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

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-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 [ DOI: doi:10.1038/s41467-019-10236-7 Pubmed: 31101900 ]

Sample:

Rna (5'-r(p*ap*gp*cp*c)-3') (1 kDa, RNA from Rotavirus A)
Dna/rna (5'-d(*(gtg))-r(p*gp*c)-3') (1 kDa, Macromolecule from Rotavirus A)
Rotavirus a (Virus from Rotavirus A)
Inner capsid protein vp2 (103 kDa, Protein from Rotavirus A)
Rna-dependent rna polymerase of rotavirus a (125 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 [ DOI: doi:10.1038/s41467-019-10236-7 Pubmed: 31101900 ]

Sample:

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

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EMD-8345

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Cryo-EM structure of the human 80S ribosome at 3.6 Angstrom resolution

Release date: Oct. 26, 2016
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 5t2c
Q-score: 0.419

Zhang X, Lai M, Chang W, Yu I, Ding K, Mrazek J, Ng HL, Yang OO, Maslov DA, Zhou ZH

Nat Commun (2016) 7 pp. 13223-13223 [ DOI: doi:10.1038/ncomms13223 Pubmed: 27752045 ]

Sample:

Human ribosome (jurkat) (Complex from Homo sapiens)

EMD-6409

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In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus

Release date: Oct. 28, 2015
Resolution: 22.0 Å
EM Method: Single-particle

Zhang X, Ding K, Yu X, Chang W, Sun J, Zhou ZH

Nature (2015) 527 pp. 531-534 [ Pubmed: 26503045 DOI: doi:10.1038/nature15767 ]

Sample:

Cpv dsrna genome with vp4 + polymerase complex (tec) (Sample)
Vp4 (Protein from Bombyx mori cypovirus 1)
Dsrna genome (RNA from Bombyx mori cypovirus 1)
Rna polymerase (Protein from Bombyx mori cypovirus 1)

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