[最近の更新]
2020-05-28 PanDDA analysis group deposition
リガンド結合メインプロテアーゼ構造 [その1]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
[2020-05-06以前の履歴は文末へ移動]

55

7BQY

The Crystal Structure of COVID-19 Main Protease in Complex with an Inhibitor N3 at 1.7 Å [Structure of Mpro 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 Mpro 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
・米国 RCDB PDBのWebサイトにてID指定、または、https://www.rcsb.org/structure/ID にて
     [例] https://www.rcsb.org/structure/6VXX
・欧州 PDBeのWebサイトにて、ID指定、または、https://www.ebi.ac.uk/pdbe/entry/IDにて
     [例] https://www.ebi.ac.uk/pdbe/entry/pdb/6VXX

[更新履歴]
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:2020-05-01 17.56.29
"Structure of Mpro 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)2020-04-29 16.13.01
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 (下図はRdRpのレムデシビル結合構造 7BV2)7BV2
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 (下図はGraphical Abstractから引用)
6LZG
2020-04-09 6LU7 (#1)をNature論文crisp_bio記事に紐付け
 2020-04-09
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 (下図はキャプチャ画面)
D. E. Shaw
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.
 6W41
2020-04-01 6W9C (The crystal structure of papain-like protease of SARS CoV-2)を#36に追加
6W9C
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
下図 左[6VW1], 右 [6MOJ]
2020-03-31 11.51.38
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 (下図参照)
2020-03-31 14.33.20
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)。