Electron Microscopy Data Bank

EMPIAR-11599

Release date: Aug. 18, 2023
Dataset size: 115.3 GB
Experiment type: EMDB

Yee NBY, Ho EML, Tun WM, Smith JLR, Dumoux M, Grange M, Darrow MC, Basham M

Biological Imaging (2023) 3 [ DOI: 10.1017/S2633903X23000107 ]

Image sets:

Unaligned multi-frame micrographs of human choriocarcinoma cells

EMD-17767

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Cryo electron tomography of human choriocarcinoma cells

Release date: July 12, 2023
EM Method: Tomography

Yee NB, Ho EML, Tun W, Smith JLR, Dumoux M, Grange M, Darrow MC, Basham M

Biol Imaging (2023) 3 pp. e10-e10 [ DOI: doi:10.1017/S2633903X23000107 Pubmed: 38487693 ]

Sample:

Jeg-3 human choriocarcinoma cell line (Cell from Homo sapiens)

EMD-14088

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Icosahedral capsid of the phicrAss001 virion

Release date: March 29, 2023
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 7qof
Q-score: 0.575

Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA

Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]

Sample:

Major capsid protein gp32 (57 kDa, Protein from Bacteroides phage crAss001)
Head fiber trimer protein gp21 (13 kDa, Protein from Bacteroides phage crAss001)
Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
Head fiber dimer protein gp29 (10 kDa, Protein from Bacteroides phage crAss001)
Auxiliary capsid protein gp36 (36 kDa, Protein from Bacteroides phage crAss001)
Magnesium ion (24 Da, Ligand)

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EMD-14089

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Portal protein assembly of the phicrAss001 virion with C12 symmetry imposed

Release date: March 29, 2023
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7qog
Q-score: 0.583

Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA

Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]

Sample:

Cargo protein 1 gp45 (90 kDa, Protein from Bacteroides phage crAss001)
Ring protein 2 gp40 (26 kDa, Protein from Bacteroides phage crAss001)
Ring protein 1 gp43 (27 kDa, Protein from Bacteroides phage crAss001)
Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)

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EMD-14090

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Unique vertex of the phicrAss001 virion with C5 symmetry imposed

Release date: March 29, 2023
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 7qoh
Q-score: 0.559

Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA

Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]

Sample:

Head fiber trimer protein gp21 (10 kDa, Protein from Bacteroides phage crAss001)
Major capsid protein gp32 (57 kDa, Protein from Bacteroides phage crAss001)
Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)
Auxiliary capsid protein gp36 (36 kDa, Protein from Bacteroides phage crAss001)
Portal vertex capsid protein gp57 (11 kDa, Protein from Bacteroides phage crAss001)
Magnesium ion (24 Da, Ligand)

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EMD-14091

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Unique vertex of the phicrAss001 virion

Release date: March 29, 2023
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 7qoi
Q-score: 0.505

Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA

Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]

Sample:

Head fiber trimer protein gp21 (10 kDa, Protein from Bacteroides phage crAss001)
Major capsid protein gp32 (57 kDa, Protein from Bacteroides phage crAss001)
Ring protein 1 gp43 (27 kDa, Protein from Bacteroides phage crAss001)
Ring protein 2 gp40 (26 kDa, Protein from Bacteroides phage crAss001)
Cargo protein 1 gp45 (90 kDa, Protein from Bacteroides phage crAss001)
Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)
Auxiliary capsid protein gp36 (36 kDa, Protein from Bacteroides phage crAss001)
Portal vertex capsid protein gp57 (11 kDa, Protein from Bacteroides phage crAss001)
Magnesium ion (24 Da, Ligand)

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EMD-14092

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Tail barrel assembly of the phicrAss001 virion with C12 symmetry imposed

Release date: March 29, 2023
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 7qoj
Q-score: 0.562

Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA

Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]

Sample:

Ring protein 2 gp40 (26 kDa, Protein from Bacteroides phage crAss001)
Tail fiber protein gp22 (92 kDa, Protein from Bacteroides phage crAss001)
Ring protein 1 gp43 (27 kDa, Protein from Bacteroides phage crAss001)
Cargo protein 1 gp45 (90 kDa, Protein from Bacteroides phage crAss001)
Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
Tail hub protein a gp38 (24 kDa, Protein from Bacteroides phage crAss001)
Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)
Ring protein 4/5 gp34 (26 kDa, Protein from Bacteroides phage crAss001)
Ring protein 3 gp35 (26 kDa, Protein from Bacteroides phage crAss001)
Water (18 Da, Ligand)
Magnesium ion (24 Da, Ligand)
Tail hub protein b gp39 (13 kDa, Protein from Bacteroides phage crAss001)

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EMD-14093

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Tail muzzle assembly of the phicrAss001 virion with C6 symmetry imposed

Release date: March 29, 2023
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 7qok
Q-score: 0.529

Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA

Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]

Sample:

Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
Ring protein 4/5 gp34 (26 kDa, Protein from Bacteroides phage crAss001)
Muzzle bound helix (1 kDa, Protein from Bacteroides phage crAss001)
Muzzle protein gp44 (156 kDa, Protein from Bacteroides phage crAss001)
Magnesium ion (24 Da, Ligand)

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EMD-14094

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Tail assembly of the phicrAss001 virion with C6 symmetry imposed

Release date: March 29, 2023
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 7qol
Q-score: 0.525

Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA

Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]

Sample:

Ring protein 2 gp40 (26 kDa, Protein from Bacteroides phage crAss001)
Tail fiber protein gp22 (92 kDa, Protein from Bacteroides phage crAss001)
Ring protein 1 gp43 (27 kDa, Protein from Bacteroides phage crAss001)
Cargo protein 1 gp45 (90 kDa, Protein from Bacteroides phage crAss001)
Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
Tail hub protein a gp38 (24 kDa, Protein from Bacteroides phage crAss001)
Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)
Ring protein 4/5 gp34 (26 kDa, Protein from Bacteroides phage crAss001)
Muzzle protein gp44 (156 kDa, Protein from Bacteroides phage crAss001)
Muzzle bound helix (1 kDa, Protein from Bacteroides phage crAss001)
Ring protein 3 gp35 (26 kDa, Protein from Bacteroides phage crAss001)
Water (18 Da, Ligand)
Magnesium ion (24 Da, Ligand)
Tail hub protein b gp39 (13 kDa, Protein from Bacteroides phage crAss001)

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EMD-14100

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Asymmetric reconstruction of the phicrAss001 virion

Release date: March 29, 2023
Resolution: 4.4 Å
EM Method: Single-particle

Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA

Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]

Sample:

Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)

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