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- PDB-6mte: Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state) -

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Entry
Database: PDB / ID: 6mte
TitleRabbit 80S ribosome with eEF2 and SERBP1 (rotated state)
Components
  • 18S rRNA18S ribosomal RNA
  • 28S rRNA28S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • RACK1Receptor for activated C kinase 1
  • SERBP1
  • eEF2
  • eL13
  • eL14
  • eL15List of Subaru engines
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL24
  • eL27
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL36
  • eL37
  • eL38
  • eL39
  • eL40
  • eL41
  • eL42
  • eL43
  • eL6
  • eL8
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • uL10
  • uL11
  • uL13
  • uL14
  • uL15
  • uL16
  • uL18
  • uL2
  • uL22
  • uL23
  • uL24
  • uL29
  • uL3
  • uL30
  • uL4
  • uL5
  • uL6
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / Ribosome / translation
Function / homologyInsertion domain in 60S ribosomal protein L10P / Ribosomal protein L36e domain superfamily / Ribosomal protein L14 / 60S ribosomal protein L19 / Ubiquitin-like protein FUBI / Ribosomal protein L30/YlxQ / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / S27a-like superfamily ...Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L36e domain superfamily / Ribosomal protein L14 / 60S ribosomal protein L19 / Ubiquitin-like protein FUBI / Ribosomal protein L30/YlxQ / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / S27a-like superfamily / Ribosomal protein S21e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein S26e superfamily / Ribosomal protein L38e superfamily / Ribosomal protein S4e, central domain superfamily / 40S Ribosomal protein S10 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L7/L30 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L32e superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L15 / ribosomal L5P family C-terminus / KOW motif / Ribosomal protein L10 / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein S8 / WD domain, G-beta repeat / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein L6 / Ribosomal protein S10p/S20e / Ribosomal protein L30p/L7e / Ribosomal protein S12/S23 / Ribosomal protein S15 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ubiquitin family / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Ribosomal L39 protein / Ribosomal protein S7, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L18e/L15P / Ribosomal protein S19 conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S9, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L23 / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin / Ubiquitin conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L30, central domain, archaeal type / Ribosomal L18e/L15P superfamily
Function and homology information
Specimen sourceOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsBrown, A. / Baird, M.R. / Yip, M.C.J. / Murray, J. / Shao, S.
CitationJournal: Elife / Year: 2018
Title: Structures of translationally inactive mammalian ribosomes.
Authors: Alan Brown / Matthew R Baird / Matthew Cj Yip / Jason Murray / Sichen Shao
Abstract: The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. ...The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 19, 2018 / Release: Nov 21, 2018

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
5: 28S rRNA
7: 5S rRNA
8: 5.8S rRNA
A: uL2
B: uL3
C: uL4
D: uL18
E: eL6
F: uL30
G: eL8
H: uL6
I: uL16
J: uL5
L: eL13
M: eL14
N: eL15
O: uL13
P: uL22
Q: eL18
R: eL19
S: eL20
T: eL21
U: eL22
V: uL14
W: eL24
X: uL23
Y: uL24
Z: eL27
a: uL15
b: eL29
c: eL30
d: eL31
e: eL32
f: eL33
g: eL34
h: uL29
i: eL36
j: eL37
k: eL38
l: eL39
m: eL40
n: eL41
o: eL42
p: eL43
r: eL28
s: uL10
t: uL11
v: eEF2
w: SERBP1
9: 18S rRNA
AA: uS2
BB: eS1
CC: uS5
DD: uS3
EE: eS4
FF: uS7
GG: eS6
HH: eS7
II: eS8
JJ: uS4
KK: eS10
LL: uS17
MM: eS12
NN: uS15
OO: uS11
PP: uS19
QQ: uS9
RR: eS17
SS: uS13
TT: eS19
UU: uS10
VV: eS21
WW: uS8
XX: uS12
YY: eS24
ZZ: eS25
aa: eS26
bb: eS27
cc: eS28
dd: uS14
ee: eS30
ff: eS31
gg: RACK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,296,960390
Polyers3,288,75183
Non-polymers8,209307
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 4 types, 4 molecules 5789

#1: RNA chain 28S rRNA / 28S ribosomal RNA


Mass: 1167366.125 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#2: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 39
#3: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 48559.699 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 548638.062 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)

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Protein/peptide , 79 types, 79 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#4: Protein/peptide uL2


Mass: 26998.613 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#5: Protein/peptide uL3


Mass: 45119.812 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#6: Protein/peptide uL4


Mass: 41114.434 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: Protein/peptide uL18


Mass: 34077.391 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#8: Protein/peptide eL6


Mass: 33028.336 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#9: Protein/peptide uL30


Mass: 26658.754 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SV32
#10: Protein/peptide eL8


Mass: 36221.516 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#11: Protein/peptide uL6


Mass: 21627.215 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX33
#12: Protein/peptide uL16


Mass: 24643.057 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#13: Protein/peptide uL5


Mass: 19399.498 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#14: Protein/peptide eL13


Mass: 24200.525 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: Protein/peptide eL14


Mass: 16217.355 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KNW6
#16: Protein/peptide eL15 / List of Subaru engines


Mass: 24076.088 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#17: Protein/peptide uL13


Mass: 23144.859 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#18: Protein/peptide uL22


Mass: 17758.678 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SCJ6
#19: Protein/peptide eL18


Mass: 21568.492 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#20: Protein/peptide eL19


Mass: 21613.033 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q3T0W9
#21: Protein/peptide eL20


Mass: 20827.561 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A287APR1
#22: Protein/peptide eL21


Mass: 18478.791 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#23: Protein/peptide eL22


Mass: 11495.275 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#24: Protein/peptide uL14


Mass: 13972.425 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#25: Protein/peptide eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#26: Protein/peptide uL23


Mass: 13727.181 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q24JY1
#27: Protein/peptide uL24


Mass: 15891.787 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#28: Protein/peptide eL27


Mass: 15704.635 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#29: Protein/peptide uL15


Mass: 16489.363 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#30: Protein/peptide eL29


Mass: 26708.707 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#31: Protein/peptide eL30


Mass: 10914.756 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#32: Protein/peptide eL31


Mass: 12635.694 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#33: Protein/peptide eL32 / CD59


Mass: 15022.021 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#34: Protein/peptide eL33


Mass: 12449.612 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#35: Protein/peptide eL34 / / Large ribosomal subunit protein eL34


Mass: 12994.621 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P49207
#36: Protein/peptide uL29


Mass: 14435.403 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#37: Protein/peptide eL36


Mass: 11888.371 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#38: Protein/peptide eL37


Mass: 10090.891 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#39: Protein/peptide eL38


Mass: 8107.752 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q32PB9
#40: Protein/peptide eL39


Mass: 6324.579 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#41: Protein/peptide eL40


Mass: 6212.593 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#42: Protein/peptide eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein/peptide eL42


Mass: 12070.474 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T040
#44: Protein/peptide eL43


Mass: 10168.153 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#45: Protein/peptide eL28


Mass: 14220.686 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#46: Protein/peptide uL10 / 60S ribosomal protein L10E


Mass: 21521.062 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q29214
#47: Protein/peptide uL11


Mass: 16561.117 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7
#48: Protein/peptide eEF2 /


Mass: 94587.258 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: Protein/peptide SERBP1


Mass: 6257.690 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#51: Protein/peptide uS2


Mass: 24361.861 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: Protein/peptide eS1


Mass: 24759.145 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#53: Protein/peptide uS5


Mass: 24441.846 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: O18789
#54: Protein/peptide uS3


Mass: 25215.586 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: E2RH47, DNA-(apurinic or apyrimidinic site) lyase
#55: Protein/peptide eS4


Mass: 29523.674 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q76N24
#56: Protein/peptide uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#57: Protein/peptide eS6


Mass: 27471.535 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#58: Protein/peptide eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#59: Protein/peptide eS8


Mass: 24003.012 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q5E958
#60: Protein/peptide uS4


Mass: 21649.633 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#61: Protein/peptide eS10


Mass: 11529.682 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#62: Protein/peptide uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#63: Protein/peptide eS12


Mass: 13048.244 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#64: Protein/peptide uS15


Mass: 17057.113 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#65: Protein/peptide uS11


Mass: 14544.659 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P13471
#66: Protein/peptide uS19


Mass: 14646.297 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#67: Protein/peptide uS9


Mass: 16032.804 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q3T0X6
#68: Protein/peptide eS17


Mass: 15250.714 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#69: Protein/peptide uS13


Mass: 16898.648 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#70: Protein/peptide eS19


Mass: 15611.003 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#71: Protein/peptide uS10


Mass: 11395.489 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q3ZBH8
#72: Protein/peptide eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q32PB8
#73: Protein/peptide uS8


Mass: 14734.357 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#74: Protein/peptide uS12


Mass: 15626.392 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q3T199
#75: Protein/peptide eS24 / Small ribosomal subunit protein eS24


Mass: 14432.125 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P62847
#76: Protein/peptide eS25


Mass: 8526.119 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#77: Protein/peptide eS26


Mass: 11645.794 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q56JV1
#78: Protein/peptide eS27


Mass: 9348.990 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q2KHT7
#79: Protein/peptide eS28


Mass: 7007.069 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#80: Protein/peptide uS14


Mass: 6559.625 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#81: Protein/peptide eS30


Mass: 6317.539 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#82: Protein/peptide eS31


Mass: 7986.440 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#83: Protein/peptide RACK1 / Receptor for activated C kinase 1


Mass: 34669.113 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4

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Non-polymers , 3 types, 307 molecules

#84: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 298 / Formula: Mg / Magnesium
#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Formula: Zn / Zinc
#86: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2 / Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)
Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Cellular location: cytoplasm / Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 104478 / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 17 / Used frames/image: 1-17

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Processing

EM software
IDNameVersionCategory
1RELION2.0particle selection
2EPUimage acquisition
4GctfCTF correction
7Coot0.8.9model fitting
9RELION2.0initial Euler assignment
10RELION2.0final Euler assignment
12RELION2.03D reconstruction
13PHENIX1.13_2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 133480 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Atomic model buildingPDB-ID: 5LZV

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