7UQZ

Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly.

Sekulski, K., Cruz, V.E., Weirich, C.S., Erzberger, J.P.

(2023) Nat Commun 14: 1207-1207

  • DOI: 10.1038/s41467-023-36867-5
  • Primary Citation of Related Structures:  
    7UOO, 7UQB, 7UQZ, 7UUI, 7V08

  • PubMed Abstract: 

    • Biogenesis of the large ribosomal (60S) subunit involves the assembly of three rRNAs and 46 proteins, a process requiring approximately 70 ribosome biogenesis factors (RBFs) that bind and release the pre-60S at specific steps along the assembly pathway. The methyltransferase Spb1 and the K-loop GTPase Nog2 are essential RBFs that engage the rRNA A-loop during sequential steps in 60S maturation ...

    Biogenesis of the large ribosomal (60S) subunit involves the assembly of three rRNAs and 46 proteins, a process requiring approximately 70 ribosome biogenesis factors (RBFs) that bind and release the pre-60S at specific steps along the assembly pathway. The methyltransferase Spb1 and the K-loop GTPase Nog2 are essential RBFs that engage the rRNA A-loop during sequential steps in 60S maturation. Spb1 methylates the A-loop nucleotide G2922 and a catalytically deficient mutant strain (spb1 D52A ) has a severe 60S biogenesis defect. However, the assembly function of this modification is currently unknown. Here, we present cryo-EM reconstructions that reveal that unmethylated G2922 leads to the premature activation of Nog2 GTPase activity and capture a Nog2-GDP-AlF 4 - transition state structure that implicates the direct involvement of unmodified G2922 in Nog2 GTPase activation. Genetic suppressors and in vivo imaging indicate that premature GTP hydrolysis prevents the efficient binding of Nog2 to early nucleoplasmic 60S intermediates. We propose that G2922 methylation levels regulate Nog2 recruitment to the pre-60S near the nucleolar/nucleoplasmic phase boundary, forming a kinetic checkpoint to regulate 60S production. Our approach and findings provide a template to study the GTPase cycles and regulatory factor interactions of the other K-loop GTPases involved in ribosome assembly.

    Organizational Affiliation: 

    Department of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd., ND10.104B, Dallas, TX, 75390-8816, USA. jan.erzberger@utsouthwestern.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-AA254Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 5
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rRNA-processing proteinE [auth 5]114Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Find proteins for A0A6A5PUZ0 (Saccharomyces cerevisiae)
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60S ribosomal protein L12-AG [auth 8]165Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Ribosome biogenesis protein ALB1H [auth 9]175Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L3I [auth B]386Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L4-AJ [auth C]362Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L5K [auth D]297Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L6-AL [auth E]176Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L7-AM [auth F]244Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L8-AN [auth G]256Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L9-AO [auth H]191Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Bud site selection protein 20P [auth I]131Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L11-AQ [auth J]171Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Proteasome-interacting protein CIC1R [auth K]339Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L13-AS [auth L]199Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L14-AT [auth M]138Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L15-AU [auth N]203Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L16-AV [auth O]197Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L17-AW [auth P]183Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L18-AX [auth Q]186Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L19-AY [auth R]189Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L20-AZ [auth S]172Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L21-AAA [auth T]160Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L22-ABA [auth U]121Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L23-ACA [auth V]137Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Ribosome assembly factor MRT4DA [auth W]236Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L25EA [auth X]142Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L26-AFA [auth Y]127Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L27-AGA [auth Z]136Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L28HA [auth a]149Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Nucleolar GTP-binding protein 1IA [auth b]647Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L30JA [auth c]105Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L31-AKA [auth d]113Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L32LA [auth e]130Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L33-AMA [auth f]107Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L34-ANA [auth g]120Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L35-AOA [auth h]120Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L36-APA [auth i]99Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L37-AQA [auth j]87Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L38RA [auth k]78Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L39SA [auth l]50Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Nucleolar GTP-binding protein 2TA [auth m]472Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Pescadillo homologUA [auth n]605Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 48
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Ribosome biogenesis protein 15VA [auth o]220Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Find proteins for P53927 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
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60S ribosomal protein L43-AWA [auth p]92Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
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Ribosome biogenesis protein NOP53XA [auth q]455Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
Find proteins for Q12080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
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Ribosome biogenesis protein NSA2YA [auth r]261Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
Find proteins for P40078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
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Nuclear GTP-binding protein NUG1ZA [auth s]520Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
Find proteins for P40010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
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Ribosome biogenesis protein RLP7AB [auth t]321Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
Find proteins for P40693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
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Ribosome biogenesis protein RLP24BB [auth u]199Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
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Entity ID: 55
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Ribosome production factor 2 homologCB [auth v]344Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
Find proteins for A0A6A5PVK5 (Saccharomyces cerevisiae)
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Entity ID: 56
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Ribosome biogenesis regulatory proteinDB [auth w]202Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 57
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RSA4 isoform 1EB [auth x]515Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 58
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Eukaryotic translation initiation factor 6FB [auth y]244Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
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UPF0642 protein YBL028CGB [auth z]105Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
Find proteins for P38202 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
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Probable metalloprotease ARX1HB [auth 4]592Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 3
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Find proteins for Q03862 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsLengthOrganismImage
25S rRNAB [auth 1]3,396Saccharomyces cerevisiae BY4741
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5.8S rRNAC [auth 2]158Saccharomyces cerevisiae BY4741
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Entity ID: 4
MoleculeChainsLengthOrganismImage
5S rRNAD [auth 3]121Saccharomyces cerevisiae BY4741
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Entity ID: 6
MoleculeChainsLengthOrganismImage
ITS2 rRNAF [auth 6]74Saccharomyces cerevisiae BY4741
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP
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NE [auth b],
RE [auth m]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
B3P
Query on B3P
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HE [auth 1],
IE [auth 1],
JE [auth 1]		2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
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KE [auth I],
PE [auth g],
QE [auth j],
UE [auth p],
VE [auth u]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
K (Subject of Investigation/LOI)
Query on K
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TE [auth m]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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AC [auth 1],
AD [auth 1],
AE [auth 1],
BC [auth 1],
BD [auth 1],
AC [auth 1],
AD [auth 1],
AE [auth 1],
BC [auth 1],
BD [auth 1],
BE [auth 1],
CC [auth 1],
CD [auth 1],
CE [auth 1],
DC [auth 1],
DD [auth 1],
DE [auth 1],
EC [auth 1],
ED [auth 1],
EE [auth 1],
FC [auth 1],
FD [auth 1],
FE [auth 1],
GC [auth 1],
GD [auth 1],
GE [auth 1],
HC [auth 1],
HD [auth 1],
IB [auth 1],
IC [auth 1],
ID [auth 1],
JB [auth 1],
JC [auth 1],
JD [auth 1],
KB [auth 1],
KC [auth 1],
KD [auth 1],
LB [auth 1],
LC [auth 1],
LD [auth 1],
LE [auth R],
MB [auth 1],
MC [auth 1],
MD [auth 1],
ME [auth V],
NB [auth 1],
NC [auth 1],
ND [auth 1],
OB [auth 1],
OC [auth 1],
OD [auth 1],
OE [auth b],
PB [auth 1],
PC [auth 1],
PD [auth 1],
QB [auth 1],
QC [auth 1],
QD [auth 1],
RB [auth 1],
RC [auth 1],
RD [auth 1],
SB [auth 1],
SC [auth 1],
SD [auth 1],
SE [auth m],
TB [auth 1],
TC [auth 1],
TD [auth 1],
UB [auth 1],
UC [auth 1],
UD [auth 1],
VB [auth 1],
VC [auth 1],
VD [auth 1],
WB [auth 1],
WC [auth 1],
WD [auth 1],
XB [auth 1],
XC [auth 1],
XD [auth 1],
YB [auth 1],
YC [auth 1],
YD [auth 1],
ZB [auth 1],
ZC [auth 1],
ZD [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM135617-01
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR150074
Robert A. Welch FoundationUnited StatesI-1897

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release