Electron Microscopy Data Bank

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Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab5F6 in two fab bind conformation

Release date: June 5, 2024
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8jiz
Q-score: 0.335

Wang H, Xie C, Deng B, Ding J, Li N, Kou Z, Jin M, He J, Wang Q, Wen H, Zhang J, Zhou Q, Chen S, Chen X, Yuan TF, Zhu S

Nat Struct Mol Biol (2024) 31 pp. 1987-1996 [ Pubmed: 39227720 DOI: doi:10.1038/s41594-024-01387-3 ]

Sample:

Fab5f6 heavy chain (27 kDa, Protein from Homo sapiens)
Cryo-em structure of glun1-2a nmdar in complex with human fab23 (Cell from Homo sapiens)
Glutamate receptor ionotropic, nmda 1 (95 kDa, Protein from Homo sapiens)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Glutamate receptor ionotropic, nmda 2a (94 kDa, Protein from Homo sapiens)
Fab5f6 light chain (25 kDa, Protein from Homo sapiens)

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EMD-36336

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Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab5F6 in one fab bind conformation

Release date: June 5, 2024
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 8jj0
Q-score: 0.25

Wang H, Xie C, Deng B, Ding J, Li N, Kou Z, Jin M, He J, Wang Q, Wen H, Zhang J, Zhou Q, Chen S, Chen X, Yuan TF, Zhu S

Nat Struct Mol Biol (2024) 31 pp. 1987-1996 [ Pubmed: 39227720 DOI: doi:10.1038/s41594-024-01387-3 ]

Sample:

Fab5f6 heavy chain (27 kDa, Protein from Homo sapiens)
Cryo-em structure of glun1-2a nmdar in complex with human fab23 (Cell from Homo sapiens)
Glutamate receptor ionotropic, nmda 1 (95 kDa, Protein from Homo sapiens)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Glutamate receptor ionotropic, nmda 2a (94 kDa, Protein from Homo sapiens)
Fab5f6 light chain (25 kDa, Protein from Homo sapiens)

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EMD-36337

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Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab2G7 in two fab conformation

Release date: June 5, 2024
Resolution: 3.77 Å
EM Method: Single-particle
Fitted PDBs: 8jj1
Q-score: 0.314

Wang H, Xie C, Deng B, Ding J, Li N, Kou Z, Jin M, He J, Wang Q, Wen H, Zhang J, Zhou Q, Chen S, Chen X, Yuan TF, Zhu S

Nat Struct Mol Biol (2024) 31 pp. 1987-1996 [ Pubmed: 39227720 DOI: doi:10.1038/s41594-024-01387-3 ]

Sample:

Glutamate receptor ionotropic, nmda 1 (95 kDa, Protein from Homo sapiens)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-em structure of glun1-2a nmdar in complex with human fab28 (Cell from Homo sapiens)
Fab 2g7 heavy chain (26 kDa, Protein from Homo sapiens)
Glutamate receptor ionotropic, nmda 2a (94 kDa, Protein from Homo sapiens)
Fab 2g7 light chain (25 kDa, Protein from Homo sapiens)

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EMD-36338

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Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab2G7 in one fab conformation

Release date: June 5, 2024
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8jj2
Q-score: 0.274

Wang H, Xie C, Deng B, Ding J, Li N, Kou Z, Jin M, He J, Wang Q, Wen H, Zhang J, Zhou Q, Chen S, Chen X, Yuan TF, Zhu S

Nat Struct Mol Biol (2024) 31 pp. 1987-1996 [ Pubmed: 39227720 DOI: doi:10.1038/s41594-024-01387-3 ]

Sample:

Fab2g7 heavy chain (26 kDa, Protein from Homo sapiens)
Fab2g7 light chain (25 kDa, Protein from Homo sapiens)
Glutamate receptor ionotropic, nmda 1 (95 kDa, Protein from Homo sapiens)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-em structure of glun1-2a nmdar in complex with human fab28 (Cell from Homo sapiens)
Glutamate receptor ionotropic, nmda 2a (94 kDa, Protein from Homo sapiens)

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EMD-40190

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Local map of B3SB3L in complex with two-RBD-up state I of soluble SARS-CoV-2 Spike trimer

Release date: March 27, 2024
Resolution: 3.9 Å
EM Method: Single-particle

Liu WP, Shokr A, Mabrouk M, Aly N, Zhang J, Aschauer P, Gao HL, Selvaraj G, Elzoghby A, Chen B, Kawano T, Nasr ML

To Be Published

Sample:

Local map of b3sb3l in complex with two-rbd-up state i of soluble sars-cov-2 spike trimer (600 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)

EMD-33650

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SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7

Release date: Aug. 2, 2023
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 7y71
Q-score: 0.415

Chia WN, Tan CW, Tan AWK, Young B, Starr TN, Lopez E, Fibriansah G, Barr J, Cheng S, Yeoh AY, Yap WC, Lim BL, Ng TS, Sia WR, Zhu F, Chen S, Zhang J, Kwek MSS, Greaney AJ, Chen M, Au GG, Paradkar PN, Peiris M, Chung AW, Bloom JD, Lye D, Lok S, Wang LF

Sci Adv (2023) 9 pp. eade3470-eade3470 [ DOI: doi:10.1126/sciadv.ade3470 Pubmed: 37494438 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Sars-cov-2 spike glycoprotein trimer complexed with fab fragment of anti-rbd antibody e7 (Complex from Homo sapiens)
Fab e7 heavy chain (23 kDa, Protein from Homo sapiens)
Spike glycoprotein (132 kDa, Protein from Homo sapiens)
Fab e7 light chain (23 kDa, Protein from Homo sapiens)

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EMD-33651

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SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7 (focused refinement on Fab-RBD interface)

Release date: Aug. 2, 2023
Resolution: 4.03 Å
EM Method: Single-particle
Fitted PDBs: 7y72
Q-score: 0.395

Chia WN, Tan CW, Tan AWK, Young B, Starr TN, Lopez E, Fibriansah G, Barr J, Cheng S, Yeoh AY, Yap WC, Lim BL, Ng TS, Sia WR, Zhu F, Chen S, Zhang J, Kwek MSS, Greaney AJ, Chen M, Au GG, Paradkar PN, Peiris M, Chung AW, Bloom JD, Lye D, Lok S, Wang LF

Sci Adv (2023) 9 pp. eade3470-eade3470 [ DOI: doi:10.1126/sciadv.ade3470 Pubmed: 37494438 ]

Sample:

Fab e7 heavy chain (23 kDa, Protein from Homo sapiens)
Sars-cov-2 spike glycoprotein trimer complexed with fab fragment of anti-rbd antibody e7 (Complex from Homo sapiens)
Spike glycoprotein (132 kDa, Protein from Homo sapiens)
Fab e7 light chain (23 kDa, Protein from Homo sapiens)

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EMD-27205

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Closed state of SARS-CoV-2 BA.2 variant spike protein

Release date: June 7, 2023
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8d55
Q-score: 0.434

Zhang J, Tang W, Gao H, Lavine CL, Shi W, Peng H, Zhu H, Anand K, Kosikova M, Kwon HJ, Tong P, Gautam A, Rits-Volloch S, Wang S, Mayer ML, Wesemann DR, Seaman MS, Lu J, Xiao T, Xie H, Chen B

Nat Struct Mol Biol (2023) 30 pp. 980-990 [ Pubmed: 37430064 DOI: doi:10.1038/s41594-023-01023-6 ]

Sample:

Closed state of pre-fusion sars-cov-2 ba.2 variant spike protein (600 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

EMD-27206

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One RBD-up state of SARS-CoV-2 BA.2 variant spike protein

Release date: June 7, 2023
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8d56
Q-score: 0.438

Zhang J, Tang W, Gao H, Lavine CL, Shi W, Peng H, Zhu H, Anand K, Kosikova M, Kwon HJ, Tong P, Gautam A, Rits-Volloch S, Wang S, Mayer ML, Wesemann DR, Seaman MS, Lu J, Xiao T, Xie H, Chen B

Nat Struct Mol Biol (2023) 30 pp. 980-990 [ Pubmed: 37430064 DOI: doi:10.1038/s41594-023-01023-6 ]

Sample:

One rbd-up state of pre-fusion sars-cov-2 ba.2 variant spike protein (600 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

EMD-27207

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Middle state of SARS-CoV-2 BA.2 variant spike protein

Release date: June 7, 2023
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8d5a
Q-score: 0.414

Zhang J, Tang W, Gao H, Lavine CL, Shi W, Peng H, Zhu H, Anand K, Kosikova M, Kwon HJ, Tong P, Gautam A, Rits-Volloch S, Wang S, Mayer ML, Wesemann DR, Seaman MS, Lu J, Xiao T, Xie H, Chen B

Nat Struct Mol Biol (2023) 30 pp. 980-990 [ Pubmed: 37430064 DOI: doi:10.1038/s41594-023-01023-6 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Middle state of pre-fusion sars-cov-2 ba.2 variant spike protein (600 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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