5T6R

Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.9 of the entry. See complete history


Literature

Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.

Malyutin, A.G.Musalgaonkar, S.Patchett, S.Frank, J.Johnson, A.W.

(2017) EMBO J 36: 854-868

  • DOI: 10.15252/embj.201696012
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 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 re ...

    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.


    Organizational Affiliation

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA jf2192@cumc.columbia.edu arlen@mail.utexas.edu.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-AD254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3E387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-AF362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5G297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-AH176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-AI244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-AJ256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-AK191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10L221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-AM174Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11ARP39ARPL16AYPR102CP8283.14
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-AN199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-AO138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-Aa204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-Ab199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-Ac184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-Ad186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-Ae189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-Af172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-Ag160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-Ai137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25k142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-Al127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-Am136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28n149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29o59Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30p105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-Aq113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32r130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-As107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-At121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-Au120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-Av100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-Aw88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38x78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39y51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40z128Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-AQ106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-AR92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein uL1S210Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Maltose binding protein, 60S ribosomal export protein Nmd3 fusionV917Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NMD3YHR170W
Find proteins for A0A0F8NYV9 (Methanosarcina mazei)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-Ah121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-Aj155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 1
MoleculeChainsLengthOrganism
25S Ribosomal RNAA3396Saccharomyces cerevisiae

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Entity ID: 2
MoleculeChainsLengthOrganism
5S Ribosomal RNAB121Saccharomyces cerevisiae

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Entity ID: 3
MoleculeChainsLengthOrganism
5.8S Ribosomal RNAC158Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, C, i
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM53655
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM29169
Howard Hughes Medical Institute (HHMI)United StatesHHMI

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Other
  • Version 1.2: 2017-02-22
    Changes: Database references
  • Version 1.3: 2017-04-12
    Changes: Database references
  • Version 1.4: 2017-09-20
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2017-11-08
    Changes: Derived calculations
  • Version 1.6: 2018-07-18
    Changes: Data collection
  • Version 1.7: 2018-10-03
    Changes: Data collection, Other, Refinement description
  • Version 1.8: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.9: 2019-12-18
    Changes: Advisory, Derived calculations, Other