[20200528更新] 新型コロナウイルスのPDB公開構造一覧

[ブログ文字数制限のため分割]
　公開構造一覧 - その４; - その３; - その２; - その１(本記事)

55	7BQY	The Crystal Structure of COVID-19 Main Protease in Complex with an Inhibitor N3 at 1.7 Å [Structure of M^pro from COVID-19 virus and discovery of its inhibitors: 6LU7と同一論文]	04/22/2020 crisp_bio記事 Nature
54	6WEY	High-resolution structure of the SARS-CoV-2 NSP3 Macro X domain	04/29/2020
53	6WLC	Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-5'-Monophosphate (関連 ID 6X1B 6VWW 6W01 6WLC 6WXC) [Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2.]	04/29/2020 Protein Sci
52	6YHU	Crystal structure of the nsp7-nsp8 complex of SARS-CoV-2	04/29/2020
51	6YM0	Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab (crystal form 1) [Potent antibody binding to an unexpected highly conserved cryptic epitope of the SARS-CoV-2 Spike, to be published] - 6YLA (released 2020-04-15)関連	04/29/2020
50	6WKP	Crystal structure of RNA-binding domain of nucleocapsid phosphoprotein from SARS CoV-2, monoclinic crystal form	04/29/2020
49	6W37	SARS-CoV-2 ORF7a encoded accessory protein accessory protein	04/29/2020
48	6LZE	SARS-CoV-2 Mpro in complex with 11a [Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease]	04/29/2020 Science
47	6M0K	SARS-CoV-2 Mpro in complex with 11b [Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease]	04/29/2020 Science
46	6WJI	2.05 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2	04/22/2020
45	6WIQ	Crystal structure of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2	04/22/2020
44	7BV1	Cryo-EM structure of the apo nsp12-nsp7-nsp8 complex	04/22/2020 bioRxiv
43	7BV2	The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP)	04/22/2020 bioRxiv
42	6WEN	Crystal Structure of ADP ribose phosphatase of NSP3 from SARS-CoV-2 in the apo form	04/15/2020
41	6YLA	Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab [Potent antibody binding to an unexpected highly conserved cryptic epitope of the SARS-CoV-2 Spike] 関連構造 6YM0	04/15/2020
40	6YI3	The N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid phosphoprotein	04/08/2020
39	6W9Q	Peptide-bound SARS-CoV-2 Nsp9 RNA-replicase [Identification of a putative peptide-binding site at the dimer interface of the SARS-CoV-2 Nsp9 RNA-replicase, to be published] 6WXD と関連 [一覧その2]	04/08/2020
38	6LZG	Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2	03/18/2020 Cell
37	7BTF	SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors in reduced condition	04/08/2020 Science crisp_bio記事
36	6W9C	The crystal structure of papain-like protease of SARS CoV-2	04/01/2020
35	6M71	SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors	04/01/2020 Science crisp_bio記事
34		PanDDA analysis group - 68 structures of COVID-19 protease with various bound fragments (2020-03-11公開分と合わせて75構造) IDリスト: crisp_bio別記事参照	03/25/2020
33	6W41	Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody CR3022 [A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV]	03/25/2020 Science
32	6W63	Structure of COVID-19 main protease bound to potent broad-spectrum non-covalent inhibitor X77 [A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main protease including SARS-CoV-2 (COVID-19)]	03/25/2020
31	6YB7	SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19) [COVID-19 main protease with unliganded active site]	03/25/2020
30	6W4B	The crystal structure of Nsp9 RNA binding protein of SARS CoV-2	03/18/2020 bioRixv
29	6M0J	Crystal structure of 2019-nCoV spike receptor-binding domain bound with ACE2	03/18/2020 Nature
28	6M3M	Crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain	03/18/2020 crisp_bio記事
27	5R7Y	PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z45617795	03/11/2020
26	5R7Z	PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z1220452176	03/11/2020
25	5R80	PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z18197050	03/11/2020
24	5R81	PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z1367324110	03/11/2020
23	5R82	PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z219104216	03/11/2020
22	5R83	PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z44592329	03/11/2020
21	5R84	PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z31792168	03/11/2020
20	6M03	The crystal structure of COVID-19 main protease in apo form	03/11/2020
19	6M17	The 2019-nCoV RBD/ACE2-B0AT1 complex	03/11/2020 crisp_bio記事 Science
18	6M18	ACE2-B0AT1 complex	03/11/2020 crisp_bio記事 Science
17	6M1D	ACE2-B0AT1 complex, open conformation	03/11/2020 crisp_bio記事 Science
16	6VXX	Structure of the SARS-CoV-2 spike glycoprotein (closed state)	03/11/2020 Cell crisp_bio記事
15	6VYB	SARS-CoV-2 spike ectodomain structure (open state)	03/11/2020 Cell crisp_bio記事
14	6VYO	Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2	03/11/2020
13	6W01	The 1.9 A Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate (関連 ID 6X1B 6VWW 6W01 6WLC 6WXC) [Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2.]	03/11/2020 Protein Sci
12	6W02	Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with ADP ribose	03/11/2020
11	6Y84	COVID-19 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, SARS-CoV-2)	03/11/2020
10	6VWW	Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2. (関連 ID 6X1B 6VWW 6W01 6WLC 6WXC) [Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2.]	03/04/2020 Protein Sci
9	6VXS	Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2	03/04/2020
8	6Y2E	Crystal structure of the free enzyme of the SARS-CoV-2 (2019-nCoV) main protease	03/04/2020 Science
7	6Y2F	Crystal structure (monoclinic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b)	03/04/2020 Science
6	6Y2G	Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b)	03/04/2020 Science
5	6VW1	Structure of 2019-nCoV chimeric receptor-binding domain complexed with its receptor human ACE2	03/04/2020 Nature
4	6LVN	Structure of the 2019-nCoV HR2 Domain	02/26/2020
3	6LXT	Structure of post fusion core of 2019-nCoV S2 subunit	02/26/2020 Cell Res crip_bio記事
2	6VSB	Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up	02/26/2020 crisp_bio記事
1	6LU7	The crystal structure of COVID-19 main protease in complex with an inhibitor N3 [Structure of M^pro from COVID-19 virus and discovery of its inhibitors: 7BQYと同一論文]	02/05/2020 crisp_bio記事 Nature

具体的な構造データの取得法：
・日本 PDBjのWebサイトにてID指定、または、https://pdbj.org/mine/summary/ID にて
　　　　　 [例] https://pdbj.org/mine/summary/6VXX
[更新履歴]

2020-05-28 PanDDA analysis group depositionのリガンド結合メインプロテアーゼ構造 [その１]とリガンド結合メインプロテアーゼ構造 [その２]へのリンクを追加

2020-05-27 "Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV ‐2" Kim Y [..] Joachimiak A.Protein Sci 2020-04-17へのリンクを、 6VWW, 6W01, 6WLC (リストその２: 6X1B,6WXC)に追加

2020-05-20 #39の6W9Qに関連構造6WXP [一覧その2に収録]の情報を付加
2020-05-16 #3の6LXTの参考文献をbioRxiv投稿からCell Research 論文へと更新 (crisp_bio 新型コロナウイルス：スパイクのサブユニットS2の構造と、細胞融合・感染を阻害する脂質化ペプチドの合成)
2020-05-06 ブログの本文記事文字数の上限を超えたため、5月6日PDB更新分から次の記事へ移行: crisp_bio 2020-05-06 新型コロナウイルスのPDB公開構造一覧 - その２

2020-05-01 既登録の6LU7(#1)と関連する新規構造7BQY (#55)を追加し掲載論文へのリンクを追加:

"Structure of M^pro from COVID-19 virus and discovery of its inhibitors" Jin Z, Du X, […] Yang H. Nature 2020-04-09

2020-04-29 Science論文の2構造 (6LZEと6M0K)を含む8構造公開 (下図はScience論文からの引用)

2020-04-23 Science論文掲載PDB IDsを収録
2020-04-22 4月22日公開の7BV2と7BV1 (bioRxiv 2020-04-10), 6WIQ, および6WJIを追加
2020-04-15 4月8日公開の6W9Qと6YI3, および、15日公開の6YLAと6WENを追加 (いずれも、論文は発表待ち)

2020-04-11 7BTF (#37)と6M71 (#35)の文献をbioRxiv投稿からScience論文へと更新 (crisp_bio記事はコチラ)

2020-04-11 6LZG (#38)を登録しとCell論文へのリンクを追加
2020-04-09 6LU7 (#1)をNature論文とcrisp_bio記事に紐付け
2020-04-09 SARS-CoV-2とACE2複合体のMDシミュレーション動画 "Trajectory 4: A 10 µs simulation of the SARS-CoV-2–ACE2 complex"へのリンクを追加

2020-04-08 SARS-CoV-2のRNA依存性RNAポリメラーゼとコファクタの複合体構造データ公開 (#37) [crisp_bio注] #35の6M71と#37の7BTFを、暫定的に同一のbioRxiv投稿に紐付けましたが、この点は、PDBに再確認中です (2020-04-08) -> 2020-04-11 Science論文に統一
2020-04-05 The New York Timesが、SARS-CoV-2の全タンパク質の配列データと簡明なアノテーションを提示 "Bad News Wrapped in Protein: Inside te Coronavirus Genome" Corum J, Zimmer C. NYT2020-04-03; How Coronavirus Hijacks Your Cells. NYT 2020-03-13 updated.
2020-04-03 6W41 (#33)にScience論文へのリンクを追加: "A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV" Yuan M, Wu NC [..] Mok CKP, Wilson IA. Science 2020-04-03.

2020-04-01 6W9C (The crystal structure of papain-like protease of SARS CoV-2)を#36に追

2020-03-31 UniProt: COVID-19プラットフォーム公開 https://covid-19.uniprot.org/
2020-03-31 通し番号修正; Nature 2020-03-30 論文2報へのリンクを追加 (一覧表の#5と#28)
[# 5] "Structural basis of receptor recognition by SARS-CoV-2" Shang J, Ye G, Shi Y, Wan Y [..] Li F. Nature 2020-03-30. [6VW1] Structure of 2019-nCoV chimeric receptor-binding domain complexed with its receptor human ACE2
[#29] "Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor" Lan J, Ge J, Yu J, Shan S[..] Zhang L, Wang X. Nature 2020-03-20. [6M0J] Crystal structure of 2019-nCoV spike receptor-binding domain bound with ACE2
2020-03-31 bioRixv投稿へのリンクを追加 (一覧表の#29) "Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9" Littler DR, Gully BS, Colson RN, Rossjohn J. bioRxiv 2020-03-30; 6W4B The crystal structure of Nsp9 RNA binding protein of SARS CoV-2
2020-03-26 03-25新規公開追加の記述修正：新規公開追加 (3件およびPanDDA analsisによるリガンド結合プロテアーゼの構造68件(2020-03-11公開分とあわせて75件)); 論文crisp_bio記事へのリンクを追加し、03-25新規公開については、未発表論文の予定タイトルと思われるテキストを[]内に付記
2020-03-23 PDB登録へのリンク整理; 6LXT (#3)にbioRxiv 2020-03-12投稿と、その紹介にあたるcrisp_bio記事へのリンクを追加
2020-03-18 PDB登録 6M3M 追加
2020-03-12 [更新] 投稿・論文発表があった構造には公開日の部分にcrisp_bio記事または論文へのリンクを埋め込み; PDBj、新型コロナウイルス特集ページ公開 (毎水曜更新) → コチラ
2020-03-12 [注] この一覧は、2002-3年のSARS CoVのPDB登録データを含んでいない ("SARS CoV"検索へのヒットは182件 (2020-03-12時点)。
2020-03-11 [初稿] COVID-19, SARS CoV-2または2019-nCoVにてRCSB PDBを検索した結果25件を一覧に (以後、毎週水曜日に更新されるPDB公開構造と、随時発表される関連論文へのリンクを追加)。

crisp_bio

[20200528更新] 新型コロナウイルスのPDB公開構造一覧 - その１

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