[20200610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(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 6X6Pと7BYR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 PDB 2020-05-27公開IDを追加; リストその２に追加した6X1Bと6WXC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;

crisp_bio

[20200610更新] 新型コロナウイルスのPDB公開構造一覧 - その2

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