5DM7 image
Deposition Date 2015-09-08
Release Date 2015-11-11
Last Version Date 2024-11-20
Entry Detail
PDB ID:
5DM7
Keywords:
RIBOSOME
Title:
Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A
Biological Source:
Source Organism:
Deinococcus radiodurans (Taxon ID: 1299)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.00 Å
R-Value Free:
0.32
R-Value Work:
0.28
R-Value Observed:
0.28
Space Group:
I 2 2 2
5DM7 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:A (auth: 0)
Chain Length:224
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSS8 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:Z (auth: 1)
Chain Length:54
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSS4 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:AA (auth: 2)
Chain Length:47
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSH2 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:BA (auth: 3)
Chain Length:65
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSW6 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:B (auth: A)
Chain Length:274
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ9 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:C (auth: B)
Chain Length:205
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXK2 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:D (auth: C)
Chain Length:197
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXK1 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:E (auth: D)
Chain Length:177
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ0 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:F (auth: E)
Chain Length:171
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSL3 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:G (auth: F)
Chain Length:144
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSS7 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:H (auth: G)
Chain Length:142
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXY1 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:I (auth: H)
Chain Length:134
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ2 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:J (auth: I)
Chain Length:141
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSK9 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:K (auth: J)
Chain Length:136
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ5 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:L (auth: K)
Chain Length:113
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSJ5 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:M (auth: L)
Chain Length:104
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSL2 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:N (auth: M)
Chain Length:109
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RWB4 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:O (auth: N)
Chain Length:117
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSW7 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:P (auth: O)
Chain Length:94
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RY64 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:Q (auth: P)
Chain Length:127
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ7 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:R (auth: Q)
Chain Length:93
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXK0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:S (auth: R)
Chain Length:110
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ1 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:T (auth: S)
Chain Length:175
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RX88 Pfam ID:PF01386, PF14693
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:U (auth: T)
Chain Length:84
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RY65 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:V (auth: U)
Chain Length:72
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RRG8 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:W (auth: V)
Chain Length:66
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ4 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:X (auth: W)
Chain Length:55
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSL0 Pfam ID:PF00327
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:CA (auth: X)
Chain Length:2881
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:DA (auth: Y)
Chain Length:122
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:Y (auth: Z)
Chain Length:57
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:P49228 Pfam ID:PF01783
Ligand Molecules
HGR
MG
Primary Citation
Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
Nucleic Acids Res. 43 10015 10025 (2015)
PMID: 26464437 DOI: 10.1093/nar/gkv975

Abstact

Hygromycin A (HygA) binds to the large ribosomal subunit and inhibits its peptidyl transferase (PT) activity. The presented structural and biochemical data indicate that HygA does not interfere with the initial binding of aminoacyl-tRNA to the A site, but prevents its subsequent adjustment such that it fails to act as a substrate in the PT reaction. Structurally we demonstrate that HygA binds within the peptidyl transferase center (PTC) and induces a unique conformation. Specifically in its ribosomal binding site HygA would overlap and clash with aminoacyl-A76 ribose moiety and, therefore, its primary mode of action involves sterically restricting access of the incoming aminoacyl-tRNA to the PTC.

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Chemical

Disease

Primary Citation of related structures
5DM7