2020-08-26 2020 年8月26日新規公開分からその6へ移行
2020-08-19 
8月19日の新規公開3エントリーならびに関連する公開済エントリーを追加
[crisp_bio注]
  • ブログ投稿1件ごとの字数制限のため, SRAS-CoV-2の構造のPDB登録エントリーを順次分割して投稿: その5(本記事);- その4; - その3; - その2; - その1
  • 7月22日 (本投稿)から、同一論文・投稿 (to be publishedを含む)ごとの形式を採用、このため、新規公開エントリーより以前に公開されたエントリーも改めてリストしている。

  • To be publishedの場合, そのTitleは仮置の場合もあり、ジャーナルからの公開時には変更されている可能性がある。
  •  カラムRelease Dateの"AUTH"は"編集処理済、登録者の確認・同意待ち"を意味する
  • 出典: PDBj 新型コロナウイルスの構造情報2020-08-05までの更新履歴

ID

Title

Release Date

投稿

X-ray Structure of SARS-CoV-2 main protease bound to …

to be published

6XR3

X-ray Structure of SARS-CoV-2 main protease bound to GRL-024-20 at 1.45 A

08/19/2020

6WNP

X-ray Structure of SARS-CoV-2 main protease bound to Boceprevir at 1.45 A

05/06/2020

6W63

Structure of COVID-19 main protease bound to potent broad-spectrum non-covalent inhibitor X77

03/25/2020

投稿

Crystal structure of the SARS-CoV-2 main protease in complex with …

to be published

7COM

Crystal structure of the SARS-CoV-2 main protease in complex with Boceprevir (space group P212121)

08/19/2020

7C7P

Crystal structure of the SARS-CoV-2 main protease in complex with Telaprevir

07/29/2020

投稿

Closing coronavirus spike glycoproteins by structure-guided design.

bioRxiv 20200603

6X79

Prefusion SARS-CoV-2 S ectodomain trimer covalently stabilized in the closed conformation

08/19/2020

投稿

Cryo-EM Structures Delineate a pH-Dependent Switch that Mediates Endosomal Positioning of SARS-CoV-2 Spike Receptor-Binding Domains

bioRxiv 20200731

6XLU

Structure of SARS-CoV-2 spike at pH 4.0

08/12/2020

6XM0

Consensus structure of SARS-CoV-2 spike at pH 5.5

08/12/2020

6XM3

Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 1

08/12/2020

6XM4

Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 2

08/12/2020

投稿

Crystal structure of SARS CoV2 main protease in complex with inhibitor …

to be published

6ZRU

Crystal structure of SARS CoV2 main protease in complex with inhibitor Boceprevir

08/12/2020

6ZRT

Crystal structure of SARS CoV2 main protease in complex with inhibitor Telaprevir

08/12/2020

投稿

Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody.

Science 20200723

7CAB

apo SARS-CoV-2 S trimer

AUTH

7CAC

SARS-CoV-2 S trimer in complex with one Fab

AUTH

7CAI

SARS-CoV-2 S trimer in complex with two Fabs

AUTH

7CAK

SARS-CoV-2 S trimer in complex with three Fabs

AUTH

7CAH

The interface of H014 Fab binds to SARS-CoV-2 S

08/12/2020

投稿

The crystal structure of papain-like protease of SARS CoV-2, ……..
(by Center for Structural Genomics of Infectious Diseases)

to be published

7JN2

The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder441

08/12/2020

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

6WRH

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

05/06/2020

6W9C

The crystal structure of papain-like protease of SARS CoV-2

05/06/2020

6WZU

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

05/27/2020

7JIW

The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder530

08/05/2020

6WRH

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

05/06/2020

6XG3

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

06/24/2020

7JIR

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder457

08/05/2020

7JIT

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder495

08/05/2020

7JIV

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder530

08/05/2020

投稿

Identification of a putative peptide-binding site at the dimer interface of the SARS-CoV-2 Nsp9 RNA-replicase.

to be published

6WXD

SARS-CoV-2 Nsp9 RNA-replicase

05/20/2020

6WC1

Peptide-bound SARS-CoV-2 Nsp9 RNA-replicase

08/05/2020

6W9Q

Peptide-bound SARS-CoV-2 Nsp9 RNA-replicase

04/08/2020

投稿

H11-H4 bound to Spike

to be published

6ZHD

H11-H4 bound to Spike

07/29/2020

投稿

Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution

to be published

6ZSL

Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution

07/29/2020

投稿

H11-D4 complex with SARS-CoV-2 RBD

to be published

6ZBP

H11-H4 complex with SARS-CoV-2

07/29/2020

投稿

Structure of SARS-CoV-2 RdRp/RNA complex at 3.4 Angstroms resolution

to be published

6XQB

SARS-CoV-2 RdRp/RNA complex

07/29/2020

投稿

Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures

bioRxiv 2020-07-08

6ZP7

SARS-COV-2 SPIKE IN PREFUSION STATE (FLEXIBILITY ANALYSIS, 1-UP OPEN CONFORMATION)

07/29/2020

6ZP5

SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed conformation)

07/29/2020

6ZOW

SARS-CoV-2 spike in prefusion state

07/29/2020

投稿

SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation

bioRxiv 2020-07-07

6ZOJ

SARS-CoV-2-Nsp1-40S complex, composite map

07/22/2020

6ZOL

SARS-CoV-2-Nsp1-40S complex, focused on head

07/22/2020

6ZOK

SARS-CoV-2-Nsp1-40S complex, focused on body

07/29/2020

投稿

Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2

Science 2020-07-17

6ZP4

SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2

07/29/2020

6ZON

SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1

07/29/2020

6ZN5

SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2

07/29/2020

6ZM7

SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex

07/29/2020

6ZLW

SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit

07/29/2020

投稿

A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike

bioRxiv 2020-07-04

6XM5

Structure of SARS-CoV-2 spike at pH 5.5, all RBDs down

07/29/2020

投稿

Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex.

bioRixv 2020-07-13

6XEZ

Structure of SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC

07/29/2020

投稿

Extreme malleability of the SARS-CoV-2 3CL Mpro active site cavity facilitates binding of clinical antivirals: Prospects for repurposing existing drugs and ramifications for inhibitor design

To be published

6XQT

3C-like proteinase, (1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl)methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropyla mino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide

07/22/2020

6XQS

3C-like proteinase, (1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide

07/22/2020

6XQU

3C-like proteinase, boceprevir (bound form) 

07/22/2020

投稿

SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation

bioRxiv 20200707

6ZOJ

SARS-CoV-2-Nsp1-40S complex, composite map

07/22/2020

6ZOL

SARS-CoV-2-Nsp1-40S complex, focused on head

07/22/2020

6ZOK

SARS-CoV-2-Nsp1-40S complex, focused on body

07/29/2020

投稿

A thermostable, closed, SARS-CoV-2 spike protein trimer

bioRxiv 20200617

6ZOX

Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x2 disulphide-bond mutant, G413C, V987C, single Arg S1/S2 cleavage site)

07/22/2020

6ZOY

Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x1 disulphide-bond mutant, S383C, D985C, K986P, V987P, single Arg S1/S2 cleavage site) in Closed State

07/22/2020

6ZOZ

Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x1 disulphide-bond mutant, S383C, D985C, K986P, V987P, single Arg S1/S2 cleavage site) in Locked State

07/22/2020

6ZP0

Structure of SARS-CoV-2 Spike Protein Trimer (single Arg S1/S2 cleavage site) in Closed State

07/22/2020

6ZP1

Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Closed State

07/22/2020

6ZP2

Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Locked State

07/22/2020

投稿

Potent Neutralizing Antibodies Directed to Multiple Epitopes on SARS-CoV-2 Spike

bioRxiv 20200716

6XEY

Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-4

07/22/2020

投稿

Distinct conformational states of SARS-CoV-2 spike protein

Science 20200721

6XR8

Distinct conformational states of SARS-CoV-2 spike protein

07/22/2020

6XRA

Distinct conformational states of SARS-CoV-2 spike protein

07/22/2020

投稿

Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

bioRxiv 20200716

crisp_bio 20200724

6XS6

SARS-CoV-2 Spike D614G variant, minus RBD

07/22/2020


更新履歴
2020-08-12 8月22日公開8エントリーを追加
2020-08-05 8月5日公開エントリーを追加
2020-07-29 7月29日公開エントリーを追加: 15 エントリ / 9 投稿 (論文, プレプリントまたはto be publsihed)
2020-07-24 7-22エントリー追加分のうち#1のPDB IDの誤記を修正:  6XRBを6XS6に修正
2020-07-22 エントリー14件追加 (#51 から#36まで); 
2020-07-15 PDB 2020-07-15 公開エントリー2件を追加
2020-07-08 PDB 2020-07-08 公開エントリーを追加
 #27と#28は2020-06-24公開であるが#29と同じbioRxiv 2020-06-13投稿掲載構造ということで再掲。
2020-07-01 PDB 2020-07-01 公開エントリーを追加
 07-01公開エントリーについては、同一投稿または論文掲載分を1行にまとめた
 (その中に07-01より以前に公開されたエントリーも再掲)
2020-06-28 PDB2020-06-24公開11エントリーを収録