Zophobas morio black wasting virus strain NJ2-molitor virion structure
Resolution: 2.0 Å
EM Method: Single-particle
Fitted PDBs: 8t9x
Q-score: 0.736
Penzes JJ, Holm M, Firlar E, Kaelber JT
To Be Published
- Dna (5'-d(p*cp*gp*a)-3') (886 Da, DNA from Zophobas morio black wasting virus)
- Major capsid protein (48 kDa, Protein from Zophobas morio black wasting virus)
- Zophobas morio densovirus (Virus from Zophobas morio densovirus)
- Dna (5'-d(p*tp*cp*gp*ap*a)-3') (1 kDa, DNA from Zophobas morio black wasting virus)
- Water (18 Da, Ligand)
- Dna (5'-d(p*cp*ap*gp*gp*cp*cp*ap*ap*a)-3') (2 kDa, DNA from Zophobas morio black wasting virus)
Icosahedral capsid of the phicrAss001 virion
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 ]
- Head fiber trimer protein gp21 (13 kDa, Protein from Bacteroides phage crAss001)
- Magnesium ion (24 Da, Ligand)
- Major capsid protein gp32 (57 kDa, Protein from Bacteroides phage crAss001)
- Auxiliary capsid protein gp36 (36 kDa, Protein from Bacteroides phage crAss001)
- Head fiber dimer protein gp29 (10 kDa, Protein from Bacteroides phage crAss001)
- Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
Unique vertex of the phicrAss001 virion with C5 symmetry imposed
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 [ DOI: doi:10.1038/s41586-023-06019-2 Pubmed: 37138077 ]
- Head fiber trimer protein gp21 (10 kDa, Protein from Bacteroides phage crAss001)
- Auxiliary capsid protein gp36 (36 kDa, Protein from Bacteroides phage crAss001)
- Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
- Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)
- Magnesium ion (24 Da, Ligand)
- Major capsid protein gp32 (57 kDa, Protein from Bacteroides phage crAss001)
- Portal vertex capsid protein gp57 (11 kDa, Protein from Bacteroides phage crAss001)
Unique vertex of the phicrAss001 virion
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 ]
- Ring protein 2 gp40 (26 kDa, Protein from Bacteroides phage crAss001)
- Portal vertex capsid protein gp57 (11 kDa, Protein from Bacteroides phage crAss001)
- Ring protein 1 gp43 (27 kDa, Protein from Bacteroides phage crAss001)
- Magnesium ion (24 Da, Ligand)
- Major capsid protein gp32 (57 kDa, Protein from Bacteroides phage crAss001)
- Head fiber trimer protein gp21 (10 kDa, Protein from Bacteroides phage crAss001)
- Auxiliary capsid protein gp36 (36 kDa, Protein from Bacteroides phage crAss001)
- Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
- Cargo protein 1 gp45 (90 kDa, Protein from Bacteroides phage crAss001)
- Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)
Virion of native gene transfer agent (GTA) particle
Resolution: 4.54 Å
EM Method: Single-particle
Fitted PDBs: 6tba
Q-score: 0.472
Bardy P, Fuzik T, Hrebik D, Pantucek R, Thomas Beatty J, Plevka P
Nat Commun (2020) 11 pp. 3034-3034 [ Pubmed: 32541663 DOI: doi:10.1038/s41467-020-16669-9 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Baseplate (Complex from Rhodobacter capsulatus SB 1003)
- Phage major capsid protein, hk97 family (40 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Uncharacterized protein (20 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Phage major tail protein, tp901-1 family (14 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Portal protein rcc01684 (42 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Uncharacterized protein (32 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Connector (Complex from Rhodobacter capsulatus SB 1003)
- Uncharacterized protein (13 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Uncharacterized protein (12 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Uncharacterized protein (22 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Head spike (Complex from Rhodobacter capsulatus SB 1003)
- Uncharacterized protein (138 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Uncharacterized protein (31 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Uncharacterized protein (9 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Capsid (Complex from Rhodobacter capsulatus SB 1003)
- Rhodobacter capsulatus sb 1003 (880 kDa, Virus from Rhodobacter capsulatus SB 1003)
- Tail (Complex from Rhodobacter capsulatus SB 1003)
Capsid structure of Penaeus monodon metallodensovirus at pH 8.2
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 6wh3
Q-score: 0.594
Penzes JJ, Pham HT, Chipman P, Bhattacharya N, McKenna R, Agbandje-McKenna M, Tijssen P
PNAS (2020) 117 pp. 20211-20222 [ DOI: doi:10.1073/pnas.2008191117 Pubmed: 32747554 ]