6FT6

Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure of the nuclear exosome captured on a maturing preribosome.

Schuller, J.M., Falk, S., Fromm, L., Hurt, E., Conti, E.

(2018) Science 360: 219-222

  • DOI: 10.1126/science.aar5428
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60 ...

    The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60 S ) during 7 S -to-5.8 S rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 S particle, which harbors the 5.8 S rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 S rRNA, captures the 3' extension of the 5.8 S rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 S substrate to process rRNA during ribosome maturation.

    Organizational Affiliation: 

    Department of Structural Cell Biology, Max Planck Institute (MPI) for Biochemistry, Munich, Germany. conti@biochem.mpg.de ed.hurt@bzh.uni-heidelberg.de.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
A
254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2A, RPL5B, YFR031C-A, YFR031BC
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
B
387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3, MAK8, TCM1, YOR063W, YOR29-14
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
C
362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4A, RPL2, RPL2A, YBR031W, YBR0315
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
D
297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5, RPL1, RPL1A, YPL131W, LPI14W
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
E
176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6A, RPL17A, YL16A, YML073C
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
F
244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7A, RPL6A, RPL8A, YL8A, YGL076C
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
G
256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8A, MAK7, RPL4A, YHL033C
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
H
191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9A, RPL8A, RPL9, YGL147C
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Bud site selection protein 20
I
166Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD20, YLR074C
Find proteins for Q08004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-A
J
174Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11A, RP39A, RPL16A, YPR102C, P8283.14
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
L
199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13A, YDL082W
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
M
138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14A, YKL006W, YKL153
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
N
204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15A, RPL10A, RPL13A, YL10A, YLR029C
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
O
199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16A, RPL13, RPL21A, YIL133C
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
P
184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17A, RPL17, RPL20A, YKL180W
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
Q
186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18A, RP28A, YOL120C
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
R
189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19A, RPL23A, YL14A, YBR084C-A, YBR084BC
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
S
172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
T
160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21A, URP1, YBR191W, YBR1401
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
U
121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22A, YLR061W, L2168
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
V
137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23A, RPL17A, RPL17AA, YBL087C, YBL0713
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosome assembly factor MRT4
W
236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MRT4, YKL009W, YKL160
Find proteins for P33201 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
X
142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25, YOL127W
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
Y
127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26A, RPL26, RPL33A, YLR344W, L8300.4
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
Z
136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27A, RPL27, YHR010W
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
a
149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28, CYH2, YGL103W
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Nucleolar GTP-binding protein 1
b
647Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG1, YPL093W, LPG15W
Find proteins for Q02892 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
c
105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30, RPL32, YGL030W
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
d
113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31A, RPL34, RPL34A, YDL075W, D2478
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
e
130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32, YBL092W, YBL0838
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
f
107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33A, RPL37A, YPL143W, LPI4W, P2625
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
g
121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34A, YER056C-A, YER056BC
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
h
120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35A, SOS1, YDL191W, D1249
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
i
100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36A, RPL39A, YMR194W, YM9646.06
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
j
88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37A, RPL35A, YLR185W, L9470.6
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
k
78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38, YLR325C, L8543.2
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
l
51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39, RPL46, SPB2, YJL189W, J0360
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Nucleolar GTP-binding protein 2
m
486Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG2, YNR053C, N3484
Find proteins for P53742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Pescadillo homolog
n
605Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP7, RRP13, YPH1, YGR103W
Find proteins for P53261 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
p
92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43A, YPR043W, YP9499.02
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein NSA2
r
261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSA2, YER126C, SYGP-ORF47
Find proteins for P40078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Nuclear GTP-binding protein NUG1
s
520Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUG1, YER006W
Find proteins for P40010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein RLP24
u
199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP24, YLR009W
Find proteins for Q07915 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein RPF2
v
344Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPF2, YKR081C, YKR401
Find proteins for P36160 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Regulator of ribosome biosynthesis
w
203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRS1, YOR294W
Find proteins for Q08746 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Ribosome assembly protein 4
x
515Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSA4, YCR072C, YCR72C
Find proteins for P25382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 6
y
245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF6, CDC95, YPR016C, LPZ15C
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
UPF0642 protein YBL028C
z
106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YBL028C, YBL0423
Find proteins for P38202 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Probable metalloprotease ARX1
4
593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARX1, YDR101C, YD8557.10c
EC: 3
Find proteins for Q03862 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
rRNA-processing protein CGR1
5
120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CGR1, YGL029W
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP6
KK
733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP6, UNC733, YOR001W
EC: 3.1.13
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Exosome complex protein LRP1
LL
184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LRP1, RRP47, YC1D, YHR081W
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase DOB1
MM
1011Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR4, DOB1, YJL050W, J1158
EC: 3.6.4.13
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
MPP6
NN
11Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
7S ribosomal RNA2162Saccharomyces cerevisiae S288C

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Entity ID: 50
MoleculeChainsLengthOrganism
25S ribosomal RNA13396Saccharomyces cerevisiae S288C

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Entity ID: 51
MoleculeChainsLengthOrganism
5S ribosomal RNA3121Saccharomyces cerevisiae S288C
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download CCD File 
b, m
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
I, j, p, u
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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b, m
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
ERCBelgiumEXORICO

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-11
    Changes: Other