Electron Microscopy Data Bank

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Cryo-EM structure of Rab29-LRRK2 complex in the LRRK2 monomer state

Release date: Jan. 3, 2024
Resolution: 4.13 Å
EM Method: Single-particle
Fitted PDBs: 8fo2
Q-score: 0.333

Zhu H, Tonelli F, Turk M, Prescott A, Alessi DR, Sun J

Science (2023) 382 pp. 1404-1411 [ DOI: doi:10.1126/science.adi9926 Pubmed: 38127736 ]

Sample:

Ras-related protein rab-7l1 (20 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
Guanosine-5'-diphosphate (443 Da, Ligand)
Adenosine-5'-triphosphate (507 Da, Ligand)
Lrrk2-rab29 (Complex from Homo sapiens)
Leucine-rich repeat serine/threonine-protein kinase 2 (286 kDa, Protein from Homo sapiens)
Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)

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EMD-29341

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Cryo-EM structure of Rab29-LRRK2 complex in the LRRK2 dimer state

Release date: Jan. 3, 2024
Resolution: 3.88 Å
EM Method: Single-particle
Fitted PDBs: 8fo8
Q-score: 0.264

Zhu H, Tonelli F, Turk M, Prescott A, Alessi DR, Sun J

Science (2023) 382 pp. 1404-1411 [ DOI: doi:10.1126/science.adi9926 Pubmed: 38127736 ]

Sample:

Ras-related protein rab-7l1 (20 kDa, Protein from Homo sapiens)
Guanosine-5'-diphosphate (443 Da, Ligand)
Adenosine-5'-triphosphate (507 Da, Ligand)
Rab29-lrrk2 (Complex from Homo sapiens)
Leucine-rich repeat serine/threonine-protein kinase 2 (286 kDa, Protein from Homo sapiens)

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EMD-29342

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Cryo-EM structure of Rab29-LRRK2 complex in the LRRK2 tetramer state

Release date: Jan. 3, 2024
Resolution: 3.48 Å
EM Method: Single-particle
Fitted PDBs: 8fo9
Q-score: 0.307

Zhu H, Tonelli F, Turk M, Prescott A, Alessi DR, Sun J

Science (2023) 382 pp. 1404-1411 [ DOI: doi:10.1126/science.adi9926 Pubmed: 38127736 ]

Sample:

Ras-related protein rab-7l1 (20 kDa, Protein from Homo sapiens)
Guanosine-5'-diphosphate (443 Da, Ligand)
Adenosine-5'-triphosphate (507 Da, Ligand)
Rab29-lrrk2 (Complex from Homo sapiens)
Leucine-rich repeat serine/threonine-protein kinase 2 (286 kDa, Protein from Homo sapiens)

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EMD-40588

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Cryo-EM structure of LRRK2 bound with type-I inhibitor DNL201

Release date: Jan. 3, 2024
Resolution: 4.02 Å
EM Method: Single-particle
Fitted PDBs: 8smc
Q-score: 0.435

Zhu H, Tonelli F, Turk M, Prescott A, Alessi DR, Sun J

Science (2023) 382 pp. 1404-1411 [ DOI: doi:10.1126/science.adi9926 Pubmed: 38127736 ]

Sample:

Non-specific serine/threonine protein kinase (136 kDa, Protein from Homo sapiens)
2-methyl-2-(3-methyl-4-{[4-(methylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1h-pyrazol-1-yl)propanenitrile (339 Da, Ligand)
Guanosine-5'-diphosphate (443 Da, Ligand)
Lrrk2 (Complex 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 [ DOI: doi:10.1038/s41594-023-01023-6 Pubmed: 37430064 ]

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 [ DOI: doi:10.1038/s41594-023-01023-6 Pubmed: 37430064 ]

Sample:

Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
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)

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 [ DOI: doi:10.1038/s41594-023-01023-6 Pubmed: 37430064 ]

Sample:

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)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)

EMD-26021

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Structural and functional impact by SARS-CoV-2 Omicron spike mutations

Release date: Feb. 16, 2022
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7tnw
Q-score: 0.44

Zhang J, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Rits-Volloch S, Wang S, Sliz P, Wesemann DR, Yang W, Seaman MS, Lu J, Xiao T, Chen B

Cell Rep (2022) 39 pp. 110729-110729 [ DOI: doi:10.1016/j.celrep.2022.110729 Pubmed: 35452593 ]

Sample:

Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Closed state of pre-fusion sars-cov-2 omicron variant spike protein (440 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)

EMD-26029

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Structural and functional impact by SARS-CoV-2 Omicron spike mutations

Release date: Feb. 16, 2022
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7to4
Q-score: 0.394

Zhang J, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Rits-Volloch S, Wang S, Sliz P, Wesemann DR, Yang W, Seaman MS, Lu J, Xiao T, Chen B

Cell Rep (2022) 39 pp. 110729-110729 [ DOI: doi:10.1016/j.celrep.2022.110729 Pubmed: 35452593 ]

Sample:

One rbd-up state of pre-fusion sars-cov-2 omicron variant spike protein (440 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)
Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)

EMD-24982

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One RBD-up 1 of pre-fusion SARS-CoV-2 Delta variant spike protein

Release date: Nov. 10, 2021
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7sbl
Q-score: 0.394

Zhang J, Xiao T, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Walsh Jr RM, Rits-Volloch S, Wesemann DR, Yang W, Seaman MS, Lu J, Chen B

Science (2021) 374 pp. 1353-1360 [ DOI: doi:10.1126/science.abl9463 Pubmed: 34698504 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
One rbd-up 1 of pre-fusion sars-cov-2 delta variant spike protein (440 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)

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