신종 코로나바이러스 특집 콘텐츠

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코로나 바이러스, 2020. David S. Goodsell @ RCSB PDB에 의한 오리지널 일러스트를 수정

신종 코로나바이러스 감염증 (Novel Coronavirus disease 2019:COVID-19)의 확산이 세계적으로 매우 큰 문제가 되고 있습니다. 시급히 새로운 바이러스（Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2）를 이해하고 효과적인 약을 개발하기 위해, 신속하게 구조 생물학 연구가 시작되고 있습니다. PDBj는 사용자의 편의를 도모하기 위해 신종 코로나바이러스의 특집 페이지를 제공하고 있습니다. 매주 수요일에 최신 항목이 추가됩니다.

바이러스 단백질에 관한 해설기사는 아래의 「이달의 분자」 페이지를 참조하십시오.

「전체 엔트리」 탭에는, 모든 PDB ID가 포함되어 있습니다. 이용자가 전체의 독립된 엔트리를 검색하고 싶을 때 사용하실 수 있으며, 동일 저자에 의한 그룹등록의 엔트리도 전부 구별되어 있습니다. 「대표구조」 탭에는, 분해능이 가장 높은 대표구조만을 표지하고 있습니다. 아미노산 서열이 100 % 일치하는 PDB 엔트리의 경우, 다른 리간드를 포함하여도 대표구조에는 제외됩니다. 「최신 엔트리」 탭은, 이번주 공개된 가장 최근의 엔트리 입니다.

Created: 2020-09-03 (last edited: more than 1 year ago)

전체 엔트리 (5207)대표구조 (2270)최신 엔트리 (10)

7VBE

1.6 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 5.0
Descriptor:	Nucleoprotein
Authors:	Zhou, X.L, Zhong, F.L, Li, J, Zhang, J.
Deposit date:	2021-08-31
Release date:	2022-07-06
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.59 Å)
Cite:	1.6 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 5.0 To Be Published

7VBF

1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 8.5
Descriptor:	Nucleoprotein
Authors:	Zhou, X.L, Zhong, F.L, Li, J, Zhang, J.
Deposit date:	2021-08-31
Release date:	2022-07-06
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.3 Å)
Cite:	1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 8.5 To Be Published

7X1M

The complex structure of Omicron BA.1 RBD with BD604, S309,and S304
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, BD-604 Fab heavy chain, BD-604 Fab light chain, ...
Authors:	Huang, M, Xie, Y.F, Qi, J.X.
Deposit date:	2022-02-24
Release date:	2022-07-06
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (2.74 Å)
Cite:	Atlas of currently available human neutralizing antibodies against SARS-CoV-2 and escape by Omicron sub-variants BA.1/BA.1.1/BA.2/BA.3. Immunity, 55, 2022

7XAZ

Crystal structure of Omicron BA.1.1 RBD complexed with hACE2
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, ...
Authors:	Liao, H, Meng, Y, Li, W.
Deposit date:	2022-03-19
Release date:	2022-07-06
Last modified:	2024-10-16
Method:	X-RAY DIFFRACTION (3 Å)
Cite:	Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell, 185, 2022

7XB0

Crystal structure of Omicron BA.2 RBD complexed with hACE2
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, ...
Authors:	Li, L, Liao, H, Meng, Y, Li, W.
Deposit date:	2022-03-19
Release date:	2022-07-06
Last modified:	2024-10-30
Method:	X-RAY DIFFRACTION (2.9 Å)
Cite:	Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell, 185, 2022

7XB1

Crystal structure of Omicron BA.3 RBD complexed with hACE2
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, ...
Authors:	Li, W, Meng, Y, Liao, H.
Deposit date:	2022-03-19
Release date:	2022-07-06
Last modified:	2024-10-23
Method:	X-RAY DIFFRACTION (2.7 Å)
Cite:	Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell, 185, 2022

7Y42

Cryo-EM structure of the SARS-CoV-2 spike glycoprotein in complex with all-trans retinoic acid
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, RETINOIC ACID, Spike glycoprotein
Authors:	Xiang, Y, Wang, L.
Deposit date:	2022-06-13
Release date:	2022-07-06
Last modified:	2024-11-20
Method:	ELECTRON MICROSCOPY (3.45 Å)
Cite:	A Retinol Derivative Inhibits SARS-CoV-2 Infection by Interrupting Spike-Mediated Cellular Entry. Mbio, 13, 2022

8CWU

Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 1-21
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, VHH 1-21
Authors:	Liu, H, Wilson, I.A.
Deposit date:	2022-05-19
Release date:	2022-07-06
Last modified:	2024-10-23
Method:	X-RAY DIFFRACTION (1.71 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CWV

Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 2-31 and a human antibody CC12.1 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.1 Fab heavy chain, CC12.1 Fab light chain, ...
Authors:	Liu, H, Wilson, I.A.
Deposit date:	2022-05-19
Release date:	2022-07-06
Last modified:	2024-10-23
Method:	X-RAY DIFFRACTION (2.51 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CXN

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-57
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, pan-sarbecovirus nanobody 2-57
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-22
Release date:	2022-07-06
Last modified:	2024-10-23
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CXQ

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-22
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 1-22
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-22
Release date:	2022-07-06
Last modified:	2024-11-13
Method:	ELECTRON MICROSCOPY (2.3 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CY6

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-65
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 2-65
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2024-11-20
Method:	ELECTRON MICROSCOPY (3.2 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CY7

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2024-10-23
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CY9

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-23
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 1-23
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2024-11-06
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CYA

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-67
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2024-10-09
Method:	ELECTRON MICROSCOPY (2.7 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CYB

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-8
Descriptor:	1-deoxy-alpha-D-mannopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2024-11-13
Method:	ELECTRON MICROSCOPY (2.7 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CYC

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 2-34
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2024-11-13
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CYD

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-45
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 2-45
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2024-11-13
Method:	ELECTRON MICROSCOPY (2.6 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CYJ

RBD of SARS-CoV-2 Spike protein in complex with pan-sarbecovirus nanobodies 2-10, 2-67, 2-62 and 1-25
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 1-25, pan-sarbecovirus nanobody 2-10, ...
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2024-11-13
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8DCC

SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 3 Bound to P2B-2F6 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, P2B-2F6 Fab heavy chain, P2B-2F6 Fab light chain, ...
Authors:	Dickey, T.D, Tolia, N.H.
Deposit date:	2022-06-16
Release date:	2022-07-06
Last modified:	2024-10-23
Method:	X-RAY DIFFRACTION (2.6 Å)
Cite:	Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response. Sci Adv, 8, 2022

7FB3

SARS-CoV-2 spike protein in one-RBD weak state after CTSL-treatment
Descriptor:	Spike glycoprotein
Authors:	Zhu, Y, Tai, L.H, Sun, F.
Deposit date:	2021-07-08
Release date:	2022-07-13
Last modified:	2025-06-18
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	Novel sites for Cathepsin L cleavage in SARS-CoV-2 spike guide treatment strategies To Be Published

7FBJ

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, New antigen receptor variable domain, ...
Authors:	Zhu, J, Xu, T, Feng, B, Liu, J.
Deposit date:	2021-07-11
Release date:	2022-07-13
Last modified:	2024-10-16
Method:	X-RAY DIFFRACTION (2.85 Å)
Cite:	A Class of Shark-Derived Single-Domain Antibodies can Broadly Neutralize SARS-Related Coronaviruses and the Structural Basis of Neutralization and Omicron Escape. Small Methods, 6, 2022

7FBK

Crystal structure of SARS-CoV-2 receptor binding domain N501Y mutant in complex with neutralizing nanobody 20G6
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, New antigen receptor variable domain, Spike protein S1
Authors:	Zhu, J, Xu, T, Feng, B, Liu, J.
Deposit date:	2021-07-11
Release date:	2022-07-13
Last modified:	2024-11-06
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	A Class of Shark-Derived Single-Domain Antibodies can Broadly Neutralize SARS-Related Coronaviruses and the Structural Basis of Neutralization and Omicron Escape. Small Methods, 6, 2022

7P19

Crystal structure of SARS-CoV-2 RBD Q498Y complexed with human ACE2
Descriptor:	1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ...
Authors:	Erausquin, E, Lopez-Sagaseta, J.
Deposit date:	2021-07-01
Release date:	2022-07-13
Last modified:	2024-11-13
Method:	X-RAY DIFFRACTION (3.24 Å)
Cite:	Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution. Acta Crystallogr D Struct Biol, 78, 2022

7WJY

Omicron spike trimer with 6m6 antibody
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 6m6 heavy chain, 6m6 light chain, ...
Authors:	Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
Deposit date:	2022-01-08
Release date:	2022-07-13
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.24 Å)
Cite:	A broadly neutralizing antibody against SARS-CoV-2 Omicron variant infection exhibiting a novel trimer dimer conformation in spike protein binding. Cell Res., 32, 2022

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