6LSR

Cryo-EM structure of a pre-60S ribosomal subunit - state B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 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

Structural snapshots of human pre-60S ribosomal particles before and after nuclear export.

Liang, X.Zuo, M.Q.Zhang, Y.Li, N.Ma, C.Dong, M.Q.Gao, N.

(2020) Nat Commun 11: 3542-3542

  • DOI: https://doi.org/10.1038/s41467-020-17237-x
  • Primary Citation of Related Structures:  
    6LQM, 6LSR, 6LSS, 6LU8

  • PubMed Abstract: 

    Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, School of Life Science, Tsinghua University, 100084, Beijing, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein 622A [auth 0]477Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173545 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large subunit GTPase 1 homologB [auth 1]658Homo sapiensMutation(s): 0 
EC: 3.6.1
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GTEx:  ENSG00000041802 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal export protein NMD3D [auth 3]534Homo sapiensMutation(s): 0 
Gene Names: NMD3CGI-07
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GTEx:  ENSG00000169251 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6F [auth 6]245Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242372 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10aH [auth A]217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198755 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3I [auth B]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29J [auth C]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4K [auth D]427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30L [auth E]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34M [auth F]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aN [auth G]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35O [auth H]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9P [auth I]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36Q [auth K]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aR [auth L]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37S [auth M]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11T [auth N]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38U [auth O]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39V [auth P]51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13W [auth Q]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14X [auth S]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31Y [auth T]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15Z [auth U]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aAA [auth V]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aBA [auth W]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aCA [auth X]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17DA [auth Y]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18EA [auth Z]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19FA [auth a]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aGA [auth b]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21HA [auth c]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22IA [auth d]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23JA [auth e]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24KA [auth f]157Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114391 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aLA [auth g]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26MA [auth h]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27NA [auth i]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28OA [auth l]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8PA [auth m]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5QA [auth r]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32RA [auth t]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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UniProt GroupP62910
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aSA [auth u]110Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P18077 (Homo sapiens)
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PHAROS:  P18077
GTEx:  ENSG00000182899 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18077
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6TA [auth v]288Homo sapiensMutation(s): 0 
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Find proteins for Q02878 (Homo sapiens)
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PHAROS:  Q02878
GTEx:  ENSG00000089009 
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UniProt GroupQ02878
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7UA [auth w]248Homo sapiensMutation(s): 0 
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Find proteins for P18124 (Homo sapiens)
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PHAROS:  P18124
GTEx:  ENSG00000147604 
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UniProt GroupP18124
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferation-associated protein 2G4VA [auth z]394Homo sapiensMutation(s): 0 
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Find proteins for Q9UQ80 (Homo sapiens)
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PHAROS:  Q9UQ80
GTEx:  ENSG00000170515 
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UniProt GroupQ9UQ80
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Entity ID: 3
MoleculeChains LengthOrganismImage
28S rRNAC [auth 2]5,070Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S rRNAE [auth 5]120Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
5.8S rRNAG [auth 8]156Homo sapiens
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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 
AB [auth 2]
AC [auth 2]
AD [auth 2]
AE [auth 2]
AF [auth 2]
AB [auth 2],
AC [auth 2],
AD [auth 2],
AE [auth 2],
AF [auth 2],
AG [auth 2],
AH [auth 2],
AI [auth 2],
AJ [auth 2],
AK [auth 5],
BB [auth 2],
BC [auth 2],
BD [auth 2],
BE [auth 2],
BF [auth 2],
BG [auth 2],
BH [auth 2],
BI [auth 2],
BJ [auth 2],
BK [auth 8],
CB [auth 2],
CC [auth 2],
CD [auth 2],
CE [auth 2],
CF [auth 2],
CG [auth 2],
CH [auth 2],
CI [auth 2],
CJ [auth 2],
CK [auth F],
DB [auth 2],
DC [auth 2],
DD [auth 2],
DE [auth 2],
DF [auth 2],
DG [auth 2],
DH [auth 2],
DI [auth 2],
DJ [auth 2],
DK [auth a],
EB [auth 2],
EC [auth 2],
ED [auth 2],
EE [auth 2],
EF [auth 2],
EG [auth 2],
EH [auth 2],
EI [auth 2],
EJ [auth 2],
EK [auth c],
FB [auth 2],
FC [auth 2],
FD [auth 2],
FE [auth 2],
FF [auth 2],
FG [auth 2],
FH [auth 2],
FI [auth 2],
FJ [auth 2],
FK [auth m],
GB [auth 2],
GC [auth 2],
GD [auth 2],
GE [auth 2],
GF [auth 2],
GG [auth 2],
GH [auth 2],
GI [auth 2],
GJ [auth 2],
GK [auth m],
HB [auth 2],
HC [auth 2],
HD [auth 2],
HE [auth 2],
HF [auth 2],
HG [auth 2],
HH [auth 2],
HI [auth 2],
HJ [auth 2],
HK [auth w],
IB [auth 2],
IC [auth 2],
ID [auth 2],
IE [auth 2],
IF [auth 2],
IG [auth 2],
IH [auth 2],
II [auth 2],
IJ [auth 2],
JB [auth 2],
JC [auth 2],
JD [auth 2],
JE [auth 2],
JF [auth 2],
JG [auth 2],
JH [auth 2],
JI [auth 2],
JJ [auth 2],
KB [auth 2],
KC [auth 2],
KD [auth 2],
KE [auth 2],
KF [auth 2],
KG [auth 2],
KH [auth 2],
KI [auth 2],
KJ [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth 2],
LE [auth 2],
LF [auth 2],
LG [auth 2],
LH [auth 2],
LI [auth 2],
LJ [auth 2],
MB [auth 2],
MC [auth 2],
MD [auth 2],
ME [auth 2],
MF [auth 2],
MG [auth 2],
MH [auth 2],
MI [auth 2],
MJ [auth 2],
NB [auth 2],
NC [auth 2],
ND [auth 2],
NE [auth 2],
NF [auth 2],
NG [auth 2],
NH [auth 2],
NI [auth 2],
NJ [auth 2],
OB [auth 2],
OC [auth 2],
OD [auth 2],
OE [auth 2],
OF [auth 2],
OG [auth 2],
OH [auth 2],
OI [auth 2],
OJ [auth 2],
PB [auth 2],
PC [auth 2],
PD [auth 2],
PE [auth 2],
PF [auth 2],
PG [auth 2],
PH [auth 2],
PI [auth 2],
PJ [auth 2],
QB [auth 2],
QC [auth 2],
QD [auth 2],
QE [auth 2],
QF [auth 2],
QG [auth 2],
QH [auth 2],
QI [auth 2],
QJ [auth 2],
RB [auth 2],
RC [auth 2],
RD [auth 2],
RE [auth 2],
RF [auth 2],
RG [auth 2],
RH [auth 2],
RI [auth 2],
RJ [auth 2],
SB [auth 2],
SC [auth 2],
SD [auth 2],
SE [auth 2],
SF [auth 2],
SG [auth 2],
SH [auth 2],
SI [auth 2],
SJ [auth 2],
TB [auth 2],
TC [auth 2],
TD [auth 2],
TE [auth 2],
TF [auth 2],
TG [auth 2],
TH [auth 2],
TI [auth 2],
TJ [auth 2],
UB [auth 2],
UC [auth 2],
UD [auth 2],
UE [auth 2],
UF [auth 2],
UG [auth 2],
UH [auth 2],
UI [auth 2],
UJ [auth 2],
VB [auth 2],
VC [auth 2],
VD [auth 2],
VE [auth 2],
VF [auth 2],
VG [auth 2],
VH [auth 2],
VI [auth 2],
VJ [auth 2],
WA [auth 2],
WB [auth 2],
WC [auth 2],
WD [auth 2],
WE [auth 2],
WF [auth 2],
WG [auth 2],
WH [auth 2],
WI [auth 2],
WJ [auth 2],
XA [auth 2],
XB [auth 2],
XC [auth 2],
XD [auth 2],
XE [auth 2],
XF [auth 2],
XG [auth 2],
XH [auth 2],
XI [auth 2],
XJ [auth 2],
YA [auth 2],
YB [auth 2],
YC [auth 2],
YD [auth 2],
YE [auth 2],
YF [auth 2],
YG [auth 2],
YH [auth 2],
YI [auth 2],
YJ [auth 5],
ZA [auth 2],
ZB [auth 2],
ZC [auth 2],
ZD [auth 2],
ZE [auth 2],
ZF [auth 2],
ZG [auth 2],
ZH [auth 2],
ZI [auth 2],
ZJ [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release