9K0Z image
Deposition Date 2024-10-16
Release Date 2025-07-09
Last Version Date 2025-07-09
Entry Detail
PDB ID:
9K0Z
Keywords:
Title:
EF-G2 bound 70S ribosome complex of M. smegmatis
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
4.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rplX
Chain IDs:EB (auth: 1)
Chain Length:105
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Polymer Type:polyribonucleotide
Molecule:P/P-site Phe-tRNA(Phe)
Chain IDs:A (auth: 2)
Chain Length:76
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL37
Gene (Uniprot):MSMEG_1916
Chain IDs:B (auth: 3)
Chain Length:23
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Polymer Type:polyribonucleotide
Molecule:mRNA fragment
Chain IDs:C (auth: 4)
Chain Length:18
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL12
Gene (Uniprot):rplL
Chain IDs:D (auth: 5)
Chain Length:69
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Translation elongation factor EF-G
Gene (Uniprot):MSMEG_6535
Chain IDs:E (auth: 7)
Chain Length:709
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:F (auth: A)
Chain Length:1511
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:G (auth: B)
Chain Length:118
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rpsC
Chain IDs:H (auth: C)
Chain Length:49
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Gene (Uniprot):rpsD
Chain IDs:I (auth: D)
Chain Length:46
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rpsE
Chain IDs:J (auth: E)
Chain Length:180
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS6
Gene (Uniprot):rpsF
Chain IDs:K (auth: F)
Chain Length:37
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rpsG
Chain IDs:L (auth: G)
Chain Length:48
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rpsH
Chain IDs:M (auth: H)
Chain Length:3127
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rpsI
Chain IDs:N (auth: I)
Chain Length:126
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rpsJ
Chain IDs:O (auth: J)
Chain Length:99
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Gene (Uniprot):rpsK
Chain IDs:P (auth: K)
Chain Length:115
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rpsL
Chain IDs:Q (auth: L)
Chain Length:182
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rpsM
Chain IDs:R (auth: M)
Chain Length:176
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14B
Gene (Uniprot):rpsZ
Chain IDs:S (auth: N)
Chain Length:151
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rpsO
Chain IDs:T (auth: O)
Chain Length:88
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS16
Gene (Uniprot):rpsP
Chain IDs:U (auth: P)
Chain Length:113
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rpsQ
Chain IDs:V (auth: Q)
Chain Length:94
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS18B
Gene (Uniprot):rpsR2
Chain IDs:W (auth: R)
Chain Length:65
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rpsS
Chain IDs:X (auth: S)
Chain Length:82
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS20
Gene (Uniprot):rpsT
Chain IDs:Y (auth: T)
Chain Length:136
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rplW
Chain IDs:Z (auth: U)
Chain Length:118
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Gene (Uniprot):rpsB
Chain IDs:AA (auth: V)
Chain Length:126
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL25
Gene (Uniprot):rplY
Chain IDs:BA (auth: W)
Chain Length:113
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:CA (auth: X)
Chain Length:79
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28
Gene (Uniprot):rpmB-3
Chain IDs:DA (auth: Y)
Chain Length:63
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpmC
Chain IDs:EA (auth: Z)
Chain Length:64
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpmD
Chain IDs:FA (auth: a)
Chain Length:1511
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32
Gene (Uniprot):rpmF
Chain IDs:GA (auth: b)
Chain Length:118
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33A
Gene (Uniprot):rpmG1
Chain IDs:HA (auth: c)
Chain Length:49
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34
Gene (Uniprot):rpmH
Chain IDs:IA (auth: d)
Chain Length:46
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35
Gene (Uniprot):rpmI
Chain IDs:JA (auth: e)
Chain Length:180
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:KA (auth: f)
Chain Length:37
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL31
Gene (Uniprot):rpmE
Chain IDs:LA (auth: g)
Chain Length:48
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:FB (auth: h)
Chain Length:3127
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rplB
Chain IDs:MA (auth: i)
Chain Length:126
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Gene (Uniprot):rplC
Chain IDs:NA (auth: j)
Chain Length:99
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Gene (Uniprot):rplD
Chain IDs:OA (auth: k)
Chain Length:115
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Gene (Uniprot):rplE
Chain IDs:PA (auth: l)
Chain Length:182
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Gene (Uniprot):rplF
Chain IDs:QA (auth: m)
Chain Length:176
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:RA (auth: n)
Chain Length:151
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL10
Gene (Uniprot):rplJ
Chain IDs:SA (auth: o)
Chain Length:88
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL11
Gene (Uniprot):rplK
Chain IDs:TA (auth: p)
Chain Length:113
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:UA (auth: q)
Chain Length:94
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:VA (auth: r)
Chain Length:65
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):rplO
Chain IDs:WA (auth: s)
Chain Length:82
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Gene (Uniprot):rplP
Chain IDs:XA (auth: t)
Chain Length:136
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17
Gene (Uniprot):rplQ
Chain IDs:YA (auth: u)
Chain Length:118
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rplR
Chain IDs:ZA (auth: v)
Chain Length:126
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:AB (auth: w)
Chain Length:113
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
Gene (Uniprot):rplT
Chain IDs:BB (auth: x)
Chain Length:79
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21
Gene (Uniprot):rplU
Chain IDs:CB (auth: y)
Chain Length:63
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Gene (Uniprot):rplV
Chain IDs:DB (auth: z)
Chain Length:64
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Primary Citation
Cryo-EM structural analyses reveal a unique role for elongation factor G2 (EF-G2) in Mycobacteria.
Febs J. ? ? ? (2025)
PMID: 40569974 DOI: 10.1111/febs.70161

Abstact

The gene-encoding translation elongation factor G (EF-G) has undergone gene duplication across various bacterial species including Mycobacteria, and in mammalian mitochondria, leading to the emergence of the paralogue elongation factor G2 (EF-G2). Our study reveals that mycobacterial EF-G2, unlike EF-G1, neither participates in ribosome-recycling nor significantly contributes to overall translation, suggesting that it plays an alternative role in Mycobacteria. Remarkably, our investigation found a significant overexpression of mycobacterial EF-G2 during the stationary growth phase. Moreover, EF-G2 lacks ribosome-dependent GTPase activity, an observation consistent with previous reports. Cryo-EM analysis of the M. smegmatis 70S ribosome purified from the nutrient-starved (stationary) phase and complexed with EF-G2 unveiled the structural basis for its inability to hydrolyse GTP in a ribosome-dependent manner. Furthermore, we report an unprecedented binding mode of two EF-G2 copies on the 50S ribosomal subunit that impedes subunit association, thereby preventing the formation of active 70S ribosomes. Thus, instead of performing canonical functions, mycobacterial EF-G2 acts as a translation repressor during nutrient starvation. Altogether, our findings shed light on the multifaceted mechanisms by which EF-G2 modulates protein synthesis under nutrient-limited conditions, providing insights into adaptive strategies employed by Mycobacteria to survive in hostile environments.

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Primary Citation of related structures
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