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- PDB-8bdn: VCB in complex with compound 23 -

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基本情報

登録情報
データベース: PDB / ID: 8bdn
タイトルVCB in complex with compound 23
要素
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
キーワードLIGASE / PROTAC / degrader / complex / E3 ligase / VHL / VCB / VH032
機能・相同性
機能・相同性情報


regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / transcription elongation factor activity / VCB complex / elongin complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / transcription elongation factor activity / VCB complex / elongin complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle / Cul2-RING ubiquitin ligase complex / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / negative regulation of signal transduction / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / protein serine/threonine kinase binding / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / transcription corepressor binding / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / cell morphogenesis / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / microtubule cytoskeleton / regulation of gene expression / Replication of the SARS-CoV-2 genome / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / cellular response to hypoxia / molecular adaptor activity / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / cilium / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol
類似検索 - 分子機能
von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B ...von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-QFR / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
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: 2.76 Å
データ登録者Sorrell, F.J. / Mueller, J.E. / Lehmann, M. / Wegener, A.
資金援助 ドイツ, 1件
組織認可番号国
Not funded ドイツ
引用ジャーナル: Chemmedchem / 年: 2023
タイトル: Systematic Potency and Property Assessment of VHL Ligands and Implications on PROTAC Design.
著者: Krieger, J. / Sorrell, F.J. / Wegener, A.A. / Leuthner, B. / Machrouhi-Porcher, F. / Hecht, M. / Leibrock, E.M. / Muller, J.E. / Eisert, J. / Hartung, I.V. / Schlesiger, S.
履歴
登録2022年10月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年2月15日Provider: repository / タイプ: Initial release
改定 1.12023年3月22日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22023年4月26日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume
改定 1.32024年2月7日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.42024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-B
H: Elongin-C
I: von Hippel-Lindau disease tumor suppressor
J: Elongin-B
K: Elongin-C
L: von Hippel-Lindau disease tumor suppressor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)168,57216
ポリマ－166,53312
非ポリマー2,0384
水73941
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
J: Elongin-B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)53,9955
ポリマ－53,4864
非ポリマー5101
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-37 kcal/mol
Surface area16860 Å2
手法PISA
2
C: von Hippel-Lindau disease tumor suppressor
D: Elongin-B
E: Elongin-C
K: Elongin-C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)53,1185
ポリマ－52,6084
非ポリマー5101
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-37 kcal/mol
Surface area16860 Å2
手法PISA
3
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-B
L: von Hippel-Lindau disease tumor suppressor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,4845
ポリマ－49,4653
非ポリマー1,0192
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-39 kcal/mol
Surface area17050 Å2
手法PISA
4
H: Elongin-C
I: von Hippel-Lindau disease tumor suppressor
L: von Hippel-Lindau disease tumor suppressor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)49,6065
ポリマ－48,5873
非ポリマー1,0192
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-38 kcal/mol
Surface area16500 Å2
手法PISA
単位格子
Length a, b, c (Å)93.173, 93.173, 358.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 1 through 35 or (resid 36...
d_2ens_1(chain "D" and ((resid 1 and (name N or name...
d_3ens_1(chain "G" and (resid 1 through 18 or (resid 19...
d_4ens_1(chain "J" and (resid 1 through 18 or (resid 19...
d_1ens_2(chain "B" and ((resid 16 through 17 and (name N...
d_2ens_2(chain "E" and ((resid 16 through 17 and (name N...
d_3ens_2(chain "H" and ((resid 16 through 17 and (name N...
d_4ens_2(chain "K" and ((resid 16 through 17 and (name N...
d_1ens_3(chain "C" and ((resid 62 and (name N or name...
d_2ens_3(chain "F" and (resid 62 through 68 or (resid 69...
d_3ens_3(chain "I" and ((resid 62 and (name N or name...
d_4ens_3(chain "L" and (resid 62 through 68 or (resid 69...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METARGA1 - 80
d_12ens_1ASPLYSA82 - 104
d_21ens_1METARGE1 - 80
d_22ens_1ASPLYSE82 - 104
d_31ens_1METARGI1 - 80
d_32ens_1ASPLYSI82 - 104
d_41ens_1METLYSM1 - 103
d_11ens_2METSERB1 - 32
d_12ens_2ASNCYSB37 - 91
d_21ens_2METSERF1 - 32
d_22ens_2ASNCYSF36 - 90
d_31ens_2METSERJ1 - 32
d_32ens_2ASNCYSJ36 - 90
d_41ens_2METSERN1 - 32
d_42ens_2ASNCYSN34 - 88
d_11ens_3VALPROC1 - 34
d_12ens_3PROASPC36 - 129
d_13ens_3PROGLUC131 - 143
d_14ens_3UNLUNLD
d_21ens_3VALPROG1 - 34
d_22ens_3PROASPG36 - 129
d_23ens_3PROGLUG131 - 143
d_24ens_3UNLUNLH
d_31ens_3VALPROK1 - 34
d_32ens_3PROASPK36 - 129
d_33ens_3PROGLUK131 - 143
d_34ens_3UNLUNLL
d_41ens_3VALPROO1 - 34
d_42ens_3PROASPO36 - 129
d_43ens_3PROGLUO131 - 143
d_44ens_3UNLUNLP

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

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要素

#1: タンパク質
Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


分子量: 11852.389 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: ELOB, TCEB2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15370
#2: タンパク質
Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


分子量: 10974.616 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: ELOC, TCEB1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15369
#3: タンパク質
von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


分子量: 18806.273 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: VHL / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P40337
#4: 化合物
ChemComp-QFR / (2~{R})-3-methyl-1-[(2~{S},4~{R})-2-[(5~{R})-5-methyl-5-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-4~{H}-1,2,4-oxadiazol-3-yl]-4-oxidanyl-pyrrolidin-1-yl]-2-(3-methyl-1,2-oxazol-5-yl)butan-1-one


分子量: 509.620 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C26H31N5O4S / タイプ: SUBJECT OF INVESTIGATION
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 41 / 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
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: 2.35 Å3/Da / 溶媒含有率: 47.66 %
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: 10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, soaked with 1mM compound

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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: SLS / ビームライン: X10SA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2021年12月19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: 1 Å / 相対比: 1
反射解像度: 2.76→358.85 Å / Num. obs: 42223 / % possible obs: 95.1 % / 冗長度: 12.9 % / Biso Wilson estimate: 71.98 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.057 / Rrim(I) all: 0.202 / Net I/σ(I): 9.1
反射 シェル解像度: 2.766→2.814 Å / 冗長度: 12.3 % / Rmerge(I) obs: 2.804 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1937 / CC1/2: 0.44 / Rpim(I) all: 0.556 / Rrim(I) all: 3.03 / % possible all: 40.2

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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精密化
XDSデータ削減
Aimless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: 5nw1

5nw1


解像度: 2.76→65.88 Å / SU ML: 0.4229 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 29.1625
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.2631 2153 5.12 %RANDOM
Rwork0.2093 39896 --
obs0.212 42049 99.77 %-
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
原子変位パラメータBiso mean: 74.7 Å2
精密化ステップサイクル: LAST / 解像度: 2.76→65.88 Å
タンパク質核酸リガンド溶媒全体
原子数10647 0 144 41 10832
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.009211069
X-RAY DIFFRACTIONf_angle_d1.488515089
X-RAY DIFFRACTIONf_chiral_restr0.08771730
X-RAY DIFFRACTIONf_plane_restr0.01561959
X-RAY DIFFRACTIONf_dihedral_angle_d10.27591616
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.692480814373
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.806745306191
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.83156295611
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.818802280976
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.837983181855
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.770924947323
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.786047380134
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.776548998064
ens_3d_4CX-RAY DIFFRACTIONTorsion NCS0.849585375675
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.820.3721470.33182610X-RAY DIFFRACTION100
2.82-2.890.36511370.31622587X-RAY DIFFRACTION99.89
2.89-2.970.39191410.29462615X-RAY DIFFRACTION99.96
2.97-3.060.34651550.27622596X-RAY DIFFRACTION99.93
3.06-3.150.34921570.27472592X-RAY DIFFRACTION99.93
3.15-3.270.31221250.25962639X-RAY DIFFRACTION99.89
3.27-3.40.33651290.25462640X-RAY DIFFRACTION99.96
3.4-3.550.25791420.22732640X-RAY DIFFRACTION99.93
3.55-3.740.27471520.22442633X-RAY DIFFRACTION99.93
3.74-3.970.26631310.20762636X-RAY DIFFRACTION99.82
3.97-4.280.26731330.1882690X-RAY DIFFRACTION99.75
4.28-4.710.19741570.16192673X-RAY DIFFRACTION99.89
4.71-5.390.21341520.17022687X-RAY DIFFRACTION99.86
5.39-6.790.28611430.21772750X-RAY DIFFRACTION99.69
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)
14.323231853470.329666045726-0.6062914072177.61500220149-0.821447545026.943465896270.1122458256150.05995488603790.241353772242-0.0100527312981-0.2965419465210.536857609583-0.509431135082-0.2365591980250.2020742565470.5554900052630.0211986221205-0.04784885142830.5453992664060.02158830250510.475965586252-20.910746877645.7653025074-39.9299046885
23.21883089365-0.0640909164069-0.1735447515796.468286450071.332542206427.21837016481-0.2350205402760.7524268148460.725209130094-2.076061297760.06734171382360.992491053738-1.26266965583-2.136268609630.1163045544841.01546081950.22526009438-0.1304216688780.883958579439-0.03182680231410.666952372526-27.529430984151.486603275-46.5059528466
36.37753537568-0.9233839754370.1468898097673.24976728043-3.584001236584.20154722589-1.411217941760.210519666174-1.04268182849-1.024960961531.04449107743-0.4542006066110.487630098906-1.7343481626-0.04541632012041.00084593182-0.0920204379331-0.05985736436991.12935340997-0.002463373008010.52849301155-16.901830472443.2474199074-51.5680457982
48.582754014493.416475882051.389863928925.183847787855.478238424158.123933093990.8160271038890.691605705720.259751278723-0.0197828757811-0.3574976361440.2634873853321.145798355650.519130095293-0.5492489113960.5203666555050.100161573378-0.05287385146740.677756797176-0.06150162293120.652697251642-20.142571332536.2276026014-44.0331186894
53.193485391691.9041998551-0.5757734880961.983820592921.088078496852.99474190625-0.1968801365151.021622662030.260603152514-0.515648261229-0.09777184309920.0437914333922-0.6387656063371.275921449370.1122156222120.914034265929-0.04338679725150.05871594757260.583697592241-0.04460003821940.509750120476-17.814257772550.0215919635-46.026559036
65.690633676581.682285169083.457427873334.557260755752.396707657795.51660930765-0.9627383261420.6831704509822.10517777438-2.237736580480.407871697161-0.547307108266-0.8042656833830.01831446137790.9437598113170.919703772274-0.1537754331390.424007288820.8546088711750.180886036871.00156467863-5.7633737776355.1726426828-40.457643605
72.96420858281-1.191288010011.584109444830.860833620647-0.2508632810373.12920995666-1.13865226448-2.66663523268-0.1081475549741.090879857810.0311367984879-1.708818694260.2327842384021.821236200920.6006605564850.7129726255960.0787066343268-0.2037229750931.174249232630.1175395763581.211885320749.6733046105450.4026899093-25.1321130407
89.375672306634.97381927097-0.7311611344284.9485365443-0.6779405457812.76377963983-0.256562074591.602789961740.4630475400170.1683736434810.4967640961020.511134120849-0.179323084806-0.527453482555-0.02319766582170.8831700311430.0214937180576-0.08270684781890.6562064369730.004737441687450.605796363968-19.746441648457.9498803458-31.6967879103
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562.38345471461-5.08212953042-4.299230989745.049499297191.173094890844.134877727180.1820498499750.9721705339040.1094238190310.506928546366-0.770724974986-0.001715494379170.842175434773-1.415050921320.4864107553850.500423358202-0.104878931262-0.09321029398790.7707126805830.0007291877515260.8119617676811.1999948646242.8086067491-68.8593048503
578.001070944162.1095038355-0.927868459596.384040376151.142769690285.50798884351-0.6910285225540.733493397835-0.622627421855-1.117248851080.08643867418930.09106272847740.310502664933-0.8078498676390.1662987113950.475524404060.0121778272674-0.1176227213430.619479354668-0.07623633583220.583812723208-32.033819552231.4227169432-92.8666559723
585.353012041062.22029202492-0.7905254865133.737361168072.975323285563.226463222190.143411958203-0.1710018538410.0621722566782-0.125667226751-0.071593914021-0.0235390898931-0.00467734998561-0.1890542184090.08561237073810.5337883160030.09626415299790.007389967595930.6061557666470.0274226950930.574656688619-27.840930815239.9425701608-80.1156387083
594.753744600580.8104576290091.595101148117.212943879793.28510706094.78801570963-0.0915066413440.0855563255707-0.469556035391-0.0706804120310.0526100371401-0.07043686351050.110686637604-0.09623122765270.1421452569080.4994774576920.06180356371670.04147905885110.5139510487170.05677831275270.340925291996-26.380548341733.4853154869-82.3980600545
606.2433131721.434509439543.250315806752.836997633012.720132024663.31363178140.492594021573-0.628684921802-0.2616904040570.322319216443-0.6059716116060.0008403060569480.323907042558-0.1733500792720.2894387797170.6057812063550.06634599505630.07653621049590.7501065089550.09592254179620.487324344988-22.856810414932.110718167-74.426973877
612.807615699280.4764789356030.8578025558283.54963082049-0.2678851355975.17702693942-0.4987894941360.9198950106940.4833946200030.0535891036850.13523837362-0.354318793094-1.334630691931.374676070430.4167377748030.639029631312-0.180769250755-0.2427638477471.073441865050.1665830842170.6691443549-2.1952769826449.9353144529-75.916570532
623.528984512321.053411122084.245919005953.846142202131.4628126426.57131645423-0.928109776480.5128486623191.53888486307-0.2921228745370.234095604887-0.331989663065-1.449502616781.339148167490.369646860990.832689737511-0.1018397735570.02582897691461.175673086260.1586027678680.855757300297-4.53882946646.732204645-82.7136662015
631.64422033019-2.54297193104-0.6282819722077.56075405648-0.2548338583242.614783726110.539481641229-0.08966812493740.00400436505771-2.90968192633-0.183455411838-2.814733925150.137473930354-0.0007577458278820.4348937124511.02788248125-0.10613104450.01716353710540.7641639546410.1369091246660.923613397259-11.818335127734.1102223366-92.0993156018
646.18882692564-0.928093594346-0.3351741211398.43135463388-0.6447477356632.658842104360.7663451195-0.2346537462520.413961927719-0.596107521271-0.6071705790851.18751614565-0.521518992595-1.166240592890.08720548391140.7698407148490.0433718884005-0.006471129410710.6483277147380.009869875627590.554565047121-15.5839559522-2.03638940823-37.8870645433
655.480897800382.51558502904-1.763784228866.5584149321-0.6404532212396.27324738380.2617639168050.05980821507460.380995463418-0.576158273732-0.3820023560841.09139614373-0.312058812501-1.518832613710.005662347961720.7066563110270.111016238729-0.06588439121680.8253644380040.1047997819350.620679693941-19.95472881983.83626541903-42.706135809
665.93257347712-1.637758226050.3841995058449.25486592979-2.036041142887.352947580711.48545739655-0.3018192918461.54078159231-2.13213324772-1.74143374318-0.269994505866-0.427072604867-0.3228786416750.145342039290.943942046228-0.0257827438175-0.2316279252471.48372053662-0.1360481844660.473550858838-15.95430424764.22668896671-51.1398080886
679.590507560911.12835039742-3.916394780667.29629236260.3973293268961.6917637530.9485390115971.021027158011.99901990684-1.749201695210.1959594645770.9462810724560.684184440694-1.68584722806-0.192069720530.897799140973-0.182743254573-0.1874649522850.9725192112120.05161148028810.388723860757-17.9961119539-4.76165073787-51.6193820536
680.03153659910390.710854373624-0.764403928893.74285838295-3.675149812523.874097396661.055047233730.342101929663-1.15304225007-0.5658067375070.706532903579-0.3737684644172.82108327693-0.991286973373-0.1090768911860.9027343613860.00418761787949-0.05094262009150.76823825997-0.08298268765030.650248196837-13.7764300212-9.15336983237-39.2810092628
694.62302997712-0.51941737531-0.6285097238318.48491662593-6.953210609495.08770643639-0.2642408530010.5954423273690.739477692625-1.44846545509-0.640641392171-0.7301290207510.7101830541131.046149396410.5095810095111.20662329336-0.0411194709408-0.1115154996240.9367616292210.09712397712120.735789097075-12.42229611968.15074796105-49.6277791059
703.370975824274.032795900263.678689565915.152376603553.018997269396.909734836190.718124543366-0.374988917107-0.842624326542-0.438377661466-0.0015347395362-1.3702423676-0.4208999153990.623954440046-1.091830298540.6470374222470.09711803529590.1351065497061.001501823140.01918356484260.9461125310185.379583939685.73226756994-30.0465173926
713.75501815653.0915994322-0.6230073094793.805312084621.067738704253.99238191614-0.2673594554880.9717259569671.063947457520.5292937353031.513808607411.99606002855-0.76389416616-0.85492028528-0.003692022064290.962739493997-0.0119127243842-0.04638321801460.8185287031060.2214784056850.873768544338-22.093178914610.296636978-32.4865156951
722.20538111854-0.268058993491-1.675030905139.52786356851-0.6568415471121.27595035615-0.4830109577020.4413145540440.334484687078-1.76692061663-0.0479940655288-2.775014385020.09592070444160.352521662106-0.06117695028260.87727802591-0.02759949400510.05897506671580.7890493168490.007566973060120.546802529758-7.3533642839814.3372847302-32.4394805091
734.3284927514-0.1184950022330.1089347632233.849582980761.924077731155.946969645760.168357291659-0.4388738585890.02232367976780.148143601731-0.1495074061430.07646816680270.00349786022985-0.5820320114860.1790682034290.8079947698890.1849493273820.06958973930510.6498646328650.09174676007920.827456506007-18.91120894729.47522959021-25.1773990462
747.05138872045-1.40144404042-0.7836582397052.654643200252.534229871633.39629864964-0.484095912237-0.2131905947033.38380288808-0.4967584082950.25256016563-0.700004468292-1.45652024381-1.44280716628-0.1208177472351.257822334060.0025037255479-0.00911678317840.806375115364-0.006378557887580.840414576352-10.32429766916.160041665-26.9371270757
753.408380262462.743512281080.2941158652534.30336720295-3.551937423247.42557828210.1918332805691.145975068750.4440066518240.4291038618951.013684058950.297559558531-0.738200942912-0.891348932141-0.5580866863620.9892481375490.06035452301580.07495342282350.5988169276950.02525399174280.666359161412-10.91544542191.90083503558-26.6370598125
766.64472115384-0.9452001058440.1881214839932.99009844483-2.71336942942.58507224130.421332449032-1.59307087917-0.322257373403-0.04461471378680.1656257287330.34475247788-0.32932565459-1.14391861745-0.8800051442680.84979582036-0.01448970540920.02810544286340.682251929547-0.0121504440720.678017962731-14.7082519133-10.0563040965-23.4508065605
779.74686159724-0.311725391708-5.053322053035.82067678677-0.2073149835812.848276100860.7199711141190.8960029118040.400180451670.211207488615-0.410213988465-0.673198365971-1.07978715612-0.281248625497-0.3167685488480.811030896703-0.05629585529280.02156600938520.5602997087870.007975468226660.823520178528-3.428462732565.42933824279-20.8604247523
783.909739283084.30202836707-0.4895390581331.998751862662.81272203892.537141337970.722342448976-1.910584955490.2880837864771.39051685421-0.572397584315-0.540811953740.0115785991304-1.852794583290.2631654704690.315317323107-0.01498850340490.01078651616951.13480000205-0.1528130662360.751975319382-13.7156889717-21.53157073126.07326267309
795.267452984011.30519610345-1.088799795795.898491077930.5959251060372.85740560058-0.252850501266-0.2120388231320.0278020720329-0.12821262264-0.141948903834-0.134121405519-0.182353302050.01357042025060.125415938870.5399390419120.0109266930415-0.02246096485130.457123685905-0.01273069089520.605533402488-7.94771057742-24.8715726363-8.08637828931
802.282720677750.911947576746-1.163110701816.53746140527-1.697668005583.959417517110.0193747600535-0.2866127938110.2077576426770.222260429071-0.0976139720629-0.0782282205155-0.5608440730530.156459078230.2940755330560.69101699564-0.0297764490659-0.1154508504520.6031016986090.01885350019570.532261438627-9.6311600675-20.1850985434-7.19140152245
813.91117096520.4951208844430.07363329587567.01829264432-1.345700602613.69597614006-0.397592519891-0.0549352063012-0.325267661142-0.3424891578711.18796272305-0.0181311608702-0.8793943462110.0629265009708-0.102691709340.6439369710480.0508036176538-0.01383358125290.6921143394770.02564686983740.640174309589-19.4537219632-24.9413379859-7.79179970384
820.2423303033082.94482343391-1.560518952514.55227104252-1.402262833681.542471119930.00214204323106-0.0107653703791-0.4975791461450.3348356166540.144580620224-0.900137359824-0.3378368790560.07607392262770.1484072872750.8204665025790.0107175547936-0.04025830200020.5839974887670.0338221384550.764106120726-5.39025430989-8.9312200307-15.300335445
830.7868014351561.18500817602-0.5712586570142.15451262314-1.709580841911.21988467530.4007670192480.01737674150880.4647276986462.60238467354-0.943178691314-1.22231906385-2.812986001570.6857190673080.7897679604691.62953001226-0.276948868069-0.2921483621430.851655516720.1485467746471.071905347891.729489388562.69589996356-7.92273739185
847.427636554061.03487352608-0.5545443138733.82093935103-0.4783856338482.93481958068-1.95645569118-0.8267636564371.215924113830.1677659783211.99718433946-0.639636955836-1.071849854571.341194209950.371860216581.53317157583-0.010225255895-0.2942325384931.06135718877-0.1850356516820.990608743863-11.9047156642-8.306371801011.39235659828
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 1:25)AA1 - 251 - 25
22(chain A and resid 26:44)AA26 - 4426 - 44
33(chain A and resid 45:52)AA45 - 5245 - 52
44(chain A and resid 53:67)AA53 - 6753 - 67
55(chain A and resid 68:88)AA68 - 8868 - 88
66(chain A and resid 89:97)AA89 - 9789 - 97
77(chain A and resid 98:104)AA98 - 10498 - 104
88(chain B and resid 16:25)BB16 - 251 - 10
99(chain B and resid 26:49)BB26 - 4911 - 34
1010(chain B and resid 56:61)BB56 - 6135 - 40
1111(chain B and resid 62:78)BB62 - 7841 - 57
1212(chain B and resid 79:89)BB79 - 8958 - 68
1313(chain B and resid 90:98)BB90 - 9869 - 77
1414(chain B and resid 99:112)BB99 - 11278 - 91
1515(chain C and resid 62:77)CC62 - 771 - 16
1616(chain C and resid 78:109)CC78 - 10917 - 48
1717(chain C and resid 110:118)CC110 - 11849 - 57
1818(chain C and resid 119:134)CC119 - 13458 - 73
1919(chain C and resid 135:177)CC135 - 17774 - 116
2020(chain C and resid 178:193)CC178 - 193117 - 132
2121(chain C and resid 194:206)CC194 - 206133 - 145
2222(chain D and resid 1:6)DE1 - 61 - 6
2323(chain D and resid 7:45)DE7 - 457 - 45
2424(chain D and resid 46:53)DE46 - 5346 - 53
2525(chain D and resid 54:61)DE54 - 6154 - 61
2626(chain D and resid 62:68)DE62 - 6862 - 68
2727(chain D and resid 69:87)DE69 - 8769 - 87
2828(chain D and resid 88:104)DE88 - 10488 - 104
2929(chain E and resid 16:21)EF16 - 211 - 6
3030(chain E and resid 22:33)EF22 - 337 - 18
3131(chain E and resid 34:39)EF34 - 3919 - 24
3232(chain E and resid 40:48)EF40 - 4825 - 33
3333(chain E and resid 56:77)EF56 - 7734 - 55
3434(chain E and resid 78:97)EF78 - 9756 - 75
3535(chain E and resid 98:112)EF98 - 11276 - 90
3636(chain F and resid 62:78)FG62 - 781 - 17
3737(chain F and resid 79:128)FG79 - 12818 - 67
3838(chain F and resid 129:137)FG129 - 13768 - 76
3939(chain F and resid 138:147)FG138 - 14777 - 86
4040(chain F and resid 148:162)FG148 - 16287 - 101
4141(chain F and resid 163:196)FG163 - 196102 - 135
4242(chain F and resid 197:206)FG197 - 206136 - 145
4343(chain G and resid 1:46)GI1 - 461 - 46
4444(chain G and resid 47:57)GI47 - 5747 - 57
4545(chain G and resid 58:68)GI58 - 6858 - 68
4646(chain G and resid 69:83)GI69 - 8369 - 83
4747(chain G and resid 84:89)GI84 - 8984 - 89
4848(chain G and resid 90:97)GI90 - 9790 - 97
4949(chain G and resid 98:104)GI98 - 10498 - 104
5050(chain H and resid 16:20)HJ16 - 201 - 5
5151(chain H and resid 21:27)HJ21 - 276 - 12
5252(chain H and resid 28:45)HJ28 - 4513 - 30
5353(chain H and resid 46:58)HJ46 - 5831 - 36
5454(chain H and resid 59:77)HJ59 - 7737 - 55
5555(chain H and resid 78:94)HJ78 - 9456 - 72
5656(chain H and resid 95:112)HJ95 - 11273 - 90
5757(chain I and resid 62:73)IK62 - 731 - 12
5858(chain I and resid 74:109)IK74 - 10913 - 48
5959(chain I and resid 110:144)IK110 - 14449 - 83
6060(chain I and resid 145:157)IK145 - 15784 - 96
6161(chain I and resid 158:183)IK158 - 18397 - 122
6262(chain I and resid 184:194)IK184 - 194123 - 133
6363(chain I and resid 195:208)IK195 - 208134 - 147
6464(chain J and resid 1:8)JM1 - 81 - 8
6565(chain J and resid 9:37)JM9 - 379 - 37
6666(chain J and resid 38:48)JM38 - 4838 - 48
6767(chain J and resid 49:57)JM49 - 5749 - 57
6868(chain J and resid 58:70)JM58 - 7058 - 70
6969(chain J and resid 71:89)JM71 - 8971 - 88
7070(chain J and resid 90:104)JM90 - 10489 - 103
7171(chain K and resid 16:20)KN16 - 201 - 5
7272(chain K and resid 21:27)KN21 - 276 - 12
7373(chain K and resid 28:47)KN28 - 4713 - 32
7474(chain K and resid 48:67)KN48 - 6733 - 43
7575(chain K and resid 68:81)KN68 - 8144 - 57
7676(chain K and resid 82:94)KN82 - 9458 - 70
7777(chain K and resid 95:112)KN95 - 11271 - 88
7878(chain L and resid 62:67)LO62 - 671 - 6
7979(chain L and resid 68:109)LO68 - 1097 - 48
8080(chain L and resid 110:131)LO110 - 13149 - 70
8181(chain L and resid 132:144)LO132 - 14471 - 83
8282(chain L and resid 145:174)LO145 - 17484 - 113
8383(chain L and resid 175:196)LO175 - 196114 - 135
8484(chain L and resid 197:204)LO197 - 204136 - 143

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万見について

-
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

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