Electron Microscopy Data Bank

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Release date: July 31, 2024
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8yb6
Q-score: 0.512

Zhang C, Chen F, Wang F, Xu H, Xue J, Li Z

Mol Cell (2024) 84 pp. 3141- [ Pubmed: 39047725 DOI: doi:10.1016/j.molcel.2024.06.033 ]

Sample:

Crispr system cascade subunit casc (41 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Zinc ion (65 Da, Ligand)
61-nt crrna (19 kDa, RNA from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Crispr system cascade subunit casd (43 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Type i-ehnh cascade complex (Complex from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Crispr-associated protein cse2 (crispr_cse2) (20 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Crispr-associated protein cse1 (crispr_cse1) (60 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Crispr-associated endoribonuclease cse3 (31 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)

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EMD-39167

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Type I-FHNH Cascade-dsDNA intermediate complex

Release date: July 31, 2024
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8ydb
Q-score: 0.443

Zhang C, Chen F, Wang F, Xu H, Xue J, Li Z

Mol Cell (2024) 84 pp. 3141- [ Pubmed: 39047725 DOI: doi:10.1016/j.molcel.2024.06.033 ]

Sample:

Cas8f fusion with hnh (39 kDa, Protein from Selenomonas sp.)
Type i-fhnh cascade-dsdna intermediate complex (Complex from Selenomonas sp.)
Cas5f (28 kDa, Protein from Selenomonas sp.)
Nts (3 kDa, Macromolecule from Selenomonas sp.)
Cas6f (20 kDa, Protein from Selenomonas sp.)
Ts (10 kDa, Macromolecule from Selenomonas sp.)
Cas7f (38 kDa, Protein from Selenomonas sp.)
60-nt crrna (19 kDa, RNA from Selenomonas sp.)

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EMD-39200

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Type I-FHNH Cascade-dsDNA R-loop complex

Release date: July 31, 2024
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8yeo
Q-score: 0.432

Zhang C, Chen F, Wang F, Xu H, Xue J, Li Z

Mol Cell (2024) 84 pp. 3141- [ Pubmed: 39047725 DOI: doi:10.1016/j.molcel.2024.06.033 ]

Sample:

Cas8f fusion with hnh (39 kDa, Protein from Selenomonas sp.)
Cas5f (28 kDa, Protein from Selenomonas sp.)
Nts (3 kDa, Macromolecule from Selenomonas sp.)
Cas6f (20 kDa, Protein from Selenomonas sp.)
Type i-fhnh cascade-dsdna r-loop complex (Complex from Selenomonas sp.)
Cas7f (38 kDa, Protein from Selenomonas sp.)
60-nt crrna (19 kDa, RNA from Selenomonas sp.)
Ts (15 kDa, Macromolecule from Selenomonas sp.)

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EMD-39285

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Type I-FHNH Cascade complex

Release date: July 31, 2024
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 8yh9
Q-score: 0.406

Zhang C, Chen F, Wang F, Xu H, Xue J, Li Z

Mol Cell (2024) 84 pp. 3141- [ Pubmed: 39047725 DOI: doi:10.1016/j.molcel.2024.06.033 ]

Sample:

Type i-fhnh cascade complex (Complex from Selenomonas sp.)
Cas8f fusion with hnh (39 kDa, Protein from Selenomonas sp.)
Cas5f (28 kDa, Protein from Selenomonas sp.)
Cas6f (20 kDa, Protein from Selenomonas sp.)
Cas7f (38 kDa, Protein from Selenomonas sp.)
60-nt crrna (19 kDa, RNA from Selenomonas sp.)

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EMD-39286

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Type I-EHNH Cascade-ssDNA complex

Release date: July 31, 2024
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8yha
Q-score: 0.508

Zhang C, Chen F, Wang F, Xu H, Xue J, Li Z

Mol Cell (2024) 84 pp. 3141- [ Pubmed: 39047725 DOI: doi:10.1016/j.molcel.2024.06.033 ]

Sample:

Crispr system cascade subunit casc (41 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Zinc ion (65 Da, Ligand)
Dna/rna (47-mer) (17 kDa, Macromolecule from Candidatus Cloacimonadota bacterium)
Type i-ehnh cascade-ssdna complex (Complex from Candidatus Cloacimonadota bacterium)
Crispr system cascade subunit casd (43 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
61-nt crrna (19 kDa, RNA from Candidatus Cloacimonadota bacterium)
Crispr-associated protein cse2 (crispr_cse2) (20 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Crispr-associated protein cse1 (crispr_cse1) (60 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Crispr-associated endoribonuclease cse3 (31 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)

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EMD-28645

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Cryo-EM structure of a riboendonclease

Release date: Aug. 30, 2023
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8ewg
Q-score: 0.518

Wang F, Zhang C, Xu H, Zeng W, Ma L, Li Z

J Mol Biol (2023) 435 pp. 168197-168197 [ DOI: doi:10.1016/j.jmb.2023.168197 Pubmed: 37442412 ]

Sample:

Crispr-associated endonuclease cas9 (143 kDa, Protein from Thermoclostridium caenicola)
Rna (56-mer) (19 kDa, RNA from Thermoclostridium caenicola)
Binary complex of a riboendonuclease with its cognate rna (Complex from Thermoclostridium caenicola)

EMD-34484

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Cryo-EM structure of a riboendonuclease

Release date: Aug. 30, 2023
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8h4u
Q-score: 0.439

Wang F, Zhang C, Xu H, Zeng W, Ma L, Li Z

J Mol Biol (2023) 435 pp. 168197-168197 [ DOI: doi:10.1016/j.jmb.2023.168197 Pubmed: 37442412 ]

Sample:

Apo-form riboendonuclease (Complex from Thermoclostridium caenicola)
Crispr-associated endonuclease cas9 (143 kDa, Protein from Thermoclostridium caenicola)

EMD-32856

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Cryo-EM structure of SARS-CoV-2 Omicron Spike protein with human ACE2 receptor, C2 state

Release date: April 6, 2022
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7wvp
Q-score: 0.143

Hong Q, Han W, Li J, Xu S, Wang Y, Xu C, Li Z, Wang Y, Zhang C, Huang Z, Cong Y

Nature (2022) 604 pp. 546-552 [ DOI: doi:10.1038/s41586-022-04581-9 Pubmed: 35228716 ]

Sample:

Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Angiotensin-converting enzyme 2 (72 kDa, Protein from Homo sapiens)
Sars-cov-2 omicron spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
Human ace2 receptor (Complex)
Cryo-em structure of sars-cov-2 omicron spike protein with human ace2 receptor, c2 state (Complex from Homo sapiens)

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EMD-32857

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Cryo-EM structure of SARS-CoV-2 Omicron Spike protein with human ACE2 receptor, C3 state

Release date: April 6, 2022
Resolution: 4.04 Å
EM Method: Single-particle
Fitted PDBs: 7wvq
Q-score: 0.057

Hong Q, Han W, Li J, Xu S, Wang Y, Xu C, Li Z, Wang Y, Zhang C, Huang Z, Cong Y

Nature (2022) 604 pp. 546-552 [ DOI: doi:10.1038/s41586-022-04581-9 Pubmed: 35228716 ]

Sample:

Cryo-em structure of sars-cov-2 omicron spike protein with human ace2 receptor, c3 state (Complex from Homo sapiens)
Omicron spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Angiotensin-converting enzyme 2 (72 kDa, Protein from Homo sapiens)
Human ace2 receptor (Complex)

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EMD-32854

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SARS-CoV-2 Omicron S-open

Release date: March 2, 2022
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7wvn
Q-score: 0.247

Hong Q, Han W, Li J, Xu S, Wang Y, Xu C, Li Z, Wang Y, Zhang C, Huang Z, Cong Y

Nature (2022) 604 pp. 546-552 [ DOI: doi:10.1038/s41586-022-04581-9 Pubmed: 35228716 ]

Sample:

Omicron s-open (Complex)
Omicron s-open (Complex from Homo sapiens)
Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus)
Sars-cov-2 omicron varient (Complex from Severe acute respiratory syndrome coronavirus 2)
Sars-cov-2 spike protein (Complex from Homo sapiens)

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