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- PDB-9b0q: In situ human top-back di-ribosome structure (Composite map) -

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Entry
Database: PDB / ID: 9b0q
TitleIn situ human top-back di-ribosome structure (Composite map)
Components
  • (40S ribosomal protein ...) x 21
  • (60S ribosomal protein ...) x 35
  • (Large ribosomal subunit protein ...) x 6
  • (Ribosomal protein ...) x 2
  • (Small ribosomal subunit protein ...) x 11
  • 18S rRNA [Homo sapiens]
  • 28S rRNA [Homo sapiens]
  • 60S acidic ribosomal protein P0
  • A/P site tRNA [Homo sapiens]
  • Elongation factor 2
  • Endothelial differentiation-related factor 1
  • Heparin-binding protein HBp15
  • P/E site tRNA [Homo sapiens]
  • RNA (120-MER)5S rRNA [Homo sapiens]
  • RNA (156-MER)5.8S rRNA [Homo sapiens]
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
KeywordsRIBOSOME / In situ
Function / homology
Function and homology information


Synthesis of diphthamide-EEF2 / endothelial cell differentiation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition ...Synthesis of diphthamide-EEF2 / endothelial cell differentiation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / axial mesoderm development / negative regulation of peptidyl-serine phosphorylation / positive regulation of respiratory burst involved in inflammatory response / ribosomal protein import into nucleus / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein-DNA complex disassembly / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / translation at postsynapse / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / mammalian oogenesis stage / GAIT complex / A band / positive regulation of DNA damage response, signal transduction by p53 class mediator / supercoiled DNA binding / activation-induced cell death of T cells / TORC2 complex binding / neural crest cell differentiation / G1 to G0 transition / NF-kappaB complex / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / aggresome / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / translation at presynapse / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of phagocytosis / erythrocyte homeostasis / rRNA modification in the nucleus and cytosol / positive regulation of DNA binding / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / pigmentation / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / lncRNA binding / homeostatic process / Translation initiation complex formation / response to aldosterone / positive regulation of mitochondrial depolarization / Uptake and function of diphtheria toxin / positive regulation of T cell receptor signaling pathway / macrophage chemotaxis / positive regulation of activated T cell proliferation / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / lung morphogenesis / male meiosis I / monocyte chemotaxis / negative regulation of translational frameshifting / Protein hydroxylation / BH3 domain binding / TOR signaling / SARS-CoV-1 modulates host translation machinery / TFIID-class transcription factor complex binding / regulation of cell division / mTORC1-mediated signalling / T cell proliferation involved in immune response / Peptide chain elongation / iron-sulfur cluster binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of lipid metabolic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / translational elongation / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / blastocyst development / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process
Similarity search - Function
Multiprotein bridging factor 1, N-terminal / Multiprotein bridging factor 1 / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Cro/C1-type helix-turn-helix domain / : / 40S ribosomal protein SA ...Multiprotein bridging factor 1, N-terminal / Multiprotein bridging factor 1 / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Cro/C1-type helix-turn-helix domain / : / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Ribosomal L15/L27a, N-terminal / Elongation factor G C-terminus / Ribosomal protein L28e / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Lambda repressor-like, DNA-binding domain superfamily / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / EF-G domain III/V-like / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L1, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L1 signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L1 / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL24 / Endothelial differentiation-related factor 1 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS17 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL24 / Endothelial differentiation-related factor 1 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Elongation factor 2 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS4, X isoform / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL22 / Ribosomal protein uL16-like / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWei, Z. / Yong, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: To Be Published
Title: In situ human top-top di-ribosome structure (Composite map)
Authors: Wei, Z. / Yong, X.
History
DepositionMar 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
CH: Endothelial differentiation-related factor 1
cH: Endothelial differentiation-related factor 1
sE: Small ribosomal subunit protein eS4, X isoform
sI: 40S ribosomal protein S8
sL: 40S ribosomal protein S11
sX: 40S ribosomal protein S23
sG: 40S ribosomal protein S6
sJ: 40S ribosomal protein S9
sY: 40S ribosomal protein S24
se: Small ribosomal subunit protein eS30
sA: 40S ribosomal protein SA
sB: 40S ribosomal protein S3a
sH: Small ribosomal subunit protein eS7
sV: 40S ribosomal protein S21
sa: 40S ribosomal protein S26
sC: 40S ribosomal protein S2
sN: 40S ribosomal protein S13
sO: Small ribosomal subunit protein uS11
sW: 40S ribosomal protein S15a
sb: Small ribosomal subunit protein eS27
l7: RNA (120-MER)5S rRNA [Homo sapiens]
l8: RNA (156-MER)5.8S rRNA [Homo sapiens]
lA: 60S ribosomal protein L8
lB: Large ribosomal subunit protein uL3
lC: 60S ribosomal protein L4
lD: Large ribosomal subunit protein uL18
lE: Large ribosomal subunit protein eL6
lF: 60S ribosomal protein L7
lG: 60S ribosomal protein L7a
lH: 60S ribosomal protein L9
lI: Ribosomal protein uL16-like
lJ: 60S ribosomal protein L11
lL: Large ribosomal subunit protein eL13
lM: 60S ribosomal protein L14
lN: 60S ribosomal protein L15
lO: 60S ribosomal protein L13a
lP: 60S ribosomal protein L17
lQ: 60S ribosomal protein L18
lR: 60S ribosomal protein L19
lS: 60S ribosomal protein L18a
lT: 60S ribosomal protein L21
lU: Heparin-binding protein HBp15
lV: 60S ribosomal protein L23
lX: 60S ribosomal protein L23a
lY: 60S ribosomal protein L26
lZ: 60S ribosomal protein L27
la: 60S ribosomal protein L27a
lb: Large ribosomal subunit protein eL29
lc: 60S ribosomal protein L30
ld: 60S ribosomal protein L31
le: 60S ribosomal protein L32
lf: 60S ribosomal protein L35a
lg: 60S ribosomal protein L34
lh: 60S ribosomal protein L35
li: 60S ribosomal protein L36
lj: 60S ribosomal protein L37
lk: 60S ribosomal protein L38
ll: 60S ribosomal protein L39
lm: Large ribosomal subunit protein eL40
ln: 60S ribosomal protein L41
lo: 60S ribosomal protein L36a
lp: 60S ribosomal protein L37a
lr: 60S ribosomal protein L28
lz: 60S ribosomal protein L10a
sR: 40S ribosomal protein S17
sD: Small ribosomal subunit protein uS3
sF: 40S ribosomal protein S5
sK: 40S ribosomal protein S10
sP: Small ribosomal subunit protein uS19
sQ: Small ribosomal subunit protein uS9
sS: 40S ribosomal protein S18
sT: 40S ribosomal protein S19
sU: 40S ribosomal protein S20
sc: 40S ribosomal protein S28
sd: 40S ribosomal protein S29
sg: Receptor of activated protein C kinase 1
sM: Small ribosomal subunit protein eS12
sZ: Small ribosomal subunit protein eS25
sf: Ubiquitin-40S ribosomal protein S27a
s2: 18S rRNA [Homo sapiens]
cB: Elongation factor 2
aP: A/P site tRNA [Homo sapiens]
pE: P/E site tRNA [Homo sapiens]
ls: 60S acidic ribosomal protein P0
lt: 60S ribosomal protein L12 [Homo sapiens]
l5: 28S rRNA [Homo sapiens]
CB: Elongation factor 2
SE: Small ribosomal subunit protein eS4, X isoform
SI: 40S ribosomal protein S8
SL: 40S ribosomal protein S11
SX: 40S ribosomal protein S23
SG: 40S ribosomal protein S6
SJ: 40S ribosomal protein S9
SY: 40S ribosomal protein S24
Se: Small ribosomal subunit protein eS30
SA: 40S ribosomal protein SA
SB: 40S ribosomal protein S3a
SH: Small ribosomal subunit protein eS7
SV: 40S ribosomal protein S21
Sa: 40S ribosomal protein S26
SC: 40S ribosomal protein S2
SN: 40S ribosomal protein S13
SO: Small ribosomal subunit protein uS11
SW: 40S ribosomal protein S15a
Sb: Small ribosomal subunit protein eS27
L5: 28S rRNA [Homo sapiens]
L7: RNA (120-MER)5S rRNA [Homo sapiens]
L8: RNA (156-MER)5.8S rRNA [Homo sapiens]
LA: 60S ribosomal protein L8
LB: Large ribosomal subunit protein uL3
LC: 60S ribosomal protein L4
LD: Large ribosomal subunit protein uL18
LE: Large ribosomal subunit protein eL6
LF: 60S ribosomal protein L7
LG: 60S ribosomal protein L7a
LH: 60S ribosomal protein L9
LI: Ribosomal protein uL16-like
LJ: 60S ribosomal protein L11
LL: Large ribosomal subunit protein eL13
LM: 60S ribosomal protein L14
LN: 60S ribosomal protein L15
LO: 60S ribosomal protein L13a
LP: 60S ribosomal protein L17
LQ: 60S ribosomal protein L18
LR: 60S ribosomal protein L19
LS: 60S ribosomal protein L18a
LT: 60S ribosomal protein L21
LU: Heparin-binding protein HBp15
LV: 60S ribosomal protein L23
LX: 60S ribosomal protein L23a
LY: 60S ribosomal protein L26
LZ: 60S ribosomal protein L27
La: 60S ribosomal protein L27a
Lb: Large ribosomal subunit protein eL29
Lc: 60S ribosomal protein L30
Ld: 60S ribosomal protein L31
Le: 60S ribosomal protein L32
Lf: 60S ribosomal protein L35a
Lg: 60S ribosomal protein L34
Lh: 60S ribosomal protein L35
Li: 60S ribosomal protein L36
Lj: 60S ribosomal protein L37
Lk: 60S ribosomal protein L38
Ll: 60S ribosomal protein L39
Lm: Large ribosomal subunit protein eL40
Ln: 60S ribosomal protein L41
Lo: 60S ribosomal protein L36a
Lp: 60S ribosomal protein L37a
Lr: 60S ribosomal protein L28
Lz: 60S ribosomal protein L10a
SR: 40S ribosomal protein S17
SD: Small ribosomal subunit protein uS3
SF: 40S ribosomal protein S5
SK: 40S ribosomal protein S10
SP: Small ribosomal subunit protein uS19
SQ: Small ribosomal subunit protein uS9
SS: 40S ribosomal protein S18
ST: 40S ribosomal protein S19
SU: 40S ribosomal protein S20
Sc: 40S ribosomal protein S28
Sd: 40S ribosomal protein S29
Sg: Receptor of activated protein C kinase 1
SM: Small ribosomal subunit protein eS12
SZ: Small ribosomal subunit protein eS25
Sf: Ubiquitin-40S ribosomal protein S27a
S2: 18S rRNA [Homo sapiens]
AP: A/P site tRNA [Homo sapiens]
PE: P/E site tRNA [Homo sapiens]
Ls: 60S acidic ribosomal protein P0
Lt: 60S ribosomal protein L12 [Homo sapiens]
lW: Ribosomal protein L24
LW: Ribosomal protein L24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,815,727694
Polymers6,802,547172
Non-polymers13,180522
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 12 molecules CHcHlULUsgSgsfSfcBCBlsLs

#1: Protein Endothelial differentiation-related factor 1 / EDF-1 / Multiprotein-bridging factor 1 / MBF1


Mass: 13780.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60869
#41: Protein Heparin-binding protein HBp15


Mass: 11722.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z4W8
#75: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 34669.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#78: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 7884.286 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979
#80: Protein Elongation factor 2 / EF-2


Mass: 95232.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P13639, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#83: Protein 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E / Large ribosomal subunit protein uL10


Mass: 21507.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05388

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Small ribosomal subunit protein ... , 11 types, 20 molecules sESEsesHSHsOSOsbSbsDSDsPSPsQSQsMSMsZSZSe

#2: Protein Small ribosomal subunit protein eS4, X isoform / 40S ribosomal protein S4 / SCR10 / Single copy abundant mRNA protein


Mass: 29523.674 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#9: Protein Small ribosomal subunit protein eS30 / 40S ribosomal protein S30


Mass: 6539.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#12: Protein Small ribosomal subunit protein eS7 / 40S ribosomal protein S7


Mass: 21603.229 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#17: Protein Small ribosomal subunit protein uS11 / 40S ribosomal protein S14


Mass: 15014.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#19: Protein Small ribosomal subunit protein eS27 / 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1


Mass: 9348.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#65: Protein Small ribosomal subunit protein uS3


Mass: 25172.561 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P23396
#68: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein


Mass: 14092.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#69: Protein Small ribosomal subunit protein uS9 / 40S ribosomal protein S16


Mass: 16249.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#76: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 13652.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#77: Protein Small ribosomal subunit protein eS25 / 40S ribosomal protein S25


Mass: 8526.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#86: Protein/peptide Small ribosomal subunit protein eS30 / 40S ribosomal protein S30


Mass: 5407.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861

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40S ribosomal protein ... , 21 types, 42 molecules sISIsLSLsXSXsGSGsJSJsYSYsASAsBSBsVSVsaSasCSCsNSNsWSWsRSRsFSF...

#3: Protein 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 24003.012 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#4: Protein 40S ribosomal protein S11 / Small ribosomal subunit protein uS17


Mass: 17785.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#5: Protein 40S ribosomal protein S23 / Small ribosomal subunit protein uS12


Mass: 15626.392 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#6: Protein 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 27471.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#7: Protein 40S ribosomal protein S9 / Small ribosomal subunit protein uS4


Mass: 21649.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#8: Protein 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 15203.022 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#10: Protein 40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 24774.365 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#11: Protein 40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 24888.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#13: Protein 40S ribosomal protein S21 / Small ribosomal subunit protein eS21


Mass: 9124.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#14: Protein 40S ribosomal protein S26 / Small ribosomal subunit protein eS26


Mass: 11742.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#15: Protein 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 24587.029 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#16: Protein 40S ribosomal protein S13 / Small ribosomal subunit protein uS15


Mass: 17128.191 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#18: Protein 40S ribosomal protein S15a / Small ribosomal subunit protein uS8


Mass: 14734.357 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#64: Protein 40S ribosomal protein S17 / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#66: Protein 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 21327.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#67: Protein 40S ribosomal protein S10 / Small ribosomal subunit protein eS10


Mass: 11773.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#70: Protein 40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 17029.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#71: Protein 40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 15822.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#72: Protein 40S ribosomal protein S20 / Small ribosomal subunit protein uS10


Mass: 11765.890 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#73: Protein 40S ribosomal protein S28 / Small ribosomal subunit protein eS28


Mass: 7263.394 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#74: Protein 40S ribosomal protein S29 / Small ribosomal subunit protein uS14


Mass: 6559.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273

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RNA chain , 6 types, 12 molecules l7L7l8L8s2S2aPAPpEPEl5L5

#20: RNA chain RNA (120-MER)5S rRNA [Homo sapiens]


Mass: 38691.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#21: RNA chain RNA (156-MER)5.8S rRNA [Homo sapiens]


Mass: 50143.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1142736641
#79: RNA chain 18S rRNA [Homo sapiens]


Mass: 561332.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#81: RNA chain A/P site tRNA [Homo sapiens]


Mass: 23277.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#82: RNA chain P/E site tRNA [Homo sapiens]


Mass: 24298.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#85: RNA chain 28S rRNA [Homo sapiens]


Mass: 1211748.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

+
60S ribosomal protein ... , 35 types, 70 molecules lALAlCLClFLFlGLGlHLHlJLJlMLMlNLNlOLOlPLPlQLQlRLRlSLSlTLTlVLV...

#22: Protein 60S ribosomal protein L8 / Large ribosomal subunit protein uL2


Mass: 26998.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#24: Protein 60S ribosomal protein L4 / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4


Mass: 41747.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#27: Protein 60S ribosomal protein L7 / Large ribosomal subunit protein uL30


Mass: 26590.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#28: Protein 60S ribosomal protein L7a / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3


Mass: 27452.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#29: Protein 60S ribosomal protein L9 / Large ribosomal subunit protein uL6


Mass: 21655.268 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#31: Protein 60S ribosomal protein L11 / CLL-associated antigen KW-12 / Large ribosomal subunit protein uL5


Mass: 20086.191 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#33: Protein 60S ribosomal protein L14 / CAG-ISL 7 / Large ribosomal subunit protein eL14


Mass: 16220.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#34: Protein 60S ribosomal protein L15 / Large ribosomal subunit protein eL15


Mass: 24076.088 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#35: Protein 60S ribosomal protein L13a / 23 kDa highly basic protein / Large ribosomal subunit protein uL13


Mass: 23431.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#36: Protein 60S ribosomal protein L17 / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1


Mass: 17757.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#37: Protein 60S ribosomal protein L18 / Large ribosomal subunit protein eL18


Mass: 21556.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#38: Protein 60S ribosomal protein L19 / Large ribosomal subunit protein eL19


Mass: 22441.021 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#39: Protein 60S ribosomal protein L18a / Large ribosomal subunit protein eL20


Mass: 20677.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#40: Protein 60S ribosomal protein L21 / Large ribosomal subunit protein eL21


Mass: 18478.791 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#42: Protein 60S ribosomal protein L23 / 60S ribosomal protein L17 / Large ribosomal subunit protein uL14


Mass: 13972.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#43: Protein 60S ribosomal protein L23a / Large ribosomal subunit protein uL23


Mass: 13985.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#44: Protein 60S ribosomal protein L26 / Large ribosomal subunit protein uL24


Mass: 15891.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#45: Protein 60S ribosomal protein L27 / Large ribosomal subunit protein eL27


Mass: 15704.635 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#46: Protein 60S ribosomal protein L27a / Large ribosomal subunit protein uL15


Mass: 16473.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#48: Protein 60S ribosomal protein L30 / Large ribosomal subunit protein eL30


Mass: 10954.884 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#49: Protein 60S ribosomal protein L31 / Large ribosomal subunit protein eL31


Mass: 12635.694 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#50: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 15022.021 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#51: Protein 60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein / Large ribosomal subunit protein eL33


Mass: 12433.548 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#52: Protein 60S ribosomal protein L34 / Large ribosomal subunit protein eL34


Mass: 12994.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#53: Protein 60S ribosomal protein L35 / Large ribosomal subunit protein uL29


Mass: 14462.429 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#54: Protein 60S ribosomal protein L36 / Large ribosomal subunit protein eL36


Mass: 11915.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#55: Protein 60S ribosomal protein L37 / G1.16 / Large ribosomal subunit protein eL37


Mass: 10090.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#56: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8107.752 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#57: Protein/peptide 60S ribosomal protein L39 / Large ribosomal subunit protein eL39


Mass: 6295.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#59: Protein/peptide 60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41


Mass: 3344.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945
#60: Protein 60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 ...60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein / Large ribosomal subunit protein eL42


Mass: 12345.776 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#61: Protein 60S ribosomal protein L37a / Large ribosomal subunit protein eL43


Mass: 10168.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#62: Protein 60S ribosomal protein L28 / Large ribosomal subunit protein eL28


Mass: 14320.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#63: Protein 60S ribosomal protein L10a / CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down- ...CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down-regulated protein 6 / NEDD-6


Mass: 24879.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62906
#84: Protein 60S ribosomal protein L12 [Homo sapiens]


Mass: 15080.397 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Large ribosomal subunit protein ... , 6 types, 12 molecules lBLBlDLDlELElLLLlbLblmLm

#23: Protein Large ribosomal subunit protein uL3


Mass: 46079.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#25: Protein Large ribosomal subunit protein uL18


Mass: 34008.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#26: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding ...60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 28378.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#32: Protein Large ribosomal subunit protein eL13


Mass: 24190.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#47: Protein Large ribosomal subunit protein eL29 / 60S ribosomal protein L29 / Cell surface heparin-binding protein HIP


Mass: 13965.825 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#58: Protein Large ribosomal subunit protein eL40 / 60S ribosomal protein L40


Mass: 6199.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987

-
Ribosomal protein ... , 2 types, 4 molecules lILIlWLW

#30: Protein Ribosomal protein uL16-like / 60S ribosomal protein L10-like / Large ribosomal subunit protein uL16-like


Mass: 24439.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96L21
#87: Protein Ribosomal protein L24


Mass: 14476.975 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A994J4A5

-
Non-polymers , 2 types, 522 molecules

#88: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#89: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 510 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: In situ human top-back di-ribosome / Type: RIBOSOME / Entity ID: #1-#87 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45867 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006492435
ELECTRON MICROSCOPYf_angle_d0.8721312
ELECTRON MICROSCOPYf_dihedral_angle_d16.799169650
ELECTRON MICROSCOPYf_chiral_restr0.0489561
ELECTRON MICROSCOPYf_plane_restr0.00747842

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