0.1379-0.5284-0.5910.8805-0.21430.59940.00561.40090.2057-0.15110.94930.10940.9543-10.29637.095665.4024
72.3508-0.5987-0.10291.7880.22861.89320.0519-0.26-0.47460.44830.0753-0.3050.17690.4902-0.22220.53450.0144-0.07690.52440.04730.58-11.210134.741443.8948
80.365-0.5554-0.61192.00610.62941.35720.0025-0.14580.06020.24250.1384-0.58490.21480.4603-0.14510.44240.05-0.14110.54320.0440.497-9.089239.372247.5278
92.4151-0.79261.84276.61442.0485.02560.4747-0.3702-0.28541.3209-0.76081.1840.5692-0.37150.01750.6786-0.00740.10060.58810.0680.5198-25.427240.177653.3859
104.6264-0.24231.01072.4870.65253.93580.12550.21460.0931-0.2726-0.10480.00010.0041-0.2216-0.04210.3635-0.01350.04950.39280.02450.4156-26.040467.694541.1115
113.2574-3.1624-3.27884.22924.32664.420.134-0.991-1.0859-0.4499-0.0637-0.91491.24731.36960.5190.8439-0.1014-0.42311.8769-0.1941.8318-8.871178.654763.8623
122.038-1.1906-2.05382.95510.83922.00850.0577-0.1551-0.348-0.0669-0.01070.0991-0.0975-0.52640.21380.40370.01870.05920.5736-0.02260.5649-33.196773.501349.4439
132.13761.36120.18725.34980.18222.992-0.10630.95630.3156-1.06720.1811-0.3352-0.08380.6629-0.09680.6219-0.05890.1690.81170.05840.5208-8.07662.61822.439
147.8356-2.2091-4.5797.5395-1.58133.89870.54460.46880.7842-1.41010.0747-1.2849-1.05180.8055-0.32260.881-0.4078-0.1311.44520.35091.1061-7.358571.142516.4177
151.82850.12140.14121.53211.09443.3791-0.04360.64130.6029-0.9834-0.07910.1654-0.9704-0.1612-0.07260.7917-0.09340.03380.72950.20910.5673-18.024368.976422.6702
166.7283-0.77540.94771.5980.04032.3775-0.121-0.43451.0906-0.06640.1278-0.3321-0.47680.5984-0.06160.5153-0.12020.09460.5753-0.05870.7116-9.727273.55941.2166
172.63391.0480.09721.93240.07933.06150.1604-0.14040.0704-0.2647-0.0027-0.5390.31050.4317-0.14610.47830.05740.06720.4935-0.01010.5952-10.85359.325939.676
182.18170.40480.62261.96571.02632.03440.01460.1793-0.0981-0.30340.1916-0.6083-0.04760.4132-0.10730.4636-0.060.09650.52620.03030.4789-9.332562.803131.2556
193.8571-1.4946-1.95336.22720.91273.1370.53391.0416-0.124-0.839-0.93270.8837-0.6976-0.44480.10420.73020.035-0.08680.6687-0.04340.4299-24.001259.697621.7191
203.9979-0.2407-1.9212.10541.13043.86290.36980.09650.4421-0.4490.0081-0.2984-0.2672-0.0215-0.40560.4739-0.03550.00830.5085-0.00790.4195-35.370229.51549.551
214.6255-0.7751-1.11643.3420.83583.80960.10530.51970.06280.0451-0.16740.00270.4132-0.3694-0.05740.4277-0.035-0.05880.42930.06410.4115-43.738426.35165.4123
223.9524-0.6645-0.75732.38760.35574.5673-0.1137-0.0557-0.5980.23020.2838-0.15841.12380.5114-0.07790.59950.0294-0.15590.4105-0.00910.6185-33.486916.86528.3459
231.42570.66851.60711.8066-0.05452.50490.1771-0.14040.2988-0.01070.142-0.36810.08350.0282-0.24110.4073-0.0344-0.02040.5662-0.03180.4884-33.448127.081119.5123
242.2448-2.32132.80232.427-3.05384.34210.75160.0742-0.5532-0.4161-0.31860.44850.0927-0.5047-0.44931.16930.2608-0.17841.6676-0.03951.1468-13.626412.28985.4475
251.9329-0.0267-0.42561.61930.67682.49010.06330.3049-1.0591-0.3205-0.09180.40721.2113-0.49430.04270.7309-0.0849-0.06250.5515-0.16590.8389-51.717512.839-7.3386
263.5818-0.7034-0.71972.10610.32473.80030.0359-0.0697-0.22650.0285-0.06010.39490.4004-0.5491-0.05230.5341-0.1165-0.07130.61520.0070.5384-54.253824.67546.2052
272.01780.1412-0.26432.0087-0.09875.35240.15630.2554-0.2943-0.0826-0.03910.22080.5815-0.34120.0140.4975-0.064-0.03030.3797-0.08820.4953-51.679420.0732-4.7975
284.14461.1901-0.17972.60720.42122.12060.14250.15430.16040.0164-0.01620.1281-0.1258-0.0684-0.07960.3880.05280.02080.40530.03420.3974-43.838346.4021-21.2327
291.8716-0.6268-1.13631.7323-0.90123.73120.04440.576-0.1975-0.1520.1459-0.265-0.2782-0.0272-0.13330.43030.1020.05760.50660.05690.3932-37.93147.5572-31.7755
301.9845-0.65411.29792.1553-0.94732.87580.1426-0.46221.1710.8976-0.23750.1522-1.0676-0.2217-0.15530.91450.17440.24780.6758-0.16940.8378-55.648754.90541.2451
312.2855-0.8190.88041.29510.12165.513-0.2258-0.11111.15040.45860.21710.4185-2.14520.39490.37740.93130.02830.13390.4678-0.07451.064-47.992760.1433-5.6643
323.11050.90560.45683.13360.23482.63940.27930.31420.31110.2127-0.20340.7105-0.2218-0.6147-0.06650.4930.11020.11790.584-0.00830.5445-57.841445.4625-14.3146
331.9936-0.28730.70762.0573-0.01482.50270.13020.2540.0950.1219-0.1410.7044-0.427-0.7290.07340.5830.17830.05280.6169-0.02250.7157-57.598253.3165-10.9849
341.76020.61421.20422.007-0.35571.49430.2554-0.5803-0.25330.31450.0480.5267-0.2566-0.7624-0.17120.57140.14790.12950.6098-0.07560.4809-55.215145.5159-0.8207
351.2072-0.9173-0.85185.2923-3.25118.71440.5591-0.01070.20620.5816-0.5602-0.1507-1.37172.45810.03580.6516-0.0796-0.03030.6032-0.07470.5096-40.396552.2679-0.3131
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 77 )A4 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 120 )A78 - 120
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 125 )A121 - 125
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 171 )A126 - 171
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 23 )B4 - 23
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 35 )B24 - 35
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 92 )B36 - 92
8X-RAY DIFFRACTION8chain 'B' and (resid 93 through 140 )B93 - 140
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 153 )B141 - 153
10X-RAY DIFFRACTION10chain 'C' and (resid 4 through 120 )C4 - 120
11X-RAY DIFFRACTION11chain 'C' and (resid 121 through 125 )C121 - 125
12X-RAY DIFFRACTION12chain 'C' and (resid 126 through 164 )C126 - 164
13X-RAY DIFFRACTION13chain 'D' and (resid 4 through 23 )D4 - 23
14X-RAY DIFFRACTION14chain 'D' and (resid 24 through 35 )D24 - 35
15X-RAY DIFFRACTION15chain 'D' and (resid 36 through 55 )D36 - 55
16X-RAY DIFFRACTION16chain 'D' and (resid 56 through 71 )D56 - 71
17X-RAY DIFFRACTION17chain 'D' and (resid 72 through 92 )D72 - 92
18X-RAY DIFFRACTION18chain 'D' and (resid 93 through 140 )D93 - 140
19X-RAY DIFFRACTION19chain 'D' and (resid 141 through 154 )D141 - 154
20X-RAY DIFFRACTION20chain 'E' and (resid 4 through 35 )E4 - 35
21X-RAY DIFFRACTION21chain 'E' and (resid 36 through 78 )E36 - 78
22X-RAY DIFFRACTION22chain 'E' and (resid 79 through 117 )E79 - 117
23X-RAY DIFFRACTION23chain 'E' and (resid 118 through 159 )E118 - 159
24X-RAY DIFFRACTION24chain 'E' and (resid 160 through 164 )E160 - 164
25X-RAY DIFFRACTION25chain 'F' and (resid 4 through 55 )F4 - 55
26X-RAY DIFFRACTION26chain 'F' and (resid 56 through 92 )F56 - 92
27X-RAY DIFFRACTION27chain 'F' and (resid 93 through 154 )F93 - 154
28X-RAY DIFFRACTION28chain 'G' and (resid 4 through 125 )G4 - 125
29X-RAY DIFFRACTION29chain 'G' and (resid 126 through 167 )G126 - 167
30X-RAY DIFFRACTION30chain 'H' and (resid 4 through 23 )H4 - 23
31X-RAY DIFFRACTION31chain 'H' and (resid 24 through 55 )H24 - 55
32X-RAY DIFFRACTION32chain 'H' and (resid 56 through 92 )H56 - 92
33X-RAY DIFFRACTION33chain 'H' and (resid 93 through 115 )H93 - 115
34X-RAY DIFFRACTION34chain 'H' and (resid 116 through 140 )H116 - 140
35X-RAY DIFFRACTION35chain 'H' and (resid 141 through 152 )H141 - 152

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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