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- PDB-6mtc: Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state) -

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Entry
Database: PDB / ID: 6mtc
TitleRabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state)
Components
  • (40S ribosomal protein ...) x 32
  • (60S ribosomal protein ...) x 43
  • 18S rRNA18S ribosomal RNA
  • 28S rRNA28S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Interferon-related developmental regulator 2
  • Receptor of activated protein C kinase 1
  • Z-site tRNA
KeywordsRIBOSOME / translation
Function / homology50S ribosomal protein L30e-like / Ribosomal protein L22/L17 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S17e-like superfamily / Winged helix-like DNA-binding domain superfamily / RNA-binding S4 domain superfamily ...50S ribosomal protein L30e-like / Ribosomal protein L22/L17 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S17e-like superfamily / Winged helix-like DNA-binding domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L32e superfamily / WD40-repeat-containing domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L7, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein L21 superfamily / 40S Ribosomal protein S10 / Ribosomal protein L5, C-terminal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S4/S9 N-terminal domain / Interferon-related developmental regulator / Ribosomal protein L7/L30 / Ribosomal protein L36e domain superfamily / Ribosomal protein L14 / 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 L5, N-terminal / Ribosomal protein L15 / Ubiquitin family / Ribosomal protein L18e/L15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S19 conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein S7, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S15P / Ribosomal protein L24e, conserved site / Ubiquitin-like domain superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal L28e/Mak16 / Ribosomal protein S28e conserved site / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 30s ribosomal protein S13, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L15e core domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein L2, archaeal-type / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L16p/L10e / Ribosomal protein S17e signature. / Ribosomal L18 C-terminal region / Ribosomal protein L39e signature. / Ribosomal protein L14 signature. / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal_S17 N-terminal / 60S ribosomal protein L4 C-terminal domain / Ribosomal L30 N-terminal domain / Ribosomal protein S8 signature. / Ribosomal S13/S15 N-terminal domain / Interferon-related developmental regulator (IFRD) / Interferon-related protein conserved region / Ribosomal protein S30 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L6, N-terminal domain / Plectin/S10 domain / Ribosomal protein S7 signature. / Ribosomal protein S17 signature. / Ribosomal protein L14 / Ribosomal protein S6e signature. / Ribosomal protein L6 signature 2. / Trp-Asp (WD) repeats signature.
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
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 21, 2018Structure modelrepositoryInitial release
1.1Nov 28, 2018Structure modelData collection / Database references / Structure summarypdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif_struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

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Assembly

Deposited unit
4: Z-site tRNA
5: 28S rRNA
7: 5S rRNA
8: 5.8S rRNA
A: 60S ribosomal protein L8
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4
D: 60S ribosomal protein L5
E: 60S ribosomal protein L6
F: 60S ribosomal protein L7
G: 60S ribosomal protein L7a
H: 60S ribosomal protein L9
I: 60S ribosomal protein L10
J: 60S ribosomal protein L11
L: 60S ribosomal protein L13
M: 60S ribosomal protein L14
N: 60S Ribosomal protein L15
O: 60S ribosomal protein L13a
P: 60S ribosomal protein L17
Q: 60S ribosomal protein L18
R: 60S ribosomal protein L19
S: 60S ribosomal protein L18a
T: 60S ribosomal protein L21
U: 60S ribosomal protein L22
V: 60S ribosomal protein L23
W: 60S ribosomal protein L24
X: 60S ribosomal protein L23a
Y: 60S ribosomal protein L26
Z: 60S ribosomal protein L27
a: 60S ribosomal protein L27a
b: 60S ribosomal protein L29
c: 60S ribosomal protein L30
d: 60S ribosomal protein L31
e: 60S ribosomal protein L32
f: 60S ribosomal protein L35a
g: 60S ribosomal protein L34
h: 60S ribosomal protein L35
i: 60S ribosomal protein L36
j: 60S ribosomal protein L37
k: 60S ribosomal protein L38
l: 60S ribosomal protein L39
m: 60S ribosomal protein L40
n: 60S ribosomal protein L41
o: 60S ribosomal protein L36a
p: 60S ribosomal protein L37a
r: 60S ribosomal protein L28
u: 60S ribosomal protein L10a
v: Interferon-related developmental regulator 2
9: 18S rRNA
AA: 40S ribosomal protein SA
BB: 40S ribosomal protein S3a
CC: 40S ribosomal protein S2
DD: 40S ribosomal protein S3
EE: 40S ribosomal protein S4, X isoform
FF: 40S ribosomal protein S5
GG: 40S ribosomal protein S6
HH: 40S ribosomal protein S7
II: 40S ribosomal protein S8
JJ: 40S ribosomal protein S9
KK: 40S ribosomal protein S10
LL: 40S ribosomal protein S11
MM: 40S ribosomal protein S12
NN: 40S ribosomal protein S13
OO: 40S ribosomal protein S14
PP: 40S ribosomal protein S15
QQ: 40S ribosomal protein S16
RR: 40S ribosomal protein S17
SS: 40S ribosomal protein S18
TT: 40S ribosomal protein S19
UU: 40S ribosomal protein S20
VV: 40S ribosomal protein S21
WW: 40S ribosomal protein S15a
XX: 40S ribosomal protein S23
YY: 40S ribosomal protein S24
ZZ: 40S ribosomal protein S25
aa: 40S ribosomal protein S26
bb: 40S ribosomal protein S27
cc: 40S ribosomal protein S28
dd: 40S ribosomal protein S29
ee: 40S ribosomal protein S30
ff: 40S ribosomal protein S27a
gg: Receptor of activated protein C kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,252,695387
Polyers3,244,95382
Non-polymers7,742305
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 , 5 types, 5 molecules 45789

#1: RNA chain Z-site tRNA


Mass: 24102.275 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#2: RNA chain 28S rRNA / 28S ribosomal RNA


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


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


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


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

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60S ribosomal protein ... , 43 types, 43 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#5: Protein/peptide 60S ribosomal protein L8 /


Mass: 26998.613 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#6: Protein/peptide 60S ribosomal protein L3 /


Mass: 45119.812 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#7: Protein/peptide 60S ribosomal protein L4 /


Mass: 41114.434 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#8: Protein/peptide 60S ribosomal protein L5 /


Mass: 34077.391 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#9: Protein/peptide 60S ribosomal protein L6 /


Mass: 33028.336 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#10: Protein/peptide 60S ribosomal protein L7 /


Mass: 26658.754 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SV32
#11: Protein/peptide 60S ribosomal protein L7a /


Mass: 36221.516 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#12: Protein/peptide 60S ribosomal protein L9 /


Mass: 21627.215 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX33
#13: Protein/peptide 60S ribosomal protein L10 /


Mass: 24643.057 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#14: Protein/peptide 60S ribosomal protein L11 /


Mass: 19399.498 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#15: Protein/peptide 60S ribosomal protein L13 /


Mass: 24200.525 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#16: Protein/peptide 60S ribosomal protein L14 /


Mass: 16217.355 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KNW6
#17: Protein/peptide 60S Ribosomal protein L15 /


Mass: 24076.088 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#18: Protein/peptide 60S ribosomal protein L13a /


Mass: 23144.859 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#19: Protein/peptide 60S ribosomal protein L17 /


Mass: 17758.678 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SCJ6
#20: Protein/peptide 60S ribosomal protein L18 /


Mass: 21568.492 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#21: Protein/peptide 60S ribosomal protein L19 /


Mass: 21613.033 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#22: Protein/peptide 60S ribosomal protein L18a /


Mass: 20827.561 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#23: Protein/peptide 60S ribosomal protein L21 /


Mass: 18478.791 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#24: Protein/peptide 60S ribosomal protein L22 /


Mass: 11495.275 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein/peptide 60S ribosomal protein L23 /


Mass: 13972.425 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#26: Protein/peptide 60S ribosomal protein L24 /


Mass: 17825.111 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#27: Protein/peptide 60S ribosomal protein L23a /


Mass: 13727.181 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#28: Protein/peptide 60S ribosomal protein L26 /


Mass: 15891.787 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#29: Protein/peptide 60S ribosomal protein L27 /


Mass: 15704.635 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#30: Protein/peptide 60S ribosomal protein L27a /


Mass: 16489.363 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#31: Protein/peptide 60S ribosomal protein L29 /


Mass: 26708.707 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#32: Protein/peptide 60S ribosomal protein L30 /


Mass: 10914.756 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#33: Protein/peptide 60S ribosomal protein L31 /


Mass: 12635.694 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#34: Protein/peptide 60S ribosomal protein L32 /


Mass: 15022.021 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#35: Protein/peptide 60S ribosomal protein L35a /


Mass: 12449.612 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#36: Protein/peptide 60S ribosomal protein L34 /


Mass: 12994.621 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: Protein/peptide 60S ribosomal protein L35 /


Mass: 14435.403 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#38: Protein/peptide 60S ribosomal protein L36 /


Mass: 11888.371 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#39: Protein/peptide 60S ribosomal protein L37 /


Mass: 10090.891 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#40: Protein/peptide 60S ribosomal protein L38 /


Mass: 8107.752 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: Protein/peptide 60S ribosomal protein L39 /


Mass: 6324.579 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#42: Protein/peptide 60S ribosomal protein L40 /


Mass: 6212.593 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein/peptide 60S ribosomal protein L41 /


Mass: 3473.451 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein/peptide 60S ribosomal protein L36a /


Mass: 12070.474 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T040
#45: Protein/peptide 60S ribosomal protein L37a /


Mass: 10168.153 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#46: Protein/peptide 60S ribosomal protein L28 /


Mass: 14220.686 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#47: Protein/peptide 60S ribosomal protein L10a /


Mass: 23599.887 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8

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Protein/peptide , 2 types, 2 molecules vgg

#48: Protein/peptide Interferon-related developmental regulator 2


Mass: 47827.254 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHD9
#82: Protein/peptide Receptor of activated protein C kinase 1


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

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40S ribosomal protein ... , 32 types, 32 molecules AABBCCDDEEFFGGHHIIJJKKLLMMNNOOPPQQRRSSTTUUVVWWXXYYZZaabbccddeeff

#50: Protein/peptide 40S ribosomal protein SA /


Mass: 24361.861 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#51: Protein/peptide 40S ribosomal protein S3a /


Mass: 24759.145 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#52: Protein/peptide 40S ribosomal protein S2 /


Mass: 24441.846 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein/peptide 40S ribosomal protein S3 /


Mass: 25215.586 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein/peptide 40S ribosomal protein S4, X isoform / Ribosome


Mass: 29523.674 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#55: Protein/peptide 40S ribosomal protein S5 /


Mass: 22913.453 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#56: Protein/peptide 40S ribosomal protein S6 /


Mass: 27471.535 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#57: Protein/peptide 40S ribosomal protein S7 /


Mass: 22168.914 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#58: Protein/peptide 40S ribosomal protein S8 /


Mass: 24003.012 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#59: Protein/peptide 40S ribosomal protein S9 /


Mass: 21649.633 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#60: Protein/peptide 40S ribosomal protein S10 /


Mass: 11529.682 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#61: Protein/peptide 40S ribosomal protein S11 /


Mass: 18468.826 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#62: Protein/peptide 40S ribosomal protein S12 /


Mass: 13048.244 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#63: Protein/peptide 40S ribosomal protein S13 /


Mass: 17057.113 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#64: Protein/peptide 40S ribosomal protein S14 /


Mass: 14544.659 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#65: Protein/peptide 40S ribosomal protein S15 /


Mass: 14246.854 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#66: Protein/peptide 40S ribosomal protein S16 /


Mass: 16032.804 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#67: Protein/peptide 40S ribosomal protein S17 /


Mass: 15250.714 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#68: Protein/peptide 40S ribosomal protein S18 /


Mass: 16898.648 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#69: Protein/peptide 40S ribosomal protein S19 /


Mass: 15611.003 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#70: Protein/peptide 40S ribosomal protein S20 /


Mass: 11395.489 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#71: Protein/peptide 40S ribosomal protein S21 /


Mass: 9124.389 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#72: Protein/peptide 40S ribosomal protein S15a /


Mass: 14734.357 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#73: Protein/peptide 40S ribosomal protein S23 /


Mass: 15626.392 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#74: Protein/peptide 40S ribosomal protein S24 /


Mass: 14432.125 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein/peptide 40S ribosomal protein S25 /


Mass: 8526.119 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#76: Protein/peptide 40S ribosomal protein S26 /


Mass: 11645.794 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#77: Protein/peptide 40S ribosomal protein S27 /


Mass: 9348.990 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#78: Protein/peptide 40S ribosomal protein S28 /


Mass: 7007.069 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#79: Protein/peptide 40S ribosomal protein S29 /


Mass: 6559.625 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#80: Protein/peptide 40S ribosomal protein S30 /


Mass: 6317.539 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#81: Protein/peptide 40S ribosomal protein S27a / Ribosome


Mass: 7986.440 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22

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Non-polymers , 2 types, 305 molecules

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


Mass: 24.305 Da / Num. of mol.: 297 / Formula: Mg / Magnesium
#84: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Formula: Zn / Zinc

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Details

Sequence detailsAccording to the authors the sample sequences cannot include all nucleotides, as the rabbit genome ...According to the authors the sample sequences cannot include all nucleotides, as the rabbit genome is incomplete for the ribosomal RNA.

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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 Z-site tRNA and IFRD2 / 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
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
VitrificationCryogen 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 / 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
1RELIONparticle selection
2EPUimage acquisition
4GctfCTF correction
7Coot0.8.9model fitting
9RELIONinitial Euler assignment
10RELION2.0final Euler assignment
11RELION2.0classification
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: 74031 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Atomic model buildingPDB-ID: 5LZV

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