7Z34

Structure of pre-60S particle bound to DRG1(AFG2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1.

Prattes, M.Grishkovskaya, I.Hodirnau, V.V.Hetzmannseder, C.Zisser, G.Sailer, C.Kargas, V.Loibl, M.Gerhalter, M.Kofler, L.Warren, A.J.Stengel, F.Haselbach, D.Bergler, H.

(2022) Nat Struct Mol Biol 29: 942-953

  • DOI: 10.1038/s41594-022-00832-5
  • Primary Citation of Related Structures:  
    7Z11, 7Z34

  • PubMed Abstract: 
  • The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation ...

    The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.


    Organizational Affiliation

    Field of Excellence BioHealth - University of Graz, Graz, Austria. helmut.bergler@uni-graz.at.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase family gene 2 protein780Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: AFG2DRG1YLR397CL8084.16
EC: 3.6.4.10
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Probable metalloprotease ARX1E [auth 4]593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARX1YDR101CYD8557.10c
EC: 3
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-AF [auth A]254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3G [auth B]387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Entity ID: 8
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60S ribosomal protein L4-AH [auth C]362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Entity ID: 9
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60S ribosomal protein L5I [auth D]297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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Entity ID: 10
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60S ribosomal protein L6-AJ [auth E]176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 11
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60S ribosomal protein L7-AK [auth F]244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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60S ribosomal protein L8-AL [auth G]256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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60S ribosomal protein L9-AM [auth H]191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 14
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Bud site selection protein 20N [auth I]166Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD20YLR074C
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Entity ID: 15
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60S ribosomal protein L11-AO [auth J]174Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11ARP39ARPL16AYPR102CP8283.14
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Entity ID: 16
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60S ribosomal protein L28P [auth K]149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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60S ribosomal protein L13-AQ [auth L]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 18
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60S ribosomal protein L14-AR [auth M]138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 19
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60S ribosomal protein L15-AS [auth N]204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 20
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60S ribosomal protein L16-AT [auth O]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 21
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60S ribosomal protein L17-AU [auth P]184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 22
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60S ribosomal protein L18-AV [auth Q]186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19-AW [auth R]189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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Entity ID: 24
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60S ribosomal protein L20-AX [auth S]172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 25
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60S ribosomal protein L21-AY [auth T]160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 26
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60S ribosomal protein L22-AZ [auth U]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 27
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60S ribosomal protein L23-AAA [auth V]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome assembly factor MRT4BA [auth W]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MRT4YKL009WYKL160
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Entity ID: 29
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60S ribosomal protein L25CA [auth X]142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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60S ribosomal protein L26-ADA [auth Y]127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 31
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60S ribosomal protein L27-AEA [auth Z]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 32
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60S ribosomal protein L12-AFA [auth a]165Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL12ARPL15BYEL054C
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Nucleolar GTP-binding protein 1GA [auth b]647Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG1YPL093WLPG15W
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Entity ID: 34
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60S ribosomal protein L30HA [auth c]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 35
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60S ribosomal protein L31-AIA [auth d]113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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60S ribosomal protein L32JA [auth e]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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60S ribosomal protein L33-AKA [auth f]107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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60S ribosomal protein L34-ALA [auth g]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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60S ribosomal protein L35-AMA [auth h]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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60S ribosomal protein L36-ANA [auth i]100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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60S ribosomal protein L37-AOA [auth j]88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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60S ribosomal protein L38PA [auth k]78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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60S ribosomal protein L39QA [auth l]51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29TA [auth o]59Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
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60S ribosomal protein L43-AUA [auth p]92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
UniProt
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L42-AVA [auth q]106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2WA [auth r]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSA2YER126CSYGP-ORF47
UniProt
Find proteins for P40078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
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Ribosome biogenesis protein RLP24YA [auth u]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP24YLR009W
UniProt
Find proteins for Q07915 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal export protein NMD3ZA [auth v]518Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NMD3YHR170W
UniProt
Find proteins for P38861 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
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Eukaryotic translation initiation factor 6CB [auth y]245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF6CDC95YPR016CLPZ15C
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Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
UPF0642 protein YBL028CDB [auth z]106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YBL028CYBL0423
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown peptideEB [auth 0]19Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 2
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35S pre-ribosomal RNAB [auth 1]3,396Saccharomyces cerevisiae S288C
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Entity ID: 3
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5S rRNAC [auth 2]121Saccharomyces cerevisiae S288C
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Entity ID: 4
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5.8S rRNAD [auth 3]158Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
BI [auth w],
CI [auth w],
DI [auth w],
EI [auth x],
FB [auth Aa],
BI [auth w],
CI [auth w],
DI [auth w],
EI [auth x],
FB [auth Aa],
GB [auth Aa],
IF [auth m],
JF [auth m],
KF [auth n],
LF [auth n],
MF [auth t]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
UNK
Query on UNK

Download Ideal Coordinates CCD File 
AC [auth 1],
AD [auth 1],
AE [auth 1],
AF [auth J],
AG [auth v],
AC [auth 1],
AD [auth 1],
AE [auth 1],
AF [auth J],
AG [auth v],
AH [auth v],
AI [auth v],
BC [auth 1],
BD [auth 1],
BE [auth 1],
BF [auth J],
BG [auth v],
BH [auth v],
CC [auth 1],
CD [auth 1],
CE [auth 1],
CF [auth J],
CG [auth v],
CH [auth v],
DC [auth 1],
DD [auth 1],
DE [auth 1],
DF [auth J],
DG [auth v],
DH [auth v],
EC [auth 1],
ED [auth 1],
EE [auth 1],
EF [auth J],
EG [auth v],
EH [auth v],
FC [auth 1],
FD [auth 1],
FE [auth 1],
FF [auth J],
FG [auth v],
FH [auth v],
GC [auth 1],
GD [auth 1],
GE [auth 1],
GF [auth L],
GG [auth v],
GH [auth v],
HB [auth 1],
HC [auth 1],
HD [auth 1],
HE [auth 1],
HG [auth v],
HH [auth v],
IB [auth 1],
IC [auth 1],
ID [auth 1],
IE [auth 1],
IG [auth v],
IH [auth v],
JB [auth 1],
JC [auth 1],
JD [auth 1],
JE [auth 1],
JG [auth v],
JH [auth v],
KB [auth 1],
KC [auth 1],
KD [auth 1],
KE [auth J],
KG [auth v],
KH [auth v],
LB [auth 1],
LC [auth 1],
LD [auth 1],
LE [auth J],
LG [auth v],
LH [auth v],
MB [auth 1],
MC [auth 1],
MD [auth 1],
ME [auth J],
MG [auth v],
MH [auth v],
NB [auth 1],
NC [auth 1],
ND [auth 1],
NE [auth J],
NF [auth v],
NG [auth v],
NH [auth v],
OB [auth 1],
OC [auth 1],
OD [auth 1],
OE [auth J],
OF [auth v],
OG [auth v],
OH [auth v],
PB [auth 1],
PC [auth 1],
PD [auth 1],
PE [auth J],
PF [auth v],
PG [auth v],
PH [auth v],
QB [auth 1],
QC [auth 1],
QD [auth 1],
QE [auth J],
QF [auth v],
QG [auth v],
QH [auth v],
RB [auth 1],
RC [auth 1],
RD [auth 1],
RE [auth J],
RF [auth v],
RG [auth v],
RH [auth v],
SB [auth 1],
SC [auth 1],
SD [auth 1],
SE [auth J],
SF [auth v],
SG [auth v],
SH [auth v],
TB [auth 1],
TC [auth 1],
TD [auth 1],
TE [auth J],
TF [auth v],
TG [auth v],
TH [auth v],
UB [auth 1],
UC [auth 1],
UD [auth 1],
UE [auth J],
UF [auth v],
UG [auth v],
UH [auth v],
VB [auth 1],
VC [auth 1],
VD [auth 1],
VE [auth J],
VF [auth v],
VG [auth v],
VH [auth v],
WB [auth 1],
WC [auth 1],
WD [auth 1],
WE [auth J],
WF [auth v],
WG [auth v],
WH [auth v],
XB [auth 1],
XC [auth 1],
XD [auth 1],
XE [auth J],
XF [auth v],
XG [auth v],
XH [auth v],
YB [auth 1],
YC [auth 1],
YD [auth 1],
YE [auth J],
YF [auth v],
YG [auth v],
YH [auth v],
ZB [auth 1],
ZC [auth 1],
ZD [auth 1],
ZE [auth J],
ZF [auth v],
ZG [auth v],
ZH [auth v]
UNKNOWN
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
HF [auth b]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustria--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references