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9DFD: Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with lasso peptide lariocidin B, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.60A resolution

PDB ID:

9DFD Download

MMDB ID:

255350

PDB Deposition Date:

2024/8/29

Updated in MMDB:

2024/11

Experimental Method:

x-ray diffraction

Resolution:

2.6 Å

Source Organism:

Thermus thermophilus HB8▼

Taxonomy	Molecule
Thermus thermophilus HB8	1A, 1B, 1D, 1E, 1F, 1G, 1H, 1I, 1N, 1O, 1P, 1Q, 1R, 1S, 1T, 1U, 1V, 1W, 1X, 1Y, 1Z, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 1a, 1b, 1c, 1d, 1e, 1f, 1g, 1h, 1i, 1j, 1k, 1l, 1m, 1n, 1o, 1p, 1q, 1r, 1s, 1t, 1u, 2A, 2B, 2D, 2E, 2F, 2G, 2H, 2I, 2N, 2O, 2P, 2Q, 2R, 2S, 2T, 2U, 2V, 2W, 2X, 2Y, 2Z, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 2a, 2b, 2c, 2d, 2e, 2f, 2g, 2h, 2i, 2j, 2k, 2l, 2m, 2n, 2o, 2p, 2q, 2r, 2s, 2t, 2u
Paenibacillus	1z, 2z
Tequatrovirus T4	1v, 2v
Escherichia coli	1w, 1x, 1y, 2w, 2x, 2y

Similar Structures:

Biological Unit for 9DFD: 57-meric; determined by author

Molecular Components in 9DFD
Label	Count	Molecule
Proteins (50 molecules)
1D	1	50S Ribosomal Protein L2
1E	1	50S Ribosomal Protein L3
1F	1	50S Ribosomal Protein L4
1G	1	50S Ribosomal Protein L5
1H	1	50S Ribosomal Protein L6
1I	1	50S Ribosomal Protein L9
1N	1	50S Ribosomal Protein L13
1O	1	50S Ribosomal Protein L14
1P	1	50S Ribosomal Protein L15
1Q	1	50S Ribosomal Protein L16
1R	1	50S Ribosomal Protein L17
1S	1	50S Ribosomal Protein L18
1T	1	50S Ribosomal Protein L19
1U	1	50S Ribosomal Protein L20
1V	1	50S Ribosomal Protein L21
1W	1	50S Ribosomal Protein L22
1X	1	50S Ribosomal Protein L23
1Y	1	50S Ribosomal Protein L24
1Z	1	50S Ribosomal Protein L25
10	1	50S Ribosomal Protein L27
11	1	50S Ribosomal Protein L28
12	1	50S Ribosomal Protein L29
13	1	50S Ribosomal Protein L30
14	1	50S Ribosomal Protein L31
15	1	50S Ribosomal Protein L32
16	1	50S Ribosomal Protein L33
17	1	50S Ribosomal Protein L34
18	1	50S Ribosomal Protein L35
19	1	50S Ribosomal Protein L36
1b	1	30S Ribosomal Protein S2
1c	1	30S Ribosomal Protein S3
1d	1	30S Ribosomal Protein S4
1e	1	30S Ribosomal Protein S5
1f	1	30S Ribosomal Protein S6
1g	1	30S Ribosomal Protein S7
1h	1	30S Ribosomal Protein S8
1i	1	30S Ribosomal Protein S9
1j	1	30S Ribosomal Protein S10
1k	1	30S Ribosomal Protein S11
1l	1	30S Ribosomal Protein S12
1m	1	30S Ribosomal Protein S13
1n	1	30S Ribosomal Protein S14 Type Z
1o	1	30S Ribosomal Protein S15
1p	1	30S Ribosomal Protein S16
1q	1	30S Ribosomal Protein S17
1r	1	30S Ribosomal Protein S18
1s	1	30S Ribosomal Protein S19
1t	1	30S Ribosomal Protein S20
1u	1	30S Ribosomal Protein THX
1z	1	Lasso Peptide Lariocidin B
Nucleotides(7 molecules)
1A	1	23S Ribosomal RNA
1B	1	5S Ribosomal RNA
1a	1	16S Ribosomal RNA
1v	1	Met-phe-mrna
1w	1	A-site Aminoacylated Phe-trnaphe
1x	1	P-site Aminoacylated Fmet-trnamet
1y	1	E-site Deacylated Trnaphe
Chemicals and Non-standard biopolymers (1429 molecules)
1	1421	MAGNESIUM ION (Link to PubChem not yet available)
2	1	POTASSIUM ION (Link to PubChem not yet available)
3	6	ZINC ION (Link to PubChem not yet available)
4	1	IRON/SULFUR CLUSTER (Link to PubChem not yet available)

* Click molecule labels to explore molecular sequence information.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303