[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(本記事); - その1


#

ID

Title

Release Date

46

6X6P

Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis

06/10/2020

45

7BYR

BD23-Fab in complex with the S ectodomain trimer [Potent neutralizing antibodies against SARS-CoV-2 identified by high-throughput single-cell sequencing of convalescent patients' B cells]

06/10/2020

Cell

crisp_bio記事

44

6YZ7

H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex [Structural characterisation of a nanobody derived from a naive library that neutralises SARS-CoV-2]

06/03/2020

Nat Struct Mol Biol 2020-07-13

43

6Z2M

H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex [Structural characterisation of a nanobody derived from a naive library that neutralises SARS-CoV-2]

06/03/2020

Nat Struct Mol Biol 2020-07-13

42

6YZ5

H11-D4 complex with SARS-CoV-2 RBD [Structural characterisation of a nanobody derived from a naive library that neutralises SARS-CoV-2]

06/03/2020

Nat Struct Mol Biol 2020-07-13

41

6X4I

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with 3'-uridinemonophosphate

06/03/2020

40

6Z43

Cryo-EM Structure of SARS-CoV-2 Spike : H11-D4 Nanobody Complex [Structural basis for a potent neutralising single-domain antibody that blocks SARS-CoV-2 binding to its receptor ACE2]

06/03/2020
Nat Struct Mol Biol 2020-07-13

39

6M1V

Crystal structure of post fusion core of 2019-nCoV S2 subunit

06/03/2020

38

7BWJ

P2B-2F6/SARS-CoV-2 RBD複合体構造 [Human neutralizing antibodies elicited by SARS-CoV-2 infection]

06/03/2020

Nature

crisp_bio記事

37

5R8T

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 main protease screened against DSI poised (Enamine), Fraglites and Peplites (Newcastle university), Mini Frags (Astex), York 3D (York university), electrophile cysteine covalent (Weizman institute) fragment libraries

01/04/2020

bioRxiv

36

6X2C

SARS-CoV-2 u1S2q All Down RBD State Spike Protein Trimer [Controlling the SARS-CoV-2 Spike Glycoprotein Conformation]

05/27/2020

35

6X2A

SARS-CoV-2 u1S2q 1 Up RBD Spike Protein Trimer [Controlling the SARS-CoV-2 Spike Glycoprotein Conformation]

05/27/2020

34

6X29

SARS-CoV-2 rS2d Down State Spike Protein Trimer [Controlling the SARS-CoV-2 Spike Glycoprotein Conformation]

05/27/2020

33

7BW4

Structure of the RNA-dependent RNA polymerase from SARS-CoV-2 [Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from SARS-CoV-2]

05/27/2020

Cell Rep

32

6WZU

The crystal structure of Papain-Like Protease of SARS CoV-2 , P3221 space group [The crystal structure of Papain-Like Protease of SARS CoV-2 , P3221 space group]

05/27/2020

31

6WZQ

Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P21 form [Structure of SARS-CoV-2 Nucleocapsid dimerization domain]

05/27/2020

30

6WZO

Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P1 form [Structure of SARS-CoV-2 Nucleocapsid dimerization domain]

05/27/2020

29

7C2I

Crystal structure of nsp16-nsp10 heterodimer from SARS-CoV-2 in complex with SAM (with additional SAM during crystallization) [Crystal structure of SARS-CoV-2 nsp10/nsp16 2'-O-methylase and its implication on antiviral drug design]

05/27/2020

28

6X1B

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU (関連 ID 6X1B 6VWW 6W01 6WLC 6WXC) [Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2.]

05/27/2020

Protein Sci

27

6WXC

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with potential refurbishing drug Tipiracil (関連 ID 6X1B 6VWW 6W01 6WLC 6WXC) [Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2.]

05/20/2020

Protein Sci

26

7C01

Molecular basis for a potent human neutralizing antibody targeting SARS-CoV-2 RBD [A potent human neutralizing monoclonal antibody targeting the receptor binding site of SARS-CoV-2 virus]

05/27/2020

Nature

crisp_bio記事

25

7C2K

COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex [Structural basis for RNA replication by the SARS-CoV-2 polymerase]

06/03/2020

Cell

24

7BZF

COVID-19 RNA-dependent RNA polymerase post-translocated catalytic complex [Structural basis for RNA replication by the SARS-CoV-2 polymerase]

06/03/2020

Cell

23

6WPS

Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment

 [Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody]

05/27/2020

Nature

22

6WPT

Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment (open state)[Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody]

05/27/2020

Nature

21

6WS6

S309 Fab [Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody]

05/27/2020

Nature

20

7C22

Crystal structure of the C-terminal domain of SARS-CoV-2 nucleocapsid protein [Crystal structure of the C-terminal domain of SARS-CoV-2 nucleocapsid protein]

05/20/2020

19

6WXD

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] 6W9Qと関連

05/20/2020

18

6WTT

Crystals Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor GC-376 [Crystals Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor GC-376]

05/20/2020

17

6YZ6

Structure of the hemiacetal complex between the SARS-CoV-2 Main Protease and Leupeptin [Structure of the hemiacetal complex between the SARS-CoV-2 Main Protease and Leupeptin]

05/20/2020

16

6YUN

1.45 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2 [1.45 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2]

05/20/2020

15

6WX4

Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR251 [Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design]

05/20/2020

bioRxiv

14

6WUU

Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR250 [Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design]

05/20/2020

bioRxiv

13

6WTC

Crystal Structure of the Second Form of the Co-factor Complex of NSP7 and the C-terminal Domain of NSP8 from SARS CoV-2

05/13/2020

12

6YZ1

The crystal structure of SARS-CoV-2 nsp10-nsp16 methyltransferase complex with Sinefungin

05/13/2020

11

7BRR

Crystal structure of the 2019-nCoV main protease complexed with GC376

05/13/2020

10

7BZ5

Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody

[A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2]

05/13/2020

Science

9

6YVA

PLpro-C111S with mISG15

[Inhibition of papain-like protease PLpro blocks SARS-CoV-2 spread and promotes anti-viral immunity]

05/13/2020

8

6YYT

Structure of replicating SARS-CoV-2 polymerase

05/13/2020

7

6YWM

Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with MES

05/06/2020

6

6WQD

The 1.95 A Crystal Structure of the Co-factor Complex of NSP7 and the C-terminal Domain of NSP8 from SARS-CoV-2

05/06/2020

5

6WOJ

Structure of the SARS-CoV-2 macrodomain (NSP3) in complex with ADP-ribose

05/06/2020

4

6WKS

Structure of SARS-CoV-2 nsp16/nsp10 ternary complex

05/06/2020

3

6WRH

The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant

05/06/2020

2

6YOR

Structure of the SARS-CoV-2 spike S1 protein in complex with CR3022 Fab

[Neutralization of SARS-CoV-2 by destruction of the prefusion Spike]  関連構造 6YLA


04/29/2020

1

6YNQ 

Structure of SARS-CoV-2 Main Protease bound to 2-Methyl-1-tetralone.

04/29/2020

[crisp_bio注] 以下の表内IDのリンク先はPDBjのエントリー; AUTHは"編集処理済、登録者の確認・同意待ち", HUPは"論文出版待ち"の意; 論文出版が先行する場合があるため、必ずしもRelease Date順に並んでいません。

[更新履歴]
2020-06-10 6X6P7BYRを追加; 7BYRは既出のCell 論文 "Potent neutralizing antibodies against SARS-CoV-2 identified by high-throughput single-cell sequencing of convalescent patients' B cells."の構造 (crisp_bio記事: 新型コロナウイルス: SARS-CoV-2中和抗体をCOVID-19から回復した患者由来モノクローナル抗体から発見)
2020-06-04 7C2Kと7BZF (Cell論文)ならびに7BWJ (Nature論文)公開; 6M1V, 6Z43, 6YZ5, 6Z2Mおよび6YZ7公開
2020-05-31 7BW4 (#33)にCell Rep論文へのリンクを追加: "Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from SARS-CoV-2" Peng Q, Peng R, Yuan B, Zhao J [..] Shi Y. Cell Rep 05-30.
2020-05-30 7C01 (#26)にNature論文とcrisp_bio記事へのリンクを追加; 新規構造7BWJ (Nature論文とcrisp_bio記事へのリンクを追加)
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 PDB 2020-05-27公開IDを追加; リストその2に追加した6X1B6WXCの掲載論文"Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV ‐2" Kim Y [..] Joachimiak. Protein Sci2020-04-17を、リストその1の6VWW, 6W01, 6WLC にも掲載論文としてリンク追加 
2020-05-23 Cell論文構造7C2Kと7BZF追加 (5/23時点でPDB未公開): "Structural basis for RNA replication by the SARS-CoV-2 polymerase" Wang Q, Wu J, Wang H [..] Guddat LW, Gong P. Cell 2020-05-22.
2020-05-20 PDB新規公開構造とNature論文掲載構造を追加
2020-05-14 7BZ5の文献をmedRxivからScienceへ更新:"A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2" Wu Y, Wang F, Shen C, Peng W, Li D [..] Gao GF, Gao F, Liu L. Science 2020-05-13.
[crisp_bio注] 本リストは、RCSB PDBを2020-03-11に"COVID-19, SARS CoV-2または2019-nCoVにて"検索した結果25件から始まり、PDBからの新規公開および論文中のPDBを順次追加してきた結果、ブログ記事の文字数制限により、2020年5月1日までのリスト (55件) [* 新型コロナウイルスのPDB公開構造一覧 - その1]から移行したもの;