8HFR

NPC-trapped pre-60S particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nuclear export of pre-60S particles through the nuclear pore complex.

Li, Z.Chen, S.Zhao, L.Huang, G.Xu, H.Yang, X.Wang, P.Gao, N.Sui, S.F.

(2023) Nature 618: 411-418

  • DOI: https://doi.org/10.1038/s41586-023-06128-y
  • Primary Citation of Related Structures:  
    8HBN, 8HFR

  • PubMed Abstract: 

    The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm 1-3 . The assembly intermediates of the ribosomal subunits, pre-60S and pre-40S particles, are among the largest cargoes of the NPC and the export of these gigantic ribonucleoproteins requires numerous export factors 4,5 . Here we report the cryo-electron microscopy structure of native pre-60S particles trapped in the channel of yeast NPCs. In addition to known assembly factors, multiple factors with export functions are also included in the structure. These factors in general bind to either the flexible regions or subunit interface of the pre-60S particle, and virtually form many anchor sites for NPC binding. Through interactions with phenylalanine-glycine (FG) repeats from various nucleoporins of NPC, these factors collectively facilitate the passage of the pre-60S particle through the central FG repeat network of the NPC. Moreover, in silico analysis of the axial and radial distribution of pre-60S particles within the NPC shows that a single NPC can take up to four pre-60S particles simultaneously, and pre-60S particles are enriched in the inner ring regions close to the wall of the NPC with the solvent-exposed surface facing the centre of the nuclear pore. Our data suggest a translocation model for the export of pre-60S particles through the NPC.


  • Organizational Affiliation

    School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AA [auth h1]120Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AB [auth g2]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29C [auth b3]59Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AD [auth B4]254Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AE [auth V5]137Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AF [auth O6]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AG [auth f7]107Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AH [auth F8]176Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 2I [auth v9]486Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1J [auth rA]647Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24K [auth tB]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30L [auth cC]105Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3M [auth CD]387Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6N [auth yE]245Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AO [auth UF]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AP [auth dG]113Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32Q [auth eH]130Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Shuttling pre-60S factor ECM1R [auth xI]212Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ALB1S [auth qJ]175Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA transport regulator MTR2AA [auth FR],
CB [auth Bt],
T [auth DK]
184Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AU [auth LL]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
YEAST 60S ribosomal protein L12-AV [auth KM]165Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA export factor MEX67FA [auth CW],
GA [auth EX],
W [auth AN]
599Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AX [auth DO]362Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AY [auth RP]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AZ [auth MQ]138Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-ABA [auth mS]106Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Probable metalloprotease ARX1CA [auth pT]593Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-ADA [auth YU]127Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal export protein NMD3EA [auth vV]518Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AHA [auth nY]92Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AIA [auth SZ]172Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AJA [auth ia]100Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AKA [auth Ib]191Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25LA [auth Xc]142Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2MA [auth xd]261Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome assembly factor MRT4PA [auth Wg]236Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AQA [auth jh]88Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39RA [auth li]51Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-ASA [auth Hj]256Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-ATA [auth Qk]186Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AUA [auth Tl]160Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Translation machinery-associated protein 16VA [auth sm]178Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AXA [auth No]204Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0642 protein YBL028CYA [auth zp]106Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38202 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AZA [auth Zq]136Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38AB [auth kr]78Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
YEAST 60S ribosomal protein L1-ABB [auth As]217Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-ADB [auth Gu]244Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AEB [auth Pv]184Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28FB [auth aw]149Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Bud site selection protein 20GB [auth ox]166Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-AHB [auth Jy]174Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5IB [auth Ez]297Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains LengthOrganismImage
25S ribosomal RNANA [auth 1e]3,396Saccharomyces cerevisiae S288C
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Entity ID: 38
MoleculeChains LengthOrganismImage
5S ribosomal RNAOA [auth 2f]121Saccharomyces cerevisiae S288C
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Entity ID: 46
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAWA [auth 3n]158Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth 1e]
AD [auth 1e]
AE [auth 1e]
AF [auth 1e]
AG [auth 1e]
AC [auth 1e],
AD [auth 1e],
AE [auth 1e],
AF [auth 1e],
AG [auth 1e],
AH [auth 1e],
AI [auth 1e],
AJ [auth 1e],
AK [auth 1e],
BC [auth 1e],
BD [auth 1e],
BE [auth 1e],
BF [auth 1e],
BG [auth 1e],
BH [auth 1e],
BI [auth 1e],
BJ [auth 1e],
BK [auth 1e],
CC [auth 1e],
CD [auth 1e],
CE [auth 1e],
CF [auth 1e],
CG [auth 1e],
CH [auth 1e],
CI [auth 1e],
CJ [auth 1e],
CK [auth 1e],
DC [auth 1e],
DD [auth 1e],
DE [auth 1e],
DF [auth 1e],
DG [auth 1e],
DH [auth 1e],
DI [auth 1e],
DJ [auth 1e],
DK [auth 2f],
EC [auth 1e],
ED [auth 1e],
EE [auth 1e],
EF [auth 1e],
EG [auth 1e],
EH [auth 1e],
EI [auth 1e],
EJ [auth 1e],
EK [auth 3n],
FC [auth 1e],
FD [auth 1e],
FE [auth 1e],
FF [auth 1e],
FG [auth 1e],
FH [auth 1e],
FI [auth 1e],
FJ [auth 1e],
FK [auth 3n],
GC [auth 1e],
GD [auth 1e],
GE [auth 1e],
GF [auth 1e],
GG [auth 1e],
GH [auth 1e],
GI [auth 1e],
GJ [auth 1e],
GK [auth 3n],
HC [auth 1e],
HD [auth 1e],
HE [auth 1e],
HF [auth 1e],
HG [auth 1e],
HH [auth 1e],
HI [auth 1e],
HJ [auth 1e],
HK [auth 3n],
IC [auth 1e],
ID [auth 1e],
IE [auth 1e],
IF [auth 1e],
IG [auth 1e],
IH [auth 1e],
II [auth 1e],
IJ [auth 1e],
IK [auth 3n],
JB [auth g2],
JC [auth 1e],
JD [auth 1e],
JE [auth 1e],
JF [auth 1e],
JG [auth 1e],
JH [auth 1e],
JI [auth 1e],
JJ [auth 1e],
JK [auth 3n],
KB [auth g2],
KC [auth 1e],
KD [auth 1e],
KE [auth 1e],
KF [auth 1e],
KG [auth 1e],
KH [auth 1e],
KI [auth 1e],
KJ [auth 1e],
KK [auth No],
LB [auth B4],
LC [auth 1e],
LD [auth 1e],
LE [auth 1e],
LF [auth 1e],
LG [auth 1e],
LH [auth 1e],
LI [auth 1e],
LJ [auth 1e],
LK [auth zp],
MB [auth CD],
MC [auth 1e],
MD [auth 1e],
ME [auth 1e],
MF [auth 1e],
MG [auth 1e],
MH [auth 1e],
MI [auth 1e],
MJ [auth 1e],
NB [auth CD],
NC [auth 1e],
ND [auth 1e],
NE [auth 1e],
NF [auth 1e],
NG [auth 1e],
NH [auth 1e],
NI [auth 1e],
NJ [auth 1e],
OB [auth 1e],
OC [auth 1e],
OD [auth 1e],
OE [auth 1e],
OF [auth 1e],
OG [auth 1e],
OH [auth 1e],
OI [auth 1e],
OJ [auth 1e],
PB [auth 1e],
PC [auth 1e],
PD [auth 1e],
PE [auth 1e],
PF [auth 1e],
PG [auth 1e],
PH [auth 1e],
PI [auth 1e],
PJ [auth 1e],
QB [auth 1e],
QC [auth 1e],
QD [auth 1e],
QE [auth 1e],
QF [auth 1e],
QG [auth 1e],
QH [auth 1e],
QI [auth 1e],
QJ [auth 1e],
RB [auth 1e],
RC [auth 1e],
RD [auth 1e],
RE [auth 1e],
RF [auth 1e],
RG [auth 1e],
RH [auth 1e],
RI [auth 1e],
RJ [auth 1e],
SB [auth 1e],
SC [auth 1e],
SD [auth 1e],
SE [auth 1e],
SF [auth 1e],
SG [auth 1e],
SH [auth 1e],
SI [auth 1e],
SJ [auth 1e],
TB [auth 1e],
TC [auth 1e],
TD [auth 1e],
TE [auth 1e],
TF [auth 1e],
TG [auth 1e],
TH [auth 1e],
TI [auth 1e],
TJ [auth 1e],
UB [auth 1e],
UC [auth 1e],
UD [auth 1e],
UE [auth 1e],
UF [auth 1e],
UG [auth 1e],
UH [auth 1e],
UI [auth 1e],
UJ [auth 1e],
VB [auth 1e],
VC [auth 1e],
VD [auth 1e],
VE [auth 1e],
VF [auth 1e],
VG [auth 1e],
VH [auth 1e],
VI [auth 1e],
VJ [auth 1e],
WB [auth 1e],
WC [auth 1e],
WD [auth 1e],
WE [auth 1e],
WF [auth 1e],
WG [auth 1e],
WH [auth 1e],
WI [auth 1e],
WJ [auth 1e],
XB [auth 1e],
XC [auth 1e],
XD [auth 1e],
XE [auth 1e],
XF [auth 1e],
XG [auth 1e],
XH [auth 1e],
XI [auth 1e],
XJ [auth 1e],
YB [auth 1e],
YC [auth 1e],
YD [auth 1e],
YE [auth 1e],
YF [auth 1e],
YG [auth 1e],
YH [auth 1e],
YI [auth 1e],
YJ [auth 1e],
ZB [auth 1e],
ZC [auth 1e],
ZD [auth 1e],
ZE [auth 1e],
ZF [auth 1e],
ZG [auth 1e],
ZH [auth 1e],
ZI [auth 1e],
ZJ [auth 1e]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary