Electron Microscopy Data Bank

EMD-20526

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CryoEM Structure of Pyocin R2 - precontracted - trunk

Release date: April 15, 2020
Resolution: 2.9 Å
EM Method: Helical reconstruction
Fitted PDBs: 6pyt
Q-score: 0.549

Ge P, Scholl D, Prokhorov NS, Avaylon J, Shneider MM, Browning C, Buth SA, Plattner M, Chakraborty U, Ding K, Leiman PG, Miller JF, Zhou ZH

Nature (2020) 580 pp. 658-662 [ Pubmed: 32350467 DOI: doi:10.1038/s41586-020-2186-z ]

Sample:

Pyocin r2 (Cellular component from Pseudomonas aeruginosa PAO1)
Pyocin sheath pa0622 (41 kDa, Protein from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Pyocin tube pa0623 (17 kDa, Protein from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))

EMD-20643

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CryoEM Structure of Pyocin R2 - precontracted - baseplate

Release date: April 15, 2020
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6u5b
Q-score: 0.448

Ge P, Scholl D, Prokhorov NS, Avaylon J, Shneider MM, Browning C, Buth SA, Plattner M, Chakraborty U, Ding K, Leiman PG, Miller JF, Zhou ZH

Nature (2020) 580 pp. 658-662 [ Pubmed: 32350467 DOI: doi:10.1038/s41586-020-2186-z ]

Sample:

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EMD-20644

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CryoEM Structure of Pyocin R2 - precontracted - collar

Release date: April 15, 2020
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6u5f
Q-score: 0.464

Ge P, Scholl D, Prokhorov NS, Avaylon J, Shneider MM, Browning C, Buth SA, Plattner M, Chakraborty U, Ding K, Leiman PG, Miller JF, Zhou ZH

Nature (2020) 580 pp. 658-662 [ Pubmed: 32350467 DOI: doi:10.1038/s41586-020-2186-z ]

Sample:

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EMD-20646

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CryoEM Structure of Pyocin R2 - precontracted - hub

Release date: April 15, 2020
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6u5h
Q-score: 0.356

Ge P, Scholl D, Prokhorov NS, Avaylon J, Shneider MM, Browning C, Buth SA, Plattner M, Chakraborty U, Ding K, Leiman PG, Miller JF, Zhou ZH

Nature (2020) 580 pp. 658-662 [ Pubmed: 32350467 DOI: doi:10.1038/s41586-020-2186-z ]

Sample:

EMD-20647

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CryoEM Structure of Pyocin R2 - postcontracted - collar

Release date: April 15, 2020
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6u5j
Q-score: 0.484

Ge P, Scholl D, Prokhorov NS, Avaylon J, Shneider MM, Browning C, Buth SA, Plattner M, Chakraborty U, Ding K, Leiman PG, Miller JF, Zhou ZH

Nature (2020) 580 pp. 658-662 [ Pubmed: 32350467 DOI: doi:10.1038/s41586-020-2186-z ]

Sample:

EMD-20648

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CryoEM Structure of Pyocin R2 - postcontracted - baseplate

Release date: April 15, 2020
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6u5k
Q-score: 0.384

Ge P, Scholl D, Prokhorov NS, Avaylon J, Shneider MM, Browning C, Buth SA, Plattner M, Chakraborty U, Ding K, Leiman PG, Miller JF, Zhou ZH

Nature (2020) 580 pp. 658-662 [ Pubmed: 32350467 DOI: doi:10.1038/s41586-020-2186-z ]

Sample:

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EMD-20398

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In situ structure of BTV RNA-dependent RNA polymerase in BTV virion

Release date: Aug. 7, 2019
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6pns
Q-score: 0.484

He Y, Shivakoti S, Ding K, Cui Y, Roy P, Zhou ZH

PNAS (2019) 116 pp. 16535-16540 [ DOI: doi:10.1073/pnas.1905849116 Pubmed: 31350350 ]

Sample:

Inner core structural protein vp3 (103 kDa, Protein from Bluetongue virus 1)
Bluetongue virus 1 (Virus from Bluetongue virus 1)
Rna-directed rna polymerase (149 kDa, Protein from Bluetongue virus 1)

EMD-20407

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In situ structure of BTV RNA-dependent RNA polymerase in BTV core

Release date: Aug. 7, 2019
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6po2
Q-score: 0.497

He Y, Shivakoti S, Ding K, Cui Y, Roy P, Zhou ZH

PNAS (2019) 116 pp. 16535-16540 [ DOI: doi:10.1073/pnas.1905849116 Pubmed: 31350350 ]

Sample:

Inner core structural protein vp3 (103 kDa, Protein from Bluetongue virus 1)
Bluetongue virus 1 (Virus from Bluetongue virus 1)
Rna-directed rna polymerase (149 kDa, Protein from Bluetongue virus 1)

EMD-20059

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In situ structure of Rotavirus RNA-dependent RNA polymerase at duplex-open state

Release date: May 22, 2019
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6ogy
Q-score: 0.537

Ding K, Celma CC, Zhang X, Chang T, Shen W, Atanasov I, Roy P, Zhou ZH

Nat Commun (2019) 10 pp. 2216-2216 [ Pubmed: 31101900 DOI: doi:10.1038/s41467-019-10236-7 ]

Sample:

Rna-dependent rna polymerase of rotavirus a (125 kDa, Protein from Rotavirus A)
Rotavirus a (Virus from Rotavirus A)
Dna/rna (5'-d(*(gtg))-r(p*gp*c)-3') (1 kDa, Macromolecule from Rotavirus A)
Rna (5'-r(p*ap*gp*cp*c)-3') (1 kDa, RNA from Rotavirus A)
Inner capsid protein vp2 (103 kDa, Protein from Rotavirus A)

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EMD-20060

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In situ structure of Rotavirus RNA-dependent RNA polymerase at transcript-elongated state

Release date: May 22, 2019
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6ogz
Q-score: 0.517

Ding K, Celma CC, Zhang X, Chang T, Shen W, Atanasov I, Roy P, Zhou ZH

Nat Commun (2019) 10 pp. 2216-2216 [ Pubmed: 31101900 DOI: doi:10.1038/s41467-019-10236-7 ]

Sample:

Uridine 5'-triphosphate (484 Da, Ligand)
Rna (5'-r(p*ap*up*ap*up*ap*up*ap*up*ap*up*ap*up*ap*up*ap*up*a)-3') (5 kDa, RNA from Rotavirus A)
Rna-dependent rna polymerase of rotavirus a (125 kDa, Protein from Rotavirus A)
Guanosine-5'-triphosphate (523 Da, Ligand)
Rotavirus a (Virus from Rotavirus A)
Rna (5'-r(p*up*ap*up*ap*up*ap*up*ap*up*ap*up*ap*up*ap*up*ap*up*a)-3') (5 kDa, RNA from Rotavirus A)
Inner capsid protein vp2 (103 kDa, Protein from Rotavirus A)

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