Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 1)
Resolution: 2.59 Å
EM Method: Single-particle
Fitted PDBs: 8jyk
Q-score: 0.567
Tamura T, Irie T, Deguchi S, Yajima H, Tsuda M, Nasser H, Mizuma K, Plianchaisuk A, Suzuki S, Uriu K, Begum MM, Shimizu R, Jonathan M, Suzuki R, Kondo T, Ito H, Kamiyama A, Yoshimatsu K, Shofa M, Hashimoto R, Anraku Y, Kimura KT, Kita S, Sasaki J, Sasaki-Tabata K, Maenaka K, Nao N, Wang L, Oda Y, Ikeda T, Saito A, Matsuno K, Ito J, Tanaka S, Sato K, Hashiguchi T, Takayama K, Fukuhara T
Nat Commun (2024) 15 pp. 1176-1176 [ DOI: doi:10.1038/s41467-024-45274-3 Pubmed: 38332154 ]
Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 2)
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8jym
Q-score: 0.505
Tamura T, Irie T, Deguchi S, Yajima H, Tsuda M, Nasser H, Mizuma K, Plianchaisuk A, Suzuki S, Uriu K, Begum MM, Shimizu R, Jonathan M, Suzuki R, Kondo T, Ito H, Kamiyama A, Yoshimatsu K, Shofa M, Hashimoto R, Anraku Y, Kimura KT, Kita S, Sasaki J, Sasaki-Tabata K, Maenaka K, Nao N, Wang L, Oda Y, Ikeda T, Saito A, Matsuno K, Ito J, Tanaka S, Sato K, Hashiguchi T, Takayama K, Fukuhara T
Nat Commun (2024) 15 pp. 1176-1176 [ DOI: doi:10.1038/s41467-024-45274-3 Pubmed: 38332154 ]
Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (1-up state)
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8jyn
Q-score: 0.388
Tamura T, Irie T, Deguchi S, Yajima H, Tsuda M, Nasser H, Mizuma K, Plianchaisuk A, Suzuki S, Uriu K, Begum MM, Shimizu R, Jonathan M, Suzuki R, Kondo T, Ito H, Kamiyama A, Yoshimatsu K, Shofa M, Hashimoto R, Anraku Y, Kimura KT, Kita S, Sasaki J, Sasaki-Tabata K, Maenaka K, Nao N, Wang L, Oda Y, Ikeda T, Saito A, Matsuno K, Ito J, Tanaka S, Sato K, Hashiguchi T, Takayama K, Fukuhara T
Nat Commun (2024) 15 pp. 1176-1176 [ DOI: doi:10.1038/s41467-024-45274-3 Pubmed: 38332154 ]
- Sars-cov-2 xbb1.5 spike glycoprotein with ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (2-up state)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8jyo
Q-score: 0.337
Tamura T, Irie T, Deguchi S, Yajima H, Tsuda M, Nasser H, Mizuma K, Plianchaisuk A, Suzuki S, Uriu K, Begum MM, Shimizu R, Jonathan M, Suzuki R, Kondo T, Ito H, Kamiyama A, Yoshimatsu K, Shofa M, Hashimoto R, Anraku Y, Kimura KT, Kita S, Sasaki J, Sasaki-Tabata K, Maenaka K, Nao N, Wang L, Oda Y, Ikeda T, Saito A, Matsuno K, Ito J, Tanaka S, Sato K, Hashiguchi T, Takayama K, Fukuhara T
Nat Commun (2024) 15 pp. 1176-1176 [ DOI: doi:10.1038/s41467-024-45274-3 Pubmed: 38332154 ]
- Sars-cov-2 xbb1.5 spike glycoprotein with ace2 (420 kDa, Complex from Homo sapiens)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
Structure of SARS-CoV-2 XBB.1.5 spike RBD in complex with ACE2
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 8jyp
Q-score: 0.43
Tamura T, Irie T, Deguchi S, Yajima H, Tsuda M, Nasser H, Mizuma K, Plianchaisuk A, Suzuki S, Uriu K, Begum MM, Shimizu R, Jonathan M, Suzuki R, Kondo T, Ito H, Kamiyama A, Yoshimatsu K, Shofa M, Hashimoto R, Anraku Y, Kimura KT, Kita S, Sasaki J, Sasaki-Tabata K, Maenaka K, Nao N, Wang L, Oda Y, Ikeda T, Saito A, Matsuno K, Ito J, Tanaka S, Sato K, Hashiguchi T, Takayama K, Fukuhara T
Nat Commun (2024) 15 pp. 1176-1176 [ DOI: doi:10.1038/s41467-024-45274-3 Pubmed: 38332154 ]
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 xbb1.5 spike glycoprotein with ace2 (420 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
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 [ Pubmed: 37452031 DOI: doi:10.1038/s41467-023-39890-8 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Niv-11 fab (50 kDa, Complex from Homo sapiens)
- Niv-11 fab light chain (23 kDa, Protein from Homo sapiens)
- Niv-11 fab heavy chain (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike glycoprotein in complex with niv-11 (570 kDa, Complex)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike glycoprotein (420 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
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 [ Pubmed: 37452031 DOI: doi:10.1038/s41467-023-39890-8 ]
- Niv-11 fab (50 kDa, Complex from Homo sapiens)
- Niv-11 fab light chain (23 kDa, Protein from Homo sapiens)
- Niv-11 fab heavy chain (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike glycoprotein in complex with niv-11 (570 kDa, Complex)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike glycoprotein (420 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 focused on RBD and NIV-8 interface
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7yh6
Q-score: 0.519
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 [ Pubmed: 37452031 DOI: doi:10.1038/s41467-023-39890-8 ]
- Niv-8 fab light chain (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike glycoprotein in complex with niv-8 (570 kDa, Complex)
- Niv-8 fab (50 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Niv-8 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike glycoprotein (420 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 1)
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 [ Pubmed: 37452031 DOI: doi:10.1038/s41467-023-39890-8 ]
- Sars-cov-2 spike glycoprotein (Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike glycoprotein in complex with niv-8 (570 kDa, Complex)
- Niv-8 fab (50 kDa, Complex from Homo sapiens)
- Niv-8 fab light chain (Protein from Homo sapiens)
- Niv-8 fab heavy chain (Protein from Homo sapiens)
- Sars-cov-2 spike glycoprotein (420 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
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 [ Pubmed: 37452031 DOI: doi:10.1038/s41467-023-39890-8 ]
- Niv-8 fab light chain (11 kDa, Protein from Homo sapiens)
- Niv-8 fab (50 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Niv-8 fab heavy chain (13 kDa, Protein 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)