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- PDB-8czg: Human BAK in complex with the dF3 peptide -

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基本情報

登録情報
データベース: PDB / ID: 8czg
タイトルHuman BAK in complex with the dF3 peptide
要素
  • Bcl-2 homologous antagonist/killer
  • dF3 peptide
キーワードAPOPTOSIS / BAK / inhibitor / Bcl-2 family
機能・相同性
機能・相同性情報


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / porin activity / pore complex / thymocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / positive regulation of proteolysis / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / blood vessel remodeling / animal organ regeneration / Pyroptosis / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / protein-folding chaperone binding / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol
類似検索 - 分子機能
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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like ...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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / 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
Bcl-2 homologous antagonist/killer
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
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Aguilar, F. / Keating, A.E.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM110048 米国
引用ジャーナル: Structure / 年: 2023
タイトル: Peptides from human BNIP5 and PXT1 and non-native binders of pro-apoptotic BAK can directly activate or inhibit BAK-mediated membrane permeabilization.
著者: Aguilar, F. / Yu, S. / Grant, R.A. / Swanson, S. / Ghose, D. / Su, B.G. / Sarosiek, K.A. / Keating, A.E.
履歴
登録2022年5月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年1月11日Provider: repository / タイプ: Initial release
改定 1.12023年2月8日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22023年3月15日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32023年10月25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-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
E: dF3 peptide
F: dF3 peptide
G: dF3 peptide
H: dF3 peptide


分子量 (理論値)分子数
合計 (水以外)87,2468
ポリマ－87,2468
非ポリマー00
水6,125340
1
A: Bcl-2 homologous antagonist/killer
E: dF3 peptide


分子量 (理論値)分子数
合計 (水以外)21,8122
ポリマ－21,8122
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-21 kcal/mol
Surface area9020 Å2
手法PISA
2
B: Bcl-2 homologous antagonist/killer
F: dF3 peptide


分子量 (理論値)分子数
合計 (水以外)21,8122
ポリマ－21,8122
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-20 kcal/mol
Surface area9030 Å2
手法PISA
3
C: Bcl-2 homologous antagonist/killer
G: dF3 peptide


分子量 (理論値)分子数
合計 (水以外)21,8122
ポリマ－21,8122
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-20 kcal/mol
Surface area9190 Å2
手法PISA
4
D: Bcl-2 homologous antagonist/killer
H: dF3 peptide


分子量 (理論値)分子数
合計 (水以外)21,8122
ポリマ－21,8122
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-20 kcal/mol
Surface area9250 Å2
手法PISA
単位格子
Length a, b, c (Å)48.290, 65.260, 111.570
Angle α, β, γ (deg.)90.000, 102.120, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 23 through 76 or (resid 77...
21(chain B and (resid 23 through 76 or (resid 77...
31(chain C and (resid 23 through 47 or resid 55...
41(chain D and (resid 23 through 47 or resid 55...
12(chain E and (resid 1 or resid 3 through 21))
22(chain F and ((resid 1 and (name CA or name C or name O )) or resid 3 through 21))
32(chain G and ((resid 1 and (name CA or name...
42(chain H and ((resid 1 and (name CA or name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 23 through 76 or (resid 77...A23 - 76
121(chain A and (resid 23 through 76 or (resid 77...A77
131(chain A and (resid 23 through 76 or (resid 77...A21 - 184
141(chain A and (resid 23 through 76 or (resid 77...A21 - 184
151(chain A and (resid 23 through 76 or (resid 77...A21 - 184
161(chain A and (resid 23 through 76 or (resid 77...A21 - 184
211(chain B and (resid 23 through 76 or (resid 77...B23 - 76
221(chain B and (resid 23 through 76 or (resid 77...B77
231(chain B and (resid 23 through 76 or (resid 77...B22 - 183
241(chain B and (resid 23 through 76 or (resid 77...B22 - 183
251(chain B and (resid 23 through 76 or (resid 77...B22 - 183
261(chain B and (resid 23 through 76 or (resid 77...B22 - 183
311(chain C and (resid 23 through 47 or resid 55...C23 - 47
321(chain C and (resid 23 through 47 or resid 55...C55 - 76
331(chain C and (resid 23 through 47 or resid 55...C77
341(chain C and (resid 23 through 47 or resid 55...C23 - 184
351(chain C and (resid 23 through 47 or resid 55...C23 - 184
361(chain C and (resid 23 through 47 or resid 55...C23 - 184
371(chain C and (resid 23 through 47 or resid 55...C23 - 184
411(chain D and (resid 23 through 47 or resid 55...D23 - 47
421(chain D and (resid 23 through 47 or resid 55...D55 - 84
431(chain D and (resid 23 through 47 or resid 55...D85
441(chain D and (resid 23 through 47 or resid 55...D22 - 185
451(chain D and (resid 23 through 47 or resid 55...D22 - 185
461(chain D and (resid 23 through 47 or resid 55...D22 - 185
471(chain D and (resid 23 through 47 or resid 55...D22 - 185
112(chain E and (resid 1 or resid 3 through 21))E0
212(chain F and ((resid 1 and (name CA or name C or name O )) or resid 3 through 21))F1
222(chain F and ((resid 1 and (name CA or name C or name O )) or resid 3 through 21))F1 - 22
232(chain F and ((resid 1 and (name CA or name C or name O )) or resid 3 through 21))F1 - 22
312(chain G and ((resid 1 and (name CA or name...G1
322(chain G and ((resid 1 and (name CA or name...G0 - 22
332(chain G and ((resid 1 and (name CA or name...G0 - 22
412(chain H and ((resid 1 and (name CA or name...H1
422(chain H and ((resid 1 and (name CA or name...H0 - 21
432(chain H and ((resid 1 and (name CA or name...H0 - 21

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


分子量: 19037.320 Da / 分子数: 4 / 変異: C166S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BAK1, BAK, BCL2L7, CDN1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q16611
#2: タンパク質・ペプチド
dF3 peptide


分子量: 2774.216 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 340 / 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: 1.97 Å3/Da / 溶媒含有率: 37.57 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: PEG 3350 (20% w/v), 0.2 M calcium acetate

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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: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年11月23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: 0.9792 Å / 相対比: 1
反射解像度: 1.99→41.85 Å / Num. obs: 43206 / % possible obs: 92.3 % / 冗長度: 3.704 % / Biso Wilson estimate: 22.25 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.17 / Χ2: 0.87 / Net I/σ(I): 6 / Num. measured all: 160024 / Scaling rejects: 96
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.99-2.043.3270.7151.779462343628440.7950.82582.8
2.04-2.13.7290.6062.3911943336232030.8590.69495.3
2.1-2.163.7180.522.7411523324830990.9220.59595.4
2.16-2.223.6120.4483.1210865316230080.9070.51495.1
2.22-2.33.3680.3953.319823309329170.9320.45794.3
2.3-2.383.6310.3633.710378298328580.9430.41595.8
2.38-2.473.8230.2954.5110357285027090.9570.33595.1
2.47-2.573.7910.2634.919932277426200.9670.29894.4
2.57-2.683.7390.2225.419468268825320.9750.25394.2
2.68-2.813.7640.1856.488835251223470.9790.2193.4
2.81-2.963.4950.1666.897767241222220.9770.19292.1
2.96-3.143.7390.1447.817931229221210.9870.16492.5
3.14-3.363.9420.1199.37912216120070.9910.13492.9
3.36-3.633.9160.09710.747213201218420.9940.1191.6
3.63-3.983.810.08511.56347184616660.9950.09690.2
3.98-4.453.5110.07711.655196169414800.9940.0987.4
4.45-5.144.0680.07812.585374147613210.9950.08989.5
5.14-6.294.0770.07812.034538127211130.9940.08987.5
6.29-8.893.8240.06712.3431599868260.9980.07783.8
8.89-41.854.2480.04416.2320015724710.9990.04982.3

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
PDB_EXTRACT3.27データ抽出
精密化構造決定の手法: 分子置換
開始モデル: PDB:5VX0

5vx0


解像度: 1.99→41.85 Å / SU ML: 0.29 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 30.51 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2673 1988 4.62 %
Rwork0.228 41061 -
obs0.2299 43049 92 %
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: 106.19 Å2 / Biso mean: 32.6415 Å2 / Biso min: 14.12 Å2
精密化ステップサイクル: final / 解像度: 1.99→41.85 Å
タンパク質核酸リガンド溶媒全体
原子数5780 0 0 340 6120
Biso mean---27.69 -
残基数----721
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2946X-RAY DIFFRACTION10.765TORSIONAL
12B2946X-RAY DIFFRACTION10.765TORSIONAL
13C2946X-RAY DIFFRACTION10.765TORSIONAL
14D2946X-RAY DIFFRACTION10.765TORSIONAL
21E388X-RAY DIFFRACTION10.765TORSIONAL
22F388X-RAY DIFFRACTION10.765TORSIONAL
23G388X-RAY DIFFRACTION10.765TORSIONAL
24H388X-RAY DIFFRACTION10.765TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.040.38581190.33232587270682
2.04-2.090.29631440.27673016316095
2.09-2.160.28731550.26173009316495
2.16-2.220.30161410.26032987312895
2.22-2.30.30271470.24852989313694
2.3-2.40.32021520.25763061321396
2.4-2.510.3071390.24432982312195
2.51-2.640.28031450.23222996314194
2.64-2.80.2631480.23362969311793
2.8-3.020.23431420.23392929307191
3.02-3.320.31511430.22122948309193
3.32-3.80.2351400.19262940308092
3.8-4.790.20941330.18032861299489
4.79-41.850.2381400.22722787292785
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)
11.3762-1.0967-0.24644.59831.83642.7265-0.252-0.06280.00660.270.15520.15310.2048-0.27490.12260.1889-0.00390.02290.4128-0.00220.2254-22.95891.0175-1.8611
28.20182.60161.64486.1418-0.15110.4104-0.26170.0264-0.3434-0.44470.49540.0596-0.04330.3042-0.2380.2862-0.06840.03690.38560.00340.189-14.0578-10.8898-9.4498
34.7671-3.4529-2.45664.60731.15874.8319-0.04870.04860.1325-0.0119-0.01910.0365-0.0091-0.08910.0690.2399-0.0455-0.02450.34790.05420.244-21.5993-6.70723.1929
43.3050.5676-3.07111.3621-0.70636.252-0.29560.1717-0.517-0.29610.03070.20330.6032-0.47770.21290.25010.0012-0.03920.4074-0.03760.3269-23.3085-1.2481-16.068
56.0067-1.41241.93676.49390.01332.0043-0.05860.64320.04070.12010.4177-0.79860.05331.4716-0.21010.2552-0.03360.00270.57560.03160.3063-3.36225.0633-14.8017
64.3469-1.5882.66412.93620.43626.4492-0.30940.23770.34050.00610.1718-0.374-0.71640.21630.18520.256-0.0048-0.01810.20170.04770.2149-12.581512.7172-13.5698
77.4711-0.46055.77852.92140.11454.6909-0.13750.3060.1954-0.78880.1319-0.1739-0.46790.30090.10510.33710.12880.0380.4514-0.00180.1884-25.457316.9003-13.5572
84.7623-1.71671.25111.5277-0.34831.6713-0.0127-0.12110.17060.05120.0885-0.1049-0.1027-0.1724-0.06390.17790.02040.03880.31520.01250.193-15.23343.8753-9.0637
94.76073.1409-2.90175.8925-0.94328.23610.34040.10890.715-0.22110.03980.2562-0.7398-0.2274-0.33250.25690.11480.01270.3748-0.01240.2288-26.462916.3096-3.2316
105.23013.21070.81995.14230.95144.0623-0.33260.5606-0.2179-0.15320.35360.0247-0.2541-0.1716-0.05270.17430.02730.01810.5856-0.01090.1956-33.97826.4706-3.1298
111.7816-0.05382.0941.66650.83182.89630.24530.2559-0.1742-0.0420.0903-0.10940.41610.4416-0.14990.26550.0815-0.03840.1922-0.02390.262-16.350928.9257-51.3725
122.0127-0.92721.47072.3792-1.03082.4233-0.23070.0695-0.43710.0810.1142-0.41971.24031.57380.07770.34350.136-0.02630.4364-0.05930.3546-7.033528.4861-48.9658
133.93620.66530.40741.25840.313.81560.0377-0.22030.02610.0752-0.0919-0.032-0.07140.04430.0510.206-0.0175-0.00010.12110.00340.1827-18.077538.6943-43.0154
141.6077-0.4794-0.01812.98380.98941.8785-0.0356-0.161-0.05610.08090.08970.08720.0886-0.2345-0.00160.2064-0.00680.02540.30310.03070.22952.447629.9734-7.6063
150.3896-0.1680.03561.45620.16021.35620.205-0.4003-0.1162-0.2566-0.0010.18110.1203-0.25050.04720.1938-0.03840.00960.31260.03840.22784.944525.6838-1.4762
162.37630.29780.8273.20422.3685.76860.1093-0.32250.16140.1057-0.09750.43270.297-1.25660.03190.2161-0.05330.00450.40880.02770.2368-5.913231.9159-7.2895
176.22530.3025-1.96292.7741-0.08796.2340.0749-0.3241-0.7419-0.2714-0.2387-0.03030.455-0.2180.08420.269-0.021-0.03650.35990.00550.22974.91229.0413-24.6235
181.6055-0.3212-0.10724.8710.51223.79030.10270.14950.187-0.0178-0.2701-0.3495-0.22490.86320.04780.2248-0.08560.01960.49720.03970.178716.408839.5475-18.0492
192.5009-1.33210.95381.97320.33111.8492-0.0188-0.01160.0736-0.0629-0.0532-0.0987-0.16690.22120.06590.2066-0.05040.02620.27380.01240.23478.874136.7924-12.9464
202.39822.9687-0.16467.4442-0.73616.88150.0048-0.30320.6908-0.3271-0.33840.1922-0.5858-0.45120.30140.2170.046-0.01380.292-0.0380.3218-4.237145.6838-7.6369
212.559-0.5152-0.02222.64220.56433.2250.09190.2357-0.0761-0.2524-0.01090.19740.17620.3834-0.09890.2032-0.04710.00670.18180.01460.23149.46842.226-49.7021
229.1988-3.51162.3314.2979-1.60296.5610.2129-0.6065-0.5339-0.1240.233-0.02110.95430.4127-0.35740.42660.0381-0.07520.20360.01790.35297.6568-13.2329-43.0247
231.9760.20981.68320.62611.00486.54990.0410.2768-0.1603-0.0345-0.1256-0.29130.40211.05690.03860.21760.06670.01110.33680.02790.277214.668-1.6003-51.1813
247.648-0.6699-1.27343.1667-0.2998.4797-0.2828-0.1956-0.26730.53520.2695-0.23740.5467-0.02670.02020.39490.0155-0.05910.25050.05540.32037.1676-4.0044-30.1685
254.93840.9990.55716.00871.31566.37730.224-0.51030.26690.0683-0.22180.41-0.5365-1.2713-0.06380.28680.09340.02420.34530.01350.2027-5.0495.8271-36.469
262.86320.98131.04571.7823-0.44642.47790.0758-0.14050.11140.1123-0.0547-0.0112-0.0674-0.2746-0.00990.2352-0.028-0.00060.1277-0.00390.1982.76913.7923-41.5962
270.99041.1605-0.35012.0371-0.47330.2429-0.0066-0.06040.5562-0.04860.0459-0.3438-0.35310.1236-0.16650.6304-0.2323-0.11850.02750.00190.414510.997317.7186-45.6536
284.57620.62791.00075.5571.2736.78160.15720.1216-0.17650.2461-0.0986-1.17030.19931.52640.38870.3248-0.02890.04710.50450.14490.42820.46437.8885-46.9663
294.55461.2327-0.32374.73580.15772.87110.13540.8680.1004-0.1890.05260.2574-0.186-0.9795-0.08080.27680.0707-0.04250.53480.01920.2175-24.89188.6316-20.3066
302.3913-2.7906-0.9495.0216-0.20725.2268-0.0436-0.3598-0.07760.2279-0.2147-0.158-0.0480.49840.25680.2891-0.102-0.04560.3240.01310.2512-12.064640.9035-34.1211
317.261-0.3595-0.10584.58640.84244.7408-0.09120.72410.4909-0.3767-0.03260.1201-0.2039-0.52780.11620.2727-0.0058-0.02420.37380.0090.19130.459639.2686-24.1635
328.0727-0.8663-0.71413.9432-0.35423.9880.0428-1.62290.11070.5905-0.1326-0.1499-0.06560.36710.07970.3218-0.0944-0.03880.31810.02680.24410.13716.3524-30.0338
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 46 )A21 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 61 )A47 - 61
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 69 )A62 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 100 )A70 - 100
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 106 )A101 - 106
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 118 )A107 - 118
7X-RAY DIFFRACTION7chain 'A' and (resid 119 through 124 )A119 - 124
8X-RAY DIFFRACTION8chain 'A' and (resid 125 through 164 )A125 - 164
9X-RAY DIFFRACTION9chain 'A' and (resid 165 through 173 )A165 - 173
10X-RAY DIFFRACTION10chain 'A' and (resid 174 through 184 )A174 - 184
11X-RAY DIFFRACTION11chain 'B' and (resid 22 through 69 )B22 - 69
12X-RAY DIFFRACTION12chain 'B' and (resid 70 through 82 )B70 - 82
13X-RAY DIFFRACTION13chain 'B' and (resid 83 through 183 )B83 - 183
14X-RAY DIFFRACTION14chain 'C' and (resid 23 through 57 )C23 - 57
15X-RAY DIFFRACTION15chain 'C' and (resid 58 through 69 )C58 - 69
16X-RAY DIFFRACTION16chain 'C' and (resid 70 through 82 )C70 - 82
17X-RAY DIFFRACTION17chain 'C' and (resid 83 through 100 )C83 - 100
18X-RAY DIFFRACTION18chain 'C' and (resid 101 through 118 )C101 - 118
19X-RAY DIFFRACTION19chain 'C' and (resid 119 through 164 )C119 - 164
20X-RAY DIFFRACTION20chain 'C' and (resid 165 through 184 )C165 - 184
21X-RAY DIFFRACTION21chain 'D' and (resid 22 through 46 )D22 - 46
22X-RAY DIFFRACTION22chain 'D' and (resid 47 through 61 )D47 - 61
23X-RAY DIFFRACTION23chain 'D' and (resid 62 through 82 )D62 - 82
24X-RAY DIFFRACTION24chain 'D' and (resid 83 through 100 )D83 - 100
25X-RAY DIFFRACTION25chain 'D' and (resid 101 through 118 )D101 - 118
26X-RAY DIFFRACTION26chain 'D' and (resid 119 through 164 )D119 - 164
27X-RAY DIFFRACTION27chain 'D' and (resid 165 through 174 )D165 - 174
28X-RAY DIFFRACTION28chain 'D' and (resid 175 through 185 )D175 - 185
29X-RAY DIFFRACTION29chain 'E' and (resid 1 through 22 )E1 - 22
30X-RAY DIFFRACTION30chain 'F' and (resid 1 through 22 )F1 - 22
31X-RAY DIFFRACTION31chain 'G' and (resid 1 through 22 )G1 - 22
32X-RAY DIFFRACTION32chain 'H' and (resid 1 through 21 )H1 - 21

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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://pdbjlvh1.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