Electron Microscopy Data Bank

EMPIAR-10876

Release date: April 1, 2022
Dataset size: 4.7 TB
Experiment type: EMDB

Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP

Nat Struct Mol Biol (2022) 29 pp. 121-129 [ DOI: 10.1038/s41594-021-00719-x Pubmed: 35173352 ]

Image sets:

EMD-25479

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2.3 A structure of the ATP-dependent chromatin remodeler Chd1 bound to the nucleosome in a nucleotide-free state

Release date: March 2, 2022
Resolution: 2.3 Å
EM Method: Single-particle

Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP

Nat Struct Mol Biol (2022) 29 pp. 121-129 [ Pubmed: 35173352 DOI: doi:10.1038/s41594-021-00719-x ]

Sample:

Chd1 atp-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state (400 kDa, Complex from Saccharomyces cerevisiae)

EMD-25480

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2.7 A structure of the ATP-dependent chromatin remodeler Chd1 bound to the nucleosome in a nucleotide-free state. This entry contains a better resolved DNA-binding domain

Release date: March 2, 2022
Resolution: 2.7 Å
EM Method: Single-particle

Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP

Nat Struct Mol Biol (2022) 29 pp. 121-129 [ DOI: doi:10.1038/s41594-021-00719-x Pubmed: 35173352 ]

Sample:

Chd1 atp-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state (400 kDa, Complex from Saccharomyces cerevisiae)

EMD-25481

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2.6 A structure of the nucleosome from a class without Chd1

Release date: March 2, 2022
Resolution: 2.6 Å
EM Method: Single-particle

Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP

Nat Struct Mol Biol (2022) 29 pp. 121-129 [ DOI: doi:10.1038/s41594-021-00719-x Pubmed: 35173352 ]

Sample:

Chd1 atp-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state (400 kDa, Complex from Saccharomyces cerevisiae)

EMD-25483

Download Map 3D View Raw data

2.9 A structure of the nucleosome-bound ChEx, part of the chromatin remodeler Chd1

Release date: March 2, 2022
Resolution: 2.9 Å
EM Method: Single-particle

Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP

Nat Struct Mol Biol (2022) 29 pp. 121-129 [ DOI: doi:10.1038/s41594-021-00719-x Pubmed: 35173352 ]

Sample:

Chd1 atp-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state (400 kDa, Complex from Saccharomyces cerevisiae)

EMD-0261

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E. coli 70S d2d8 stapled ribosome

Release date: Dec. 19, 2018
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 6hrm
Q-score: 0.557

Schmied WH, Tnimov Z, Uttamapinant C, Rae CD, Fried SD, Chin JW

Nature (2018) 564 pp. 444-448 [ Pubmed: 30518861 DOI: doi:10.1038/s41586-018-0773-z ]

Sample:

E. coli 70s d2d8 stapled ribosome (Complex from Escherichia coli)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
50s ribosomal protein l10 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (25 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli)
Stapled 16s-23s rrna,stapled 16s-23s rrna,stapled 16s-23s rrna,stapled 16s-23s rrna (1 MDa, RNA from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
5s ribosomal rna (38 kDa, RNA from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
Water (18 Da, Ligand)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli)
30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)

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