Structure of the SARS-CoV-2 BA.2.86 spike glycoprotein (closed state)
Resolution: 2.59 Å
EM Method: Single-particle
Fitted PDBs: 8wxl
Q-score: 0.53
Yajima H, Anraku Y, Kaku Y, Kimura KT, Plianchaisuk A, Okumura K, Nakada-Nakura Y, Atarashi Y, Hemmi T, Kuroda D, Takahashi Y, Kita S, Sasaki J, Sumita H, Ito J, Maenaka K, Sato K, Hashiguchi T
Nat Commun (2024) 15 pp. 8574-8574 [ DOI: doi:10.1038/s41467-024-52808-2 Pubmed: 39375326 ]
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up state)
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 8xuy
Q-score: 0.369
Yajima H, Anraku Y, Kaku Y, Kimura KT, Plianchaisuk A, Okumura K, Nakada-Nakura Y, Atarashi Y, Hemmi T, Kuroda D, Takahashi Y, Kita S, Sasaki J, Sumita H, Ito J, Maenaka K, Sato K, Hashiguchi T
Nat Commun (2024) 15 pp. 8574-8574 [ DOI: doi:10.1038/s41467-024-52808-2 Pubmed: 39375326 ]
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 ba.2.86 spike glycoprotein with ace2 (600 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up and 1-down state)
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8xuz
Q-score: 0.435
Yajima H, Anraku Y, Kaku Y, Kimura KT, Plianchaisuk A, Okumura K, Nakada-Nakura Y, Atarashi Y, Hemmi T, Kuroda D, Takahashi Y, Kita S, Sasaki J, Sumita H, Ito J, Maenaka K, Sato K, Hashiguchi T
Nat Commun (2024) 15 pp. 8574-8574 [ DOI: doi:10.1038/s41467-024-52808-2 Pubmed: 39375326 ]
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 xbb1.5 spike glycoprotein with ace2 (420 kDa, Complex from Homo sapiens)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (up state)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8xv0
Q-score: 0.508
Yajima H, Anraku Y, Kaku Y, Kimura KT, Plianchaisuk A, Okumura K, Nakada-Nakura Y, Atarashi Y, Hemmi T, Kuroda D, Takahashi Y, Kita S, Sasaki J, Sumita H, Ito J, Maenaka K, Sato K, Hashiguchi T
Nat Commun (2024) 15 pp. 8574-8574 [ DOI: doi:10.1038/s41467-024-52808-2 Pubmed: 39375326 ]
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
- Sars-cov-2 xbb1.5 spike glycoprotein with ace2 (420 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (down state)
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8xv1
Q-score: 0.515
Yajima H, Anraku Y, Kaku Y, Kimura KT, Plianchaisuk A, Okumura K, Nakada-Nakura Y, Atarashi Y, Hemmi T, Kuroda D, Takahashi Y, Kita S, Sasaki J, Sumita H, Ito J, Maenaka K, Sato K, Hashiguchi T
Nat Commun (2024) 15 pp. 8574-8574 [ DOI: doi:10.1038/s41467-024-52808-2 Pubmed: 39375326 ]
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
- Sars-cov-2 xbb1.5 spike glycoprotein with ace2 (420 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Structure of SARS-CoV-2 JN.1 spike RBD in complex with ACE2 (up state)
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 9iu1
Q-score: 0.332
Yajima H, Anraku Y, Kaku Y, Kimura KT, Plianchaisuk A, Okumura K, Nakada-Nakura Y, Atarashi Y, Hemmi T, Kuroda D, Takahashi Y, Kita S, Sasaki J, Sumita H, Ito J, Maenaka K, Sato K, Hashiguchi T
Nat Commun (2024) 15 pp. 8574-8574 [ DOI: doi:10.1038/s41467-024-52808-2 Pubmed: 39375326 ]
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
- Sars-cov-2 xbb1.5 spike glycoprotein with ace2 (420 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 spike in complex with neutralizing antibody NIV-11
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8hgl
Q-score: 0.368
Moriyama S, Anraku Y, Taminishi S, Adachi Y, Kuroda D, Kita S, Higuchi Y, Kirita Y, Kotaki R, Tonouchi K, Yumoto K, Suzuki T, Someya T, Fukuhara H, Kuroda Y, Yamamoto T, Onodera T, Fukushi S, Maeda K, Nakamura-Uchiyama F, Hashiguchi T, Hoshino A, Maenaka K, Takahashi Y
Nat Commun (2023) 14 pp. 4198-4198 [ DOI: doi:10.1038/s41467-023-39890-8 Pubmed: 37452031 ]
- Niv-11 fab heavy chain (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Niv-11 fab light chain (23 kDa, Protein from Homo sapiens)
- Niv-11 fab (50 kDa, Complex from Homo sapiens)
- Sars-cov-2 spike glycoprotein (420 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike glycoprotein in complex with niv-11 (570 kDa, Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 spike in complex with neutralizing antibody NIV-11 focused on RBD and NIV-11 interface
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8hgm
Q-score: 0.459
Moriyama S, Anraku Y, Taminishi S, Adachi Y, Kuroda D, Kita S, Higuchi Y, Kirita Y, Kotaki R, Tonouchi K, Yumoto K, Suzuki T, Someya T, Fukuhara H, Kuroda Y, Yamamoto T, Onodera T, Fukushi S, Maeda K, Nakamura-Uchiyama F, Hashiguchi T, Hoshino A, Maenaka K, Takahashi Y
Nat Commun (2023) 14 pp. 4198-4198 [ DOI: doi:10.1038/s41467-023-39890-8 Pubmed: 37452031 ]
- Niv-11 fab heavy chain (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Niv-11 fab light chain (23 kDa, Protein from Homo sapiens)
- Niv-11 fab (50 kDa, Complex from Homo sapiens)
- Sars-cov-2 spike glycoprotein (420 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike glycoprotein in complex with niv-11 (570 kDa, Complex)
SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7yh7
Q-score: 0.394
Moriyama S, Anraku Y, Taminishi S, Adachi Y, Kuroda D, Kita S, Higuchi Y, Kirita Y, Kotaki R, Tonouchi K, Yumoto K, Suzuki T, Someya T, Fukuhara H, Kuroda Y, Yamamoto T, Onodera T, Fukushi S, Maeda K, Nakamura-Uchiyama F, Hashiguchi T, Hoshino A, Maenaka K, Takahashi Y
Nat Commun (2023) 14 pp. 4198-4198 [ DOI: doi:10.1038/s41467-023-39890-8 Pubmed: 37452031 ]
- Niv-8 fab (50 kDa, Complex from Homo sapiens)
- Sars-cov-2 spike glycoprotein in complex with niv-8 (570 kDa, Complex)
- Sars-cov-2 spike glycoprotein (420 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (132 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Niv-8 fab light chain (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Niv-8 fab heavy chain (13 kDa, Protein from Homo sapiens)