Electron Microscopy Data Bank

EMD-39076

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ATAT-2 bound MEC-12/MEC-7 microtubule

Release date: Nov. 6, 2024
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8y9f

Luo J, Lam WH, Yu D, Chao VC, Zopfi MN, Khoo CJ, Zhao C, Yan S, Liu Z, Li XD, Zheng C, Zhai Y, Ti SC

Nat Struct Mol Biol (2025) 32 pp. 358-368 [ Pubmed: 39496813 DOI: doi:10.1038/s41594-024-01406-3 ]

Sample:

Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
Tubulin alpha-3 chain (50 kDa, Protein from Caenorhabditis elegans)
Alpha-tubulin n-acetyltransferase 2 (30 kDa, Protein from Caenorhabditis elegans)
Guanosine-5'-triphosphate (523 Da, Ligand)
Mec-12/mec-7 microtubule in complex with full-length atat-2 (Complex from Caenorhabditis elegans)
Tubulin beta-1 chain (49 kDa, Protein from Caenorhabditis elegans)
Tubulin alpha-3 chain (50 kDa, Protein from Caenorhabditis elegans)

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EMD-39100

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ATAT-2 bound MEC-12/MEC-7 microtubule without acetyl-CoA

Release date: Nov. 6, 2024
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8yaj

Luo J, Lam WH, Yu D, Chao VC, Zopfi MN, Khoo CJ, Zhao C, Yan S, Liu Z, Li XD, Zheng C, Zhai Y, Ti SC

Nat Struct Mol Biol (2025) 32 pp. 358-368 [ Pubmed: 39496813 DOI: doi:10.1038/s41594-024-01406-3 ]

Sample:

Alpha tat2 bound mec-12/mec-7 microtubules withour acetyl-coa (Complex from Caenorhabditis elegans)
Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
Tubulin alpha-3 chain (50 kDa, Protein from Caenorhabditis elegans)
Alpha-tubulin n-acetyltransferase 2 (30 kDa, Protein from Caenorhabditis elegans)
Guanosine-5'-triphosphate (523 Da, Ligand)
Tubulin beta-1 chain (49 kDa, Protein from Caenorhabditis elegans)
Piperazine-n,n'-bis(2-ethanesulfonic acid) (302 Da, Ligand)

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EMD-39102

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ATAT-2 bound K40Q MEC-12/MEC-7 microtubule

Release date: Nov. 6, 2024
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8yal

Luo J, Lam WH, Yu D, Chao VC, Zopfi MN, Khoo CJ, Zhao C, Yan S, Liu Z, Li XD, Zheng C, Zhai Y, Ti SC

Nat Struct Mol Biol (2025) 32 pp. 358-368 [ Pubmed: 39496813 DOI: doi:10.1038/s41594-024-01406-3 ]

Sample:

K40q mec-12/mec-7 microtubule complexed with alpha tat2 (Complex from Caenorhabditis elegans)
Tubulin alpha-3 chain (50 kDa, Protein from Caenorhabditis elegans)
Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
Alpha-tubulin n-acetyltransferase 2 (30 kDa, Protein from Caenorhabditis elegans)
Guanosine-5'-triphosphate (523 Da, Ligand)
Acetyl coenzyme *a (809 Da, Ligand)
Tubulin beta-1 chain (49 kDa, Protein from Caenorhabditis elegans)

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EMD-39105

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ATAT-2 bound K40R MEC-12/MEC-7 microtubule

Release date: Nov. 6, 2024
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8yar

Luo J, Lam WH, Yu D, Chao VC, Zopfi MN, Khoo CJ, Zhao C, Yan S, Liu Z, Li XD, Zheng C, Zhai Y, Ti SC

Nat Struct Mol Biol (2025) 32 pp. 358-368 [ Pubmed: 39496813 DOI: doi:10.1038/s41594-024-01406-3 ]

Sample:

Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
Tubulin alpha-3 chain (50 kDa, Protein from Caenorhabditis elegans)
Alpha-tubulin n-acetyltransferase 2 (30 kDa, Protein from Caenorhabditis elegans)
Guanosine-5'-triphosphate (523 Da, Ligand)
Acetyl coenzyme *a (809 Da, Ligand)
Tubulin beta-1 chain (49 kDa, Protein from Caenorhabditis elegans)
K40r mec-12/mec-7 microtubule in complex with luminal atat-2 (Complex from Caenorhabditis elegans)

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EMD-33861

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Cryo-EM structure of human Alpha-fetoprotein

Release date: Jan. 18, 2023
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7yim
Q-score: 0.484

Zheng L, Liu N, Gao X, Zhu W, Liu K, Wu C, Yan R, Zhang J, Gao X, Yao Y, Deng B, Xu J, Lu Y, Liu Z, Li M, Wei X, Wang HW, Peng H

Nat Methods (2023) 20 pp. 123-130 [ DOI: doi:10.1038/s41592-022-01693-y Pubmed: 36522503 ]

Sample:

Alpha-fetoprotein with no symmetry (67 kDa, Complex from Homo sapiens)
Alpha-fetoprotein (68 kDa, Protein from Homo sapiens)

EMD-33189

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cryo-EM structure of hemoglobin

Release date: Nov. 9, 2022
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7xgy
Q-score: 0.407

Zheng L, Liu N, Gao X, Zhu W, Liu K, Wu C, Yan R, Zhang J, Gao X, Yao Y, Deng B, Xu J, Lu Y, Liu Z, Li M, Wei X, Wang HW, Peng H

Nat Methods (2023) 20 pp. 123-130 [ DOI: doi:10.1038/s41592-022-01693-y Pubmed: 36522503 ]

Sample:

Protoporphyrin ix containing fe (616 Da, Ligand)
Hemoglobin (Complex from Homo sapiens)
Hemoglobin subunit beta (16 kDa, Protein from Homo sapiens)
Hemoglobin subunit alpha (15 kDa, Protein from Homo sapiens)

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EMD-31146

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Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading

Release date: Sept. 22, 2021
EM Method: Single-particle
Fitted PDBs: 7eiz

Yan L, Yang Y, Li M, Zhang Y, Zheng L, Ge J, Huang YC, Liu Z, Wang T, Gao S, Zhang R, Huang YY, Guddat LW, Gao Y, Rao Z, Lou Z

Cell (2021) 184 pp. 3474-3485.e11 [ Pubmed: 34143953 DOI: doi:10.1016/j.cell.2021.05.033 ]

Sample:

Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Proofreading exoribonuclease (59 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Magnesium ion (24 Da, Ligand)
Primer rna, template rna (Complex)
Non-structural protein 10 (14 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)
Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Nsp 7, 8, 9, 10, 12, 13, 14 (Complex from Severe acute respiratory syndrome coronavirus 2)
Mcap(0)-rtc (Complex from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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EMD-31138

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Co-transcriptional capping machineries in SARS-CoV-2 RTC: Coupling of N7-methyltransferase and 3'-5' exoribonuclease with polymerase reveals mechanisms for capping and proofreading

Release date: July 21, 2021
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 7egq
Q-score: 0.384

Yan L, Yang Y, Li M, Zhang Y, Zheng L, Ge J, Huang YC, Liu Z, Wang T, Gao S, Zhang R, Huang YY, Guddat LW, Gao Y, Rao Z, Lou Z

Cell (2021) 184 pp. 3474-3485.e11 [ Pubmed: 34143953 DOI: doi:10.1016/j.cell.2021.05.033 ]

Sample:

Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Proofreading exoribonuclease (59 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cap(0)-rtc (Complex from Severe acute respiratory syndrome coronavirus 2)
Magnesium ion (24 Da, Ligand)
Primer rna, template rna (Complex)
Primer rna (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Template rna (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 10 (14 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)
Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Nsp 7, 8, 9, 10, 12, 13, 14 (Complex from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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EMD-30504

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Cryo-EM structure of an extended SARS-CoV-2 replication and transcription complex reveals an intermediate state in cap synthesis

Release date: Dec. 9, 2020
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 7cyq
Q-score: 0.384

Yan L, Ge J, Zheng L, Zhang Y, Gao Y, Wang T, Huang Y, Yang Y, Gao S, Li M, Liu Z, Wang H, Li Y, Chen Y, Guddat LW, Wang Q, Rao Z, Lou Z

Cell (2021) 184 pp. 184-193.e10 [ Pubmed: 33232691 DOI: doi:10.1016/j.cell.2020.11.016 ]

Sample:

Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Template (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Guanosine-5'-diphosphate (443 Da, Ligand)
Magnesium ion (24 Da, Ligand)
Rna (Complex from Severe acute respiratory syndrome coronavirus 2)
Primer (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)
Sars-cov-2 extended rtc (Complex)
Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Nsp7, nsp8, nsp9, nsp12 and nsp13 (Complex from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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EMD-30178

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SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors in reduced conditions

Release date: April 8, 2020
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 7btf
Q-score: 0.569

Gao Y, Yan L, Huang Y, Liu F, Zhao Y, Cao L, Wang T, Sun Q, Ming Z, Zhang L, Ge J, Zheng L, Zhang Y, Wang H, Zhu Y, Zhu C, Hu T, Hua T, Zhang B, Yang X, Li J, Yang H, Liu Z, Xu W, Guddat LW, Wang Q, Lou Z, Rao Z

Science (2020) 368 pp. 779-782 [ Pubmed: 32277040 DOI: doi:10.1126/science.abb7498 ]

Sample:

Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Structure of sars-cov-2 rna-dependent rna polymerase in complex with cofactors in reduced condition (155 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)
Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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