5T62 image
Deposition Date 2016-09-01
Release Date 2017-02-08
Last Version Date 2024-11-13
Entry Detail
PDB ID:
5T62
Keywords:
RIBOSOME
Title:
Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex
Biological Source:
Source Organism:
Saccharomyces cerevisiae S288C (Taxon ID: 559292)
Saccharomyces cerevisiae (Taxon ID: 4932)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5T62 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence
Chain IDs:B (auth: A)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:C (auth: B)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5.8S Ribosomal RNA
Chain IDs:D (auth: C)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:E (auth: D)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX45 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:F (auth: E)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P14126 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:G (auth: F)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P10664 Pfam ID:PF00573, PF14374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:H (auth: G)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P26321 Pfam ID:PF17144, PF14204
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:I (auth: H)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q02326 Pfam ID:PF01159
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:J (auth: I)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:K (auth: J)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P17076 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:L (auth: K)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05738 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:M (auth: L)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P41805 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-A
Gene (Uniprot):RPL11A
Chain IDs:N (auth: M)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:O (auth: N)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q12690 Pfam ID:PF01294
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:P (auth: O)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:QA (auth: Q)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX27 Pfam ID:PF00935
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:RA (auth: R)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX25 Pfam ID:PF01780
Polymer Type:polypeptide(L)
Molecule:Ribosomal Protein uL1
Chain IDs:SA (auth: S)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal export protein NMD3
Gene (Uniprot):NMD3
Chain IDs:TA (auth: V)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P38861 Pfam ID:PF04981, PF21193, PF21192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large subunit GTPase 1
Gene (Uniprot):LSG1
Chain IDs:UA (auth: W)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P53145 Pfam ID:PF01926
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):TIF6
Chain IDs:A (auth: X)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q12522 Pfam ID:PF01912
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:Q (auth: a)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05748 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:R (auth: b)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P26784 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:S (auth: c)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05740 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:T (auth: d)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX49 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:U (auth: e)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX82 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):RPL20A
Chain IDs:V (auth: f)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX23 Pfam ID:PF01775
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:W (auth: g)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q02753 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:X (auth: h)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05749 Pfam ID:PF01776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:Y (auth: i)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX41 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24-A
Gene (Uniprot):RPL24A
Chain IDs:Z (auth: j)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P04449 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:AA (auth: k)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:BA (auth: l)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:CA (auth: m)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0C2H6 Pfam ID:PF01777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:DA (auth: n)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P02406 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:EA (auth: o)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05747 Pfam ID:PF01779
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:FA (auth: p)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P14120 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:GA (auth: q)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0C2H8 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:HA (auth: r)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P38061 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:IA (auth: s)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05744 Pfam ID:PF01247
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:JA (auth: t)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P87262 Pfam ID:PF01199
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:KA (auth: u)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX84 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:LA (auth: v)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05745 Pfam ID:PF01158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:MA (auth: w)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P49166 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:NA (auth: x)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P49167 Pfam ID:PF01781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:OA (auth: y)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P04650 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):RPL40A
Chain IDs:PA (auth: z)
Chain Length:128
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CH08 Pfam ID:PF00240, PF01020
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
PSU B U modified residue
Ligand Molecules
GNP
K
MG
Primary Citation
Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.
EMBO J. 36 854 868 (2017)
PMID: 28179369 DOI: 10.15252/embj.201696012

Abstact

During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. The last known events in the cytoplasm are the release of Tif6 by Efl1 and Sdo1 and the release of the export adapter, Nmd3, by the GTPase Lsg1. Here, we have used cryo-electron microscopy to determine the structure of the 60S subunit bound by Nmd3, Lsg1, and Tif6. We find that a central domain of Nmd3 mimics the translation elongation factor eIF5A, inserting into the E site of the ribosome and pulling the L1 stalk into a closed position. Additional domains occupy the P site and extend toward the sarcin-ricin loop to interact with Tif6. Nmd3 and Lsg1 together embrace helix 69 of the B2a intersubunit bridge, inducing base flipping that we suggest may activate the GTPase activity of Lsg1.

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Protein

Chemical

Disease

Primary Citation of related structures
5T6R