5T62

Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Resolution: 3.30 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: https://doi.org/10.15252/embj.201696012
  • Primary Citation of Related Structures:  
    5T62, 5T6R

  • 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 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 Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6A [auth X]264Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF6CDC95YPR016CLPZ15C
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AE [auth D]254Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3F [auth E]387Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AG [auth F]362Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5H [auth G]297Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AI [auth H]176Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AJ [auth I]244Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AK [auth J]256Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AL [auth K]191Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10M [auth L]221Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-AN [auth M]174Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AO [auth N]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AP [auth O]138Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AQ [auth a]204Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AR [auth b]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AS [auth c]184Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AT [auth d]186Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AU [auth e]189Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AV [auth f]172Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AW [auth g]160Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AX [auth h]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AY [auth i]137Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-AZ [auth j]155Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25AA [auth k]142Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-ABA [auth l]127Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-ACA [auth m]136Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28DA [auth n]149Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29EA [auth o]59Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30FA [auth p]105Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AGA [auth q]113Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32HA [auth r]130Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AIA [auth s]107Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AJA [auth t]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AKA [auth u]120Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ALA [auth v]100Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AMA [auth w]88Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38NA [auth x]78Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39OA [auth y]51Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40PA [auth z]128Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AQA [auth Q]106Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-ARA [auth R]92Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal Protein uL1SA [auth S]217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal export protein NMD3TA [auth V]524Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Large subunit GTPase 1UA [auth W]651Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.1
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Entity ID: 2
MoleculeChains LengthOrganismImage
25S Ribosomal RNAB [auth A]3,396Saccharomyces cerevisiae S288C
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S Ribosomal RNAC [auth B]121Saccharomyces cerevisiae
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Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S Ribosomal RNAD [auth C]158Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

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AH [auth W]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
K
Query on K

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NG [auth A],
OG [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth W],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth B],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth B],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth B],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth B],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth B],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth C],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth C],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth D],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth a],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth c],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth i]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
RECONSTRUCTIONRELION1.4
RECONSTRUCTIONRELION2.0 Open Beta

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  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Database references
  • 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: 2018-06-13
    Changes: Data collection, Other, Structure summary
  • Version 1.7: 2018-07-18
    Changes: Data collection
  • Version 1.8: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.9: 2019-12-18
    Changes: Other