5H4P

Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 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

Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1

Ma, C.Wu, S.Li, N.Chen, Y.Yan, K.Li, Z.Zheng, L.Lei, J.Woolford, J.L.Gao, N.

(2017) Nat. Struct. Mol. Biol. 24: 214-220

  • DOI: 10.1038/nsmb.3364

  • PubMed Abstract: 
  • A key step in ribosome biogenesis is the nuclear export of pre-ribosomal particles. Nmd3, a highly conserved protein in eukaryotes, is a specific adaptor required for the export of pre-60S particles. Here we used cryo-electron microscopy (cryo-EM) to ...

    A key step in ribosome biogenesis is the nuclear export of pre-ribosomal particles. Nmd3, a highly conserved protein in eukaryotes, is a specific adaptor required for the export of pre-60S particles. Here we used cryo-electron microscopy (cryo-EM) to characterize Saccharomyces cerevisiae pre-60S particles purified with epitope-tagged Nmd3. Our structural analysis indicates that these particles belong to a specific late stage of cytoplasmic pre-60S maturation in which ribosomal proteins uL16, uL10, uL11, eL40 and eL41 are deficient, but ribosome assembly factors Nmd3, Lsg1, Tif6 and Reh1 are present. Nmd3 and Lsg1 are located near the peptidyl-transferase center (PTC). In particular, Nmd3 recognizes the PTC in its near-mature conformation. In contrast, Reh1 is anchored to the exit of the polypeptide tunnel, with its C terminus inserted into the tunnel. These findings pinpoint a structural checkpoint role for Nmd3 in PTC assembly, and provide information about functional and mechanistic roles of these assembly factors in the maturation of the 60S ribosomal subunit.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
A
246Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL2A (RPL5B)
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX45
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
B
387Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL3 (MAK8, TCM1)
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL3
Go to UniProtKB:  P14126
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
C
361Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL4A (RPL2, RPL2A)
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P10664
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
D
297Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL5 (RPL1, RPL1A)
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL5
Go to UniProtKB:  P26321
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
E
176Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL6A (RPL17A, YL16A)
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02326
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
F
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL7A (RPL6A, RPL8A, YL8A)
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL7A
Go to UniProtKB:  P05737
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
G
256Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17076
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
H
191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05738
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-A
J
174Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL11A (RP39A, RPL16A)
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W9
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
L
199Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL13A
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL13A
Go to UniProtKB:  Q12690
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
M
138Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL14A
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36105
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
N
204Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL15A (RPL10A, RPL13A, YL10A)
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05748
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
O
199Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL16A (RPL13, RPL21A)
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26784
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
P
184Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL17A (RPL17, RPL20A)
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05740
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
Q
186Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL18A (RP28A)
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL18A
Go to UniProtKB:  P0CX49
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
R
189Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL19A (RPL23A, YL14A)
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX82
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
S
172Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL20A (RPL18A, RPL18A2)
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX23
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
T
160Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL21A (URP1)
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02753
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
U
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL22A
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05749
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
V
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL23A (RPL17A, RPL17AA)
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL23A
Go to UniProtKB:  P0CX41
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
W
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04449
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
X
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL25
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04456
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
Y
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL26A (RPL26, RPL33A)
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05743
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
Z
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL27A (RPL27)
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL27A
Go to UniProtKB:  P0C2H6
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
a
149Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL28 (CYH2)
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL28
Go to UniProtKB:  P02406
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
b
59Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL29 (YL43)
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL29
Go to UniProtKB:  P05747
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
c
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL30 (RPL32)
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL30
Go to UniProtKB:  P14120
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
d
113Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL31A (RPL34, RPL34A)
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C2H8
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
e
130Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL32
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL32
Go to UniProtKB:  P38061
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
f
107Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL33A (RPL37A)
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05744
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
g
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL34A
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P87262
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
h
120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL35A (SOS1)
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL35A
Go to UniProtKB:  P0CX84
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
i
100Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL36A (RPL39A)
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL36A
Go to UniProtKB:  P05745
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
j
88Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL37A (RPL35A)
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL37A
Go to UniProtKB:  P49166
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
k
78Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL38
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL38
Go to UniProtKB:  P49167
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
l
51Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL39 (RPL46, SPB2)
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL39
Go to UniProtKB:  P04650
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
o
106Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL42A (RPL41A, SCL41A)
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX27
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
p
92Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL43A
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX25
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal export protein NMD3
w
248Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NMD3
Find proteins for P38861 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: NMD3
Go to UniProtKB:  P38861
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 6
y
227Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TIF6 (CDC95)
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12522
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Cytoplasmic 60S subunit biogenesis factor REH1
z
56Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: REH1
Find proteins for Q06709 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06709
Entity ID: 1
MoleculeChainsLengthOrganism
25S ribosomal RNA13396Saccharomyces cerevisiae
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNA3121Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
5.8S ribosomal RNA4158Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references
  • Version 1.2: 2017-06-14
    Type: Other