[日本語] English
万見
- PDB-7yz8: Triclinic crystal structure of YTHDF1 YTH domain (544AVV546 mutant) -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7yz8
タイトルTriclinic crystal structure of YTHDF1 YTH domain (544AVV546 mutant)
要素YTH domain-containing family protein 1
キーワードRNA BINDING PROTEIN / mRNA binding and stability
機能・相同性
機能・相同性情報


regulation of axon guidance / organelle assembly / regulation of antigen processing and presentation / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / mRNA destabilization / positive regulation of translational initiation / immune system process / regulation of mRNA stability / stress granule assembly ...regulation of axon guidance / organelle assembly / regulation of antigen processing and presentation / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / mRNA destabilization / positive regulation of translational initiation / immune system process / regulation of mRNA stability / stress granule assembly / positive regulation of translation / learning / P-body / memory / cytoplasmic stress granule / ribosome binding / mRNA binding / RNA binding / cytoplasm
類似検索 - 分子機能
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
類似検索 - ドメイン・相同性
THIOCYANATE ION / YTH domain-containing family 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: 2.5 Å
データ登録者Dalle Vedove, A. / Cazzanelli, G. / Lolli, G.
資金援助 イタリア, 1件
組織認可番号国
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 イタリア
引用ジャーナル: J.Chem.Inf.Model. / 年: 2024
タイトル: Pliability in the m 6 A-Binding Region Extends Druggability of YTH Domains.
著者: Cazzanelli, G. / Dalle Vedove, A. / Spagnolli, G. / Terruzzi, L. / Colasurdo, E. / Boldrini, A. / Patsilinakos, A. / Sturlese, M. / Grottesi, A. / Biasini, E. / Provenzani, A. / Quattrone, A. / Lolli, G.
履歴
登録2022年2月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年3月1日Provider: repository / タイプ: Initial release
改定 1.12024年2月7日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.22024年3月13日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
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

-
集合体

登録構造単位
A: YTH domain-containing family protein 1
B: YTH domain-containing family protein 1
C: YTH domain-containing family protein 1
D: YTH domain-containing family protein 1
E: YTH domain-containing family protein 1
F: YTH domain-containing family protein 1
G: YTH domain-containing family protein 1
H: YTH domain-containing family protein 1
I: YTH domain-containing family protein 1
J: YTH domain-containing family protein 1
K: YTH domain-containing family protein 1
L: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)278,47524
ポリマ－277,77812
非ポリマー69712
水5,459303
1
A: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
9
I: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
10
J: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
11
K: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
12
L: YTH domain-containing family protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2062
ポリマ－23,1481
非ポリマー581
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)71.225, 92.571, 113.940
Angle α, β, γ (deg.)72.870, 79.050, 67.870
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
21(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
31(chain C and (resid 366 through 396 or resid 398 through 557))
41(chain D and (resid 366 through 396 or resid 398 through 557))
51(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
61(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
71(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
81(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
91(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
101(chain J and (resid 366 through 396 or resid 398 through 557))
111(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
121(chain L and (resid 366 through 396 or resid 398 through 557))

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROSERSER(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))AA366 - 3967 - 37
12SERSERTYRTYR(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))AA398 - 45839 - 99
13TRPTRPASNASN(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))AA470 - 557111 - 198
21PROPROSERSER(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))BB366 - 3967 - 37
22SERSERTYRTYR(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))BB398 - 45839 - 99
23TRPTRPASNASN(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))BB470 - 557111 - 198
31PROPROSERSER(chain C and (resid 366 through 396 or resid 398 through 557))CC366 - 3967 - 37
32SERSERASNASN(chain C and (resid 366 through 396 or resid 398 through 557))CC398 - 55739 - 198
41PROPROSERSER(chain D and (resid 366 through 396 or resid 398 through 557))DD366 - 3967 - 37
42SERSERASNASN(chain D and (resid 366 through 396 or resid 398 through 557))DD398 - 55739 - 198
51PROPROSERSER(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))EE366 - 3967 - 37
52SERSERTYRTYR(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))EE398 - 45839 - 99
53TRPTRPASNASN(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))EE470 - 557111 - 198
61PROPROSERSER(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))FF366 - 3967 - 37
62SERSERTYRTYR(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))FF398 - 45839 - 99
63TRPTRPASNASN(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))FF470 - 557111 - 198
71PROPROSERSER(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))GG366 - 3967 - 37
72SERSERTYRTYR(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))GG398 - 45839 - 99
73TRPTRPASNASN(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))GG470 - 557111 - 198
81PROPROSERSER(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))HH366 - 3967 - 37
82SERSERTYRTYR(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))HH398 - 45839 - 99
83TRPTRPASNASN(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))HH470 - 557111 - 198
91PROPROSERSER(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))II366 - 3967 - 37
92SERSERTYRTYR(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))II398 - 45839 - 99
93TRPTRPASNASN(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))II470 - 557111 - 198
101PROPROSERSER(chain J and (resid 366 through 396 or resid 398 through 557))JJ366 - 3967 - 37
102SERSERASNASN(chain J and (resid 366 through 396 or resid 398 through 557))JJ398 - 55739 - 198
111PROPROSERSER(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))KK366 - 3967 - 37
112SERSERTYRTYR(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))KK398 - 45839 - 99
113TRPTRPASNASN(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))KK470 - 557111 - 198
121PROPROSERSER(chain L and (resid 366 through 396 or resid 398 through 557))LL366 - 3967 - 37
122SERSERASNASN(chain L and (resid 366 through 396 or resid 398 through 557))LL398 - 55739 - 198

-
要素

#1: タンパク質
YTH domain-containing family protein 1 / DF1 / Dermatomyositis associated with cancer putative autoantigen 1 / DACA-1


分子量: 23148.166 Da / 分子数: 12 / 断片: YTH domain (residues 361-559)
変異: First residue G derives from the expression tag: E544A/E545V/E546V
由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: YTHDF1, C20orf21 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q9BYJ9
#2: 化合物
ChemComp-SCN / THIOCYANATE ION / チオシアン酸アニオン


分子量: 58.082 Da / 分子数: 12 / 由来タイプ: 合成 / 式: CNS
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 303 / 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

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.38 Å3/Da / 溶媒含有率: 48.42 % / Mosaicity: 0.09 °
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 / pH: 9.5 / 詳細: 6-12% PEG3350, 0.2 M KSCN

-
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: ELETTRA / ビームライン: 11.2C / 波長: 0.9429 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2020年2月20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: 0.9429 Å / 相対比: 1
反射解像度: 2.5→49.05 Å / Num. obs: 87250 / % possible obs: 98.3 % / 冗長度: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rrim(I) all: 0.061 / Net I/σ(I): 11.2 / Num. measured all: 301916
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.543.50.5771564644710.8120.360.6831.697.8
13.46-49.052.90.02215095150.9930.0160.02832.491.3

-
位相決定

位相決定手法: 分子置換

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1精密化
XDSデータ削減
Aimless0.7.4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: 4RCI

4rci


解像度: 2.5→48.095 Å / SU ML: 0.39 / 交差検証法: FREE R-VALUE / σ(F): 2 / 位相誤差: 28.16 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2427 4291 4.92 %
Rwork0.1843 82912 -
obs0.1872 87203 98.22 %
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: 144.46 Å2 / Biso mean: 62.7219 Å2 / Biso min: 24.61 Å2
精密化ステップサイクル: final / 解像度: 2.5→48.095 Å
タンパク質核酸リガンド溶媒全体
原子数18362 0 36 303 18701
Biso mean--87.57 50.82 -
残基数----2229
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0118940
X-RAY DIFFRACTIONf_angle_d1.17325479
X-RAY DIFFRACTIONf_chiral_restr0.0642643
X-RAY DIFFRACTIONf_plane_restr0.0093256
X-RAY DIFFRACTIONf_dihedral_angle_d17.07111446
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A10932X-RAY DIFFRACTION13.727TORSIONAL
12B10932X-RAY DIFFRACTION13.727TORSIONAL
13C10932X-RAY DIFFRACTION13.727TORSIONAL
14D10932X-RAY DIFFRACTION13.727TORSIONAL
15E10932X-RAY DIFFRACTION13.727TORSIONAL
16F10932X-RAY DIFFRACTION13.727TORSIONAL
17G10932X-RAY DIFFRACTION13.727TORSIONAL
18H10932X-RAY DIFFRACTION13.727TORSIONAL
19I10932X-RAY DIFFRACTION13.727TORSIONAL
110J10932X-RAY DIFFRACTION13.727TORSIONAL
111K10932X-RAY DIFFRACTION13.727TORSIONAL
112L10932X-RAY DIFFRACTION13.727TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.52840.38071530.2935275598
2.5284-2.55820.35321430.2766275698
2.5582-2.58930.33251740.2722269697
2.5893-2.62210.33141320.2686274698
2.6221-2.65660.35511420.2596275798
2.6566-2.6930.33261580.2562273198
2.693-2.73150.31091530.2408280198
2.7315-2.77220.29261470.2306271698
2.7722-2.81560.28741190.2329279098
2.8156-2.86170.30661460.2359274898
2.8617-2.91110.31121380.2451280198
2.9111-2.9640.34831370.2562277198
2.964-3.0210.30041360.2444275298
3.021-3.08260.31131490.2211278798
3.0826-3.14970.27981420.2176271798
3.1497-3.22290.30011490.2152281899
3.2229-3.30350.28671370.2094275898
3.3035-3.39280.25881270.2003276398
3.3928-3.49260.23131520.2004274199
3.4926-3.60530.26451310.1952278899
3.6053-3.73410.27071310.1842283299
3.7341-3.88350.25711460.1826275399
3.8835-4.06020.25361450.1634278599
4.0602-4.27410.19721400.1494276899
4.2741-4.54170.18171500.1377278599
4.5417-4.89210.17341490.1269272998
4.8921-5.38380.20561540.1364277199
5.3838-6.16150.18451420.1581279499
6.1615-7.75760.21711300.1735279599
7.7576-48.0950.18751390.1596270896
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)
14.29740.8341.8045.73341.69275.92190.0342-0.913-0.22780.6388-0.8022-0.3771.04340.09190.67340.6176-0.09980.07090.53710.18070.478524.49780.477367.2293
21.8059-0.83810.60050.91650.41322.22170.1394-0.28250.00460.2511-0.10720.18780.5284-0.0457-0.09750.5052-0.07940.04480.336-0.0030.409915.653-7.067649.6288
31.473-0.37890.8091.93470.21212.70870.00480.18730.1875-0.0588-0.1441-0.03450.0985-0.0390.0950.27610.00210.09060.310.02610.35717.31392.192646.5828
43.20051.01960.45830.7299-0.33790.64240.1224-0.20381.5191-0.0136-0.4764-0.8888-0.77010.96420.47240.7694-0.20080.04330.5947-0.00230.870618.944913.777347.5432
51.3478-0.56710.51991.0529-0.19841.799-0.12470.2629-0.2499-0.0394-0.0381-0.02220.66470.27910.07610.58070.02940.07850.3134-0.03570.472622.0042-11.195242.1113
65.8275-0.49352.22827.5033.14994.9491-0.1544-0.07750.0037-0.5129-0.18590.57390.49150.32840.08970.40290.00920.05580.38210.01490.420418.0473-4.150136.628
73.855-0.37660.97972.75630.19943.2887-0.1767-0.2882-0.44570.2255-0.0698-0.06820.9262-0.21270.20860.7844-0.04240.1510.29810.04640.502819.0237-15.108448.8607
81.04320.9184-0.12693.6988-0.3991.8809-0.15740.10750.06110.040.2862-0.03340.07040.038-0.1730.29680.046-0.00230.39650.0550.380635.774413.043156.1526
91.8795-0.0595-0.85594.37631.08132.474-0.0436-0.0234-0.1771-0.07350.0926-0.1213-0.06770.0749-0.06520.2564-0.0358-0.06850.35610.04360.3836.88830.228568.9165
100.6981-0.22370.21012.48570.33251.2467-0.0335-0.2154-0.10.61070.0628-0.40530.14670.18130.00440.35110.0003-0.07240.39880.06280.39436.116325.963876.9949
113.10110.44191.99944.8013-0.36143.42440.1405-0.8233-0.35740.9855-0.4158-0.4080.0708-0.07930.03420.43030.07450.06360.56130.11190.684456.255614.363544.2239
121.3431-0.78051.21542.02040.31013.0114-0.1109-0.0510.1639-0.3874-0.1414-0.44910.0480.24570.24810.33690.05610.10570.43790.10820.463641.570622.207730.603
132.45230.39840.84010.8115-0.14611.1350.0127-0.009-0.70090.26640.2807-0.3193-0.0275-0.1939-0.26620.43970.08680.08940.41150.07450.561541.22099.335438.6866
141.4043-1.00820.09852.29130.68383.0490.11390.2088-0.1271-0.3449-0.17020.177-0.2046-0.32350.06830.30420.02290.06140.5194-0.02810.488536.277115.508628.1733
152.4383-0.59230.31360.55761.05662.2749-0.1676-0.0123-0.2762-0.0139-0.12080.11970.0983-0.10670.23620.27760.01310.0680.48450.08940.509134.810619.982133.0841
162.2874-0.7723-0.58261.93771.13830.6751-0.0561-0.1270.176-0.6772-0.01631.24660.3184-0.63720.19560.31830.0180.01440.70340.03590.390728.390119.493829.3585
171.80230.12840.78291.5055-0.11332.96270.23740.3256-0.081-0.26890.0918-0.2936-0.34750.7216-0.06040.32560.02860.04740.50730.07730.509540.06830.176534.1228
181.87830.9903-0.59043.9061-0.99131.3515-0.1812-0.1442-0.51090.0110.1062-0.29340.54640.31920.01740.50130.1695-0.03120.49980.12750.6542.22281.744450.7038
192.28551.14610.57253.4383-0.16253.3592-0.3936-0.6579-0.22670.9396-0.19290.99760.545-0.80710.45770.7057-0.15440.25350.5893-0.1890.6581-0.295915.69679.9737
201.81340.38-0.65643.05420.62143.0144-0.027-0.32350.34280.2354-0.31940.0632-0.0327-0.14360.34880.3342-0.0785-0.00560.3418-0.01540.412110.329928.05479.5717
211.3069-0.6104-0.97562.82090.6763.4536-0.0444-0.01470.00470.0252-0.43150.3147-0.0891-0.17770.44440.2891-0.0818-0.0190.3774-0.05790.51535.228628.149472.2248
223.11780.64860.60881.09870.11681.50380.2774-0.00450.1660.5396-0.256-0.17440.78130.45610.04070.73990.0424-0.00570.48730.13430.562626.687512.006380.8477
231.5936-0.37311.05690.94740.19382.73020.25210.2143-0.6207-0.26340.48410.33950.475-1.5563-0.61080.6867-0.30380.00311.02360.03680.8172-12.5259-6.78820.884
241.8838-0.79061.67911.85570.0521.88830.05820.13580.1311-0.04660.1850.2194-0.3176-0.21430.31640.3402-0.04810.02010.44080.00590.422.75263.928423.3366
252.21550.5261.87090.30930.51281.8813-0.24070.0232-0.389-0.34670.25380.0124-0.1936-0.6637-0.0170.4045-0.0869-0.00860.8235-0.01910.49770.893-1.364713.0188
262.9405-1.42010.21942.11920.50032.22920.0718-0.0165-0.0042-0.06030.0383-0.16830.1947-0.1241-0.05510.2801-0.08380.02250.3617-0.03980.50642.7168-1.573425.9808
272.5556-1.410.17912.5956-0.54612.18930.25380.33060.0773-0.6038-0.0788-0.16550.2151-0.1866-0.22190.4252-0.06850.05820.5175-0.03950.52050.3146-2.129319.108
281.51280.59760.87021.42840.3761.530.0492-0.0003-0.01620.142-0.08340.1116-0.1429-0.47260.03280.26970.02810.04080.5871-0.01130.5264-5.25458.148930.9073
293.58340.5099-1.9841.41460.04132.84110.14130.67470.0016-0.45660.1969-0.0233-0.1518-0.7171-0.06440.6331-0.1353-0.07310.740.04360.47012.03841.8017-0.5958
300.6371-0.0532-0.02170.1499-0.14430.1269-0.12590.86640.5925-0.587-0.1622-0.682-0.40390.62060.05680.8445-0.20310.30540.8169-0.04930.987519.57571.116893.2051
310.7997-0.1419-0.19161.5736-0.37072.6911-0.0655-0.05540.40290.10840.0239-0.50110.11880.53180.10280.5197-0.0346-0.00630.5877-0.07890.523916.3313-10.5636110.5979
321.88080.3817-0.66570.5544-1.00861.8392-0.4357-0.09780.0394-0.2420.0431-0.4055-0.60670.24650.17250.6506-0.19120.04160.48080.00930.41397.88940.5453104.815
331.9492-0.21150.06263.09741.10333.3870.2034-0.38750.0530.09310.264-0.4326-0.47670.2421-0.45520.5388-0.15470.05240.5306-0.06450.479710.5666-6.1458115.6643
340.8472-0.21160.16762.6801-0.09742.9784-0.33360.07780.2476-0.14020.14110.7517-0.918-0.32280.06341.0668-0.01920.04120.5102-0.1650.66928.57775.2104114.4279
350.56670.61270.22811.5878-0.29912.1219-0.09750.0764-0.0678-0.07290.2047-0.16650.24070.1474-0.09950.4925-0.06620.04650.43-0.04090.355510.7349-17.5665110.1416
362.8467-1.82070.27484.06140.43870.61370.17340.08260.4185-0.4752-0.0835-0.2859-0.3484-0.08470.06670.9078-0.13320.1920.52570.02640.4581.1057.207694.352
371.8187-0.2611-0.96843.86340.29064.4684-0.0619-0.227-0.07170.13310.20880.1815-0.13530.1916-0.18850.42010.1480.03640.3937-0.02110.3925.0518-29.601731.1697
381.5935-0.7879-0.18641.86680.14212.4287-0.3424-0.4064-0.24760.43080.1815-0.3187-0.02680.13990.05860.45660.10880.0350.38430.00480.449827.3443-32.065432.1302
394.28120.5535-0.96563.52971.58712.583-0.4526-0.1129-0.0254-0.1212-0.08770.62881.26390.28210.50010.74030.0329-0.05590.4159-0.01880.651625.4724-45.648818.6566
401.6974-0.2775-0.37152.07870.09433.1077-0.21550.1669-0.51730.00230.01020.15090.4378-0.19290.24660.43640.0653-0.02970.4462-0.04150.593619.8878-39.620825.9856
413.52070.07340.8251.63810.36680.7315-0.08-0.8830.57350.64090.3824-0.07820.22570.6048-0.39310.94220.3964-0.11441.195-0.16030.562939.088-32.354249.2595
420.42570.7267-0.29571.2556-0.56261.00130.3959-0.15070.5366-0.07150.30880.1251-0.3146-0.13030.35861.8969-0.49970.8604-0.0802-0.02391.12061.0999-4.403180.7035
430.0295-0.04140.02213.11391.31710.55120.77130.11750.3187-0.5864-0.2435-1.6514-1.03340.57270.24631.5733-0.20880.52180.61520.16010.696410.2862-19.089668.5233
442.73570.0157-0.45963.26131.98353.55130.3932-0.1367-0.0593-0.4297-0.22680.0013-0.842-0.1616-0.15450.7611-0.08740.0130.36540.04010.3394-3.6025-25.481377.9034
453.0715-0.8184-0.53831.2716-0.81011.34830.86860.7736-0.1308-1.3757-0.6184-0.1487-1.778-0.44940.08811.53990.14830.18320.57420.05450.3018-1.7573-24.142563.0476
462.6882-0.1088-1.26470.3722-0.63182.44380.2519-0.06370.065-0.9079-0.2999-0.0151-0.488-0.22010.37361.40970.02630.12370.4258-0.10820.494-17.87-9.572586.311
471.4533-0.64440.86361.28790.37861.4482-0.13810.19150.0675-0.3250.02180.0175-0.41380.03190.08390.6166-0.1040.09050.55290.0430.448520.446419.38460.0526
481.1077-0.05661.36321.5283-0.9762.2670.14290.19970.0483-0.3116-0.3981-0.1902-0.11850.13020.16310.4621-0.0832-0.0470.6451-0.00440.492210.165317.11466.5449
492.9434-0.66010.00351.95650.83513.7089-0.3297-0.17-0.15190.1970.0836-0.1201-0.22160.0210.180.5156-0.01020.01840.39340.03730.408323.344819.706514.9252
500.97110.280.70511.84110.2971.3083-0.2992-0.2977-0.27710.23710.08390.19740.4738-0.47370.12280.4913-0.03420.04930.40370.02890.464415.325117.934710.4756
511.55180.30260.38611.68450.08541.7972-0.16620.2676-0.277-0.4780.1274-0.36210.27980.3645-0.01360.6094-0.08180.16290.5473-0.05530.540427.31698.94023.6114
522.5456-0.1211-1.1011.4204-0.81151.45-0.34110.46370.0019-0.03160.22480.5409-0.3624-0.3875-0.02490.6921-0.0429-0.15390.9724-0.04270.8981-3.444813.99453.6833
531.45140.2285-0.72992.09150.01633.3950.1482-0.17160.1797-0.3231-0.09410.1102-0.3526-0.0781-0.0260.72640.0360.02640.4202-0.05340.3803-19.18734.7794108.2845
542.3023-1.2236-0.55521.61510.69211.7890.0757-0.1063-0.0968-0.57080.05-0.1836-0.1276-0.0006-0.07610.9312-0.1280.11550.4155-0.00720.4657-2.9331-5.82691.3141
557.48560.3047-2.85842.3071-2.39183.9341-0.0479-0.0129-0.45930.31270.43910.53240.23510.35870.02890.75950.3917-0.08441.3261-0.08730.57719.894536.04850.18
561.53351.1767-0.36211.7223-0.65081.7317-0.27480.1845-0.6512-0.05030.458-1.21450.27570.4128-0.27180.57130.1799-0.09981.073-0.27420.811433.011745.39336.8619
572.10680.5327-0.89733.5992-0.05823.461-0.54330.39290.23010.17680.32550.1664-1.0475-0.74030.1880.54490.1855-0.13210.8131-0.05240.506117.393850.564230.0952
580.5413-0.2606-0.11751.0128-0.17491.8367-0.0943-0.67890.06250.64720.34520.3127-0.1610.1653-0.16970.68780.32310.00960.94870.03660.423512.370542.377637.7618
592.31520.5193-0.71983.46150.953.5279-0.2647-0.27020.3019-0.48920.5273-0.1151-0.07680.1516-0.21640.48570.1396-0.04690.4917-0.01160.311220.498644.473624.3057
600.3308-0.1004-0.47311.3120.02421.3857-0.5485-0.44740.0623-0.18030.25150.5933-0.0933-0.11170.30550.48610.2433-0.0520.7814-0.01630.612814.773243.361132.0939
610.96330.1468-0.01492.3170.13252.6381-0.2146-0.7440.455-0.02390.4836-0.2569-0.30270.4915-0.19730.51650.1866-0.12340.8832-0.22840.600824.727456.658833.9293
624.58151.01120.83781.4994-0.04121.1723-0.0201-0.30690.22850.42690.11670.21890.55160.3946-0.09080.80540.37540.04991.0190.01570.54661.517440.451446.4595
631.04450.0682-0.01492.1706-0.28421.79790.27330.19150.1753-0.1238-0.46780.9258-0.7548-0.49990.21270.94850.1729-0.19540.5923-0.23350.821235.9979-23.917381.2499
643.10621.94210.65673.3952-2.5184.44210.63570.6592-1.1688-1.0702-1.33070.4799-0.2219-0.4769-0.00960.60230.2202-0.44840.6879-0.41980.860542.3613-38.642273.9437
651.61341.056-0.45672.0258-0.10242.08380.55730.2267-0.3189-0.009-0.50620.8173-0.3761-0.23730.03460.73230.0949-0.29960.5141-0.23920.774738.4914-29.786583.8553
662.0089-0.19580.57513.8710.35572.30860.2997-0.04410.01550.0915-0.5790.6743-0.2354-0.21860.17690.67320.0017-0.09530.5625-0.21320.644940.1411-30.733488.2431
670.6735-0.54930.18650.5929-0.25140.9191-0.17850.70790.2774-0.6966-0.06830.03470.2004-0.18350.29271.58360.146-0.15880.6313-0.00380.714549.4626-9.07572.7155
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 365 through 374 )A365 - 374
2X-RAY DIFFRACTION2chain 'A' and (resid 375 through 398 )A375 - 398
3X-RAY DIFFRACTION3chain 'A' and (resid 399 through 457 )A399 - 457
4X-RAY DIFFRACTION4chain 'A' and (resid 458 through 475 )A458 - 475
5X-RAY DIFFRACTION5chain 'A' and (resid 476 through 504 )A476 - 504
6X-RAY DIFFRACTION6chain 'A' and (resid 505 through 512 )A505 - 512
7X-RAY DIFFRACTION7chain 'A' and (resid 513 through 531 )A513 - 531
8X-RAY DIFFRACTION8chain 'A' and (resid 532 through 559 )A532 - 559
9X-RAY DIFFRACTION9chain 'B' and (resid 365 through 475 )B365 - 475
10X-RAY DIFFRACTION10chain 'B' and (resid 476 through 559 )B476 - 559
11X-RAY DIFFRACTION11chain 'C' and (resid 364 through 374 )C364 - 374
12X-RAY DIFFRACTION12chain 'C' and (resid 375 through 398 )C375 - 398
13X-RAY DIFFRACTION13chain 'C' and (resid 399 through 414 )C399 - 414
14X-RAY DIFFRACTION14chain 'C' and (resid 415 through 452 )C415 - 452
15X-RAY DIFFRACTION15chain 'C' and (resid 453 through 504 )C453 - 504
16X-RAY DIFFRACTION16chain 'C' and (resid 505 through 512 )C505 - 512
17X-RAY DIFFRACTION17chain 'C' and (resid 513 through 531 )C513 - 531
18X-RAY DIFFRACTION18chain 'C' and (resid 532 through 558 )C532 - 558
19X-RAY DIFFRACTION19chain 'D' and (resid 364 through 388 )D364 - 388
20X-RAY DIFFRACTION20chain 'D' and (resid 389 through 452 )D389 - 452
21X-RAY DIFFRACTION21chain 'D' and (resid 453 through 531 )D453 - 531
22X-RAY DIFFRACTION22chain 'D' and (resid 532 through 558 )D532 - 558
23X-RAY DIFFRACTION23chain 'E' and (resid 365 through 388 )E365 - 388
24X-RAY DIFFRACTION24chain 'E' and (resid 389 through 398 )E389 - 398
25X-RAY DIFFRACTION25chain 'E' and (resid 399 through 414 )E399 - 414
26X-RAY DIFFRACTION26chain 'E' and (resid 415 through 452 )E415 - 452
27X-RAY DIFFRACTION27chain 'E' and (resid 453 through 488 )E453 - 488
28X-RAY DIFFRACTION28chain 'E' and (resid 489 through 531 )E489 - 531
29X-RAY DIFFRACTION29chain 'E' and (resid 532 through 558 )E532 - 558
30X-RAY DIFFRACTION30chain 'F' and (resid 364 through 374 )F364 - 374
31X-RAY DIFFRACTION31chain 'F' and (resid 375 through 398 )F375 - 398
32X-RAY DIFFRACTION32chain 'F' and (resid 399 through 414 )F399 - 414
33X-RAY DIFFRACTION33chain 'F' and (resid 415 through 452 )F415 - 452
34X-RAY DIFFRACTION34chain 'F' and (resid 453 through 475 )F453 - 475
35X-RAY DIFFRACTION35chain 'F' and (resid 476 through 531 )F476 - 531
36X-RAY DIFFRACTION36chain 'F' and (resid 532 through 558 )F532 - 558
37X-RAY DIFFRACTION37chain 'G' and (resid 365 through 440 )G365 - 440
38X-RAY DIFFRACTION38chain 'G' and (resid 441 through 488 )G441 - 488
39X-RAY DIFFRACTION39chain 'G' and (resid 489 through 504 )G489 - 504
40X-RAY DIFFRACTION40chain 'G' and (resid 505 through 531 )G505 - 531
41X-RAY DIFFRACTION41chain 'G' and (resid 532 through 557 )G532 - 557
42X-RAY DIFFRACTION42chain 'H' and (resid 365 through 374 )H365 - 374
43X-RAY DIFFRACTION43chain 'H' and (resid 375 through 388 )H375 - 388
44X-RAY DIFFRACTION44chain 'H' and (resid 389 through 475 )H389 - 475
45X-RAY DIFFRACTION45chain 'H' and (resid 476 through 531 )H476 - 531
46X-RAY DIFFRACTION46chain 'H' and (resid 532 through 559 )H532 - 559
47X-RAY DIFFRACTION47chain 'I' and (resid 364 through 398 )I364 - 398
48X-RAY DIFFRACTION48chain 'I' and (resid 399 through 414 )I399 - 414
49X-RAY DIFFRACTION49chain 'I' and (resid 415 through 440 )I415 - 440
50X-RAY DIFFRACTION50chain 'I' and (resid 441 through 475 )I441 - 475
51X-RAY DIFFRACTION51chain 'I' and (resid 476 through 531 )I476 - 531
52X-RAY DIFFRACTION52chain 'I' and (resid 532 through 558 )I532 - 558
53X-RAY DIFFRACTION53chain 'J' and (resid 365 through 531 )J365 - 531
54X-RAY DIFFRACTION54chain 'J' and (resid 532 through 559 )J532 - 559
55X-RAY DIFFRACTION55chain 'K' and (resid 365 through 374 )K365 - 374
56X-RAY DIFFRACTION56chain 'K' and (resid 375 through 388 )K375 - 388
57X-RAY DIFFRACTION57chain 'K' and (resid 389 through 398 )K389 - 398
58X-RAY DIFFRACTION58chain 'K' and (resid 399 through 414 )K399 - 414
59X-RAY DIFFRACTION59chain 'K' and (resid 415 through 440 )K415 - 440
60X-RAY DIFFRACTION60chain 'K' and (resid 441 through 475 )K441 - 475
61X-RAY DIFFRACTION61chain 'K' and (resid 476 through 531 )K476 - 531
62X-RAY DIFFRACTION62chain 'K' and (resid 532 through 558 )K532 - 558
63X-RAY DIFFRACTION63chain 'L' and (resid 366 through 414 )L366 - 414
64X-RAY DIFFRACTION64chain 'L' and (resid 415 through 428 )L415 - 428
65X-RAY DIFFRACTION65chain 'L' and (resid 429 through 452 )L429 - 452
66X-RAY DIFFRACTION66chain 'L' and (resid 453 through 531 )L453 - 531
67X-RAY DIFFRACTION67chain 'L' and (resid 532 through 558 )L532 - 558

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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