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- PDB-9qzp: Mouse Ribosome Classical Pre translocation state -

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Basic information

Entry
Database: PDB / ID: 9qzp
TitleMouse Ribosome Classical Pre translocation state
Components
  • (Large ribosomal subunit protein ...) x 41
  • (Small ribosomal subunit protein ...) x 30
  • (Ubiquitin-ribosomal protein ...) x 2
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 40S ribosomal protein S3a
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S ribosomal protein L41
  • Nascent protein chain
  • Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
  • messenger RNA
  • transfer RNA
KeywordsRIBOSOME / Translating Ribosomes / Classical Pre state / Mouse / Ba/F3 / Polysomes
Function / homology
Function and homology information


Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / TNFR1-mediated ceramide production / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / 5.8S rRNA binding / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of myoblast fusion / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A ...Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / TNFR1-mediated ceramide production / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / 5.8S rRNA binding / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of myoblast fusion / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / negative regulation of protein neddylation / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of expression of SLITs and ROBOs / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Alpha-protein kinase 1 signaling pathway / Pexophagy / Regulation of pyruvate metabolism / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Formation of a pool of free 40S subunits / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / SCF-beta-TrCP mediated degradation of Emi1 / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / SRP-dependent cotranslational protein targeting to membrane / p75NTR recruits signalling complexes / Interferon alpha/beta signaling / Negative regulation of MAPK pathway / Major pathway of rRNA processing in the nucleolus and cytosol / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / E3 ubiquitin ligases ubiquitinate target proteins / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Ubiquitin-dependent degradation of Cyclin D / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / Downregulation of ERBB2 signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Dual incision in TC-NER / Oncogene Induced Senescence / Degradation of CRY and PER proteins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / TNFR1-induced NF-kappa-B signaling pathway / HDR through Homologous Recombination (HRR) / Gap-filling DNA repair synthesis and ligation in TC-NER / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Metalloprotease DUBs / Formation of Incision Complex in GG-NER / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of BACH1 activity / EGFR downregulation / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / mammalian oogenesis stage / Degradation of AXIN / Protein methylation / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins
Similarity search - Function
40S ribosomal protein SA / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : ...40S ribosomal protein SA / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L2, archaeal-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal L29e protein family / Ribosomal protein S12e / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S19e, conserved site / : / Ribosomal protein S19e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L6e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / 40S Ribosomal protein S10 / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / S27a-like superfamily / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 1. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal L40e family / Ribosomal protein S30 / Ribosomal protein L36e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal protein L35Ae, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S25 / : / S25 ribosomal protein / Ribosomal_L40e / Ribosomal protein L44e / Ribosomal protein L27e
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL20 / 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 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsSanto, P.E. / Astier, A. / Plisson-Chastang, C.
Funding support France, 1items
OrganizationGrant numberCountry
Institut National du Cancer (inCA)PLBIO20-003 France
CitationJournal: Hemasphere / Year: 2026
Title: A RiboCancer cell line panel reveals that CLL-associated Rps15 mutations translationally rewire transcription through codon-specific tRNA accommodation defects.
Authors: Anaïs Astier / Marino Caruso / Stijn Vereecke / Paulo E Santo / Coralie Capron / Carine Froment / Dana Rinaldi / David Cabrerizo Granados / Marine Leclercq / Jonathan Royaert / Jelle ...Authors: Anaïs Astier / Marino Caruso / Stijn Vereecke / Paulo E Santo / Coralie Capron / Carine Froment / Dana Rinaldi / David Cabrerizo Granados / Marine Leclercq / Jonathan Royaert / Jelle Verbeeck / Naomy Pasau / Laura Plassart / Daniele Pepe / Steven Verbruggen / Hermes Paraqindes / Simon Lebaron / Virginie Marcel / Sébastien Durand / Clément Chapat / Gerben Menschaert / Pierre Close / Francesca Rapino / Frédéric Catez / Julien Marcoux / Célia Plisson-Chastang / Kim De Keersmaecker /
Abstract: Recurrent point mutations in ribosomal proteins (RPs) RPL10 and RPS15 are found in T-cell acute lymphoblastic leukemia (T-ALL) and chronic lymphocytic leukemia (CLL), respectively. Furthermore, ...Recurrent point mutations in ribosomal proteins (RPs) RPL10 and RPS15 are found in T-cell acute lymphoblastic leukemia (T-ALL) and chronic lymphocytic leukemia (CLL), respectively. Furthermore, deletions of RPL5, RPL11, and RPL22 are frequent in hematologic diseases such as Diamond Blackfan Anemia, T-ALL, multiple myeloma, and in a variety of solid tumors. Yet, the role of these RP defects in dysregulation of the ribosomal translation function remains poorly understood. We engineered an isogenic RiboCancer cell line library modeling the most recurrent RP defects in blood and solid cancers and characterized it by a multi-omics translatome analysis (proteome, Ribo-seq, and total RNA-seq) as well as RiboMethSeq. Within this RiboCancer panel, CLLassociated Rps15 mutations induced the strongest alterations in mRNA translation, affecting up to 10% of expressed genes. Cryo-electron microscopy revealed that these mutations destabilize the Rps15 C-terminus and affect the translation elongation cycle dynamics by deregulating accommodation of aminoacylated tRNAs at the ribosomal A-site. This accommodation defect showed specificity for 11 codons, explaining the reduced translation efficiency of genes with high presence of these codons in Rps15-mutant cells. Notably, these genes were enriched for epigenetic and transcriptional regulators such as transcription factor Runx3, resulting in downregulation of Runx3 target genes involved in immune regulation. By developing and characterizing a unique RiboCancer cell line panel, we mapped translational rewiring driven by the most frequent somatic RP mutations. We provide unprecedented mechanistic insights into translation defects induced by CLL-associated Rps15 mutations, and reveal an intriguing translation-based rewiring of transcription in CLL.
History
DepositionApr 23, 2025Deposition site: PDBE / Processing site: PDBE
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: Large ribosomal subunit protein uL30
A2: 28S ribosomal RNA
A3: Small ribosomal subunit protein uS13
B1: Large ribosomal subunit protein eL8
B2: 5S ribosomal RNA
B3: Small ribosomal subunit protein eS19
Bv: transfer RNA
Bx: messenger RNA
By: Nascent protein chain
Bz: transfer RNA
C1: Large ribosomal subunit protein uL6
C2: 5.8S ribosomal RNA
C3: Small ribosomal subunit protein uS10
D1: Large ribosomal subunit protein uL16
D2: Large ribosomal subunit protein uL2
D3: Small ribosomal subunit protein eS21
E1: Large ribosomal subunit protein uL5
E2: Large ribosomal subunit protein uL3
E3: Small ribosomal subunit protein uS12
F1: Large ribosomal subunit protein eL13
F2: Large ribosomal subunit protein uL4
F3: Small ribosomal subunit protein eS26
G1: Large ribosomal subunit protein eL14
G2: Large ribosomal subunit protein uL18
G3: Small ribosomal subunit protein eS28
H1: Large ribosomal subunit protein eL15
H2: Large ribosomal subunit protein eL6
H3: Small ribosomal subunit protein uS14
I2: Large ribosomal subunit protein uL13
I3: Small ribosomal subunit protein RACK1
J2: Large ribosomal subunit protein uL22
J3: Small ribosomal subunit protein uS5
K2: Large ribosomal subunit protein eL18
K3: Small ribosomal subunit protein eS6
L1: Large ribosomal subunit protein uL1
L2: Large ribosomal subunit protein eL19
L3: Small ribosomal subunit protein uS4
M2: Large ribosomal subunit protein eL20
M3: Small ribosomal subunit protein eS12
N2: Large ribosomal subunit protein eL21
N3: Small ribosomal subunit protein uS15
O2: Large ribosomal subunit protein eL22
O3: Small ribosomal subunit protein uS11
P2: Large ribosomal subunit protein uL14
P3: Small ribosomal subunit protein uS8
Q2: Large ribosomal subunit protein eL24
Q3: Small ribosomal subunit protein eS24
R2: Large ribosomal subunit protein uL23
R3: Small ribosomal subunit protein eS25
S2: Large ribosomal subunit protein uL24
S3: Small ribosomal subunit protein eS27
T2: Large ribosomal subunit protein eL27
T3: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
U2: Large ribosomal subunit protein uL15
U3: Ubiquitin-ribosomal protein eS31 fusion protein
V2: Large ribosomal subunit protein eL29
W2: Large ribosomal subunit protein eL30
X2: Large ribosomal subunit protein eL31
Y2: Large ribosomal subunit protein eL32
Z2: Large ribosomal subunit protein eL33
a2: Large ribosomal subunit protein eL34
b2: Large ribosomal subunit protein uL29
c2: Large ribosomal subunit protein eL36
d2: Large ribosomal subunit protein eL37
e2: Large ribosomal subunit protein eL38
f2: Large ribosomal subunit protein eL39
g2: Ubiquitin-ribosomal protein eL40 fusion protein
h2: 60S ribosomal protein L41
i2: Large ribosomal subunit protein eL42
j2: Large ribosomal subunit protein eL43
k2: Large ribosomal subunit protein eL28
n2: transfer RNA
o2: Small ribosomal subunit protein uS2
p2: 40S ribosomal protein S3a
q2: Small ribosomal subunit protein uS3
r2: Small ribosomal subunit protein eS4
s2: Small ribosomal subunit protein uS7
t2: Small ribosomal subunit protein eS7
u2: Small ribosomal subunit protein eS8
v2: Small ribosomal subunit protein eS10
w2: Small ribosomal subunit protein uS17
x2: Small ribosomal subunit protein uS19
y2: Small ribosomal subunit protein uS9
z2: Small ribosomal subunit protein eS17
m2: 18S ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,353,723209
Polymers3,350,46385
Non-polymers3,260124
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Large ribosomal subunit protein ... , 41 types, 41 molecules A1B1C1D1D2E1E2F1F2G1G2H1H2I2J2K2L1L2M2N2O2P2Q2R2S2T2U2V2W2X2...

#1: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 31492.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14148
#4: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a / Surfeit locus protein 3


Mass: 30042.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P12970
#10: Protein Large ribosomal subunit protein uL6 / 60S ribosomal protein L9


Mass: 21917.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51410
#13: Protein Large ribosomal subunit protein uL16 / 60S ribosomal protein L10 / Protein QM homolog / Ribosomal protein L10


Mass: 24657.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWV3
#14: Protein Large ribosomal subunit protein uL2 / 60S ribosomal protein L8


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62918
#16: Protein Large ribosomal subunit protein uL5 / 60S ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CXW4
#17: Protein Large ribosomal subunit protein uL3 / 60S ribosomal protein L3 / J1 protein


Mass: 46212.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P27659
#19: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / A52


Mass: 24364.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47963
#20: Protein Large ribosomal subunit protein uL4 / 60S ribosomal protein L4


Mass: 47259.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D8E6
#22: Protein Large ribosomal subunit protein eL14 / 60S ribosomal protein L14


Mass: 23620.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR57
#23: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34464.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47962
#25: Protein Large ribosomal subunit protein eL15 / 60S ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZM2
#26: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / TAX-responsive enhancer element-binding protein 107 / TAXREB107


Mass: 33593.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47911
#28: Protein Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a / Transplantation antigen P198 / Tum-P198 antigen


Mass: 23519.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P19253
#30: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPR4
#32: Protein Large ribosomal subunit protein eL18 / 60S ribosomal protein L18


Mass: 21698.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35980
#34: Protein Large ribosomal subunit protein uL1 / 60S ribosomal protein L10a / CSA-19 / Neural precursor cell expressed developmentally down- ...60S ribosomal protein L10a / CSA-19 / Neural precursor cell expressed developmentally down-regulated protein 6 / NEDD-6


Mass: 24965.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P53026
#35: Protein Large ribosomal subunit protein eL19 / 60S ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P84099
#37: Protein Large ribosomal subunit protein eL20 / 60S ribosomal protein L18a


Mass: 20778.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62717
#39: Protein Large ribosomal subunit protein eL21 / 60S ribosomal protein L21


Mass: 18624.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O09167
#41: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22 / Heparin-binding protein HBp15


Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P67984
#43: Protein Large ribosomal subunit protein uL14 / 60S ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62830
#45: Protein Large ribosomal subunit protein eL24 / 60S ribosomal protein L24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BP67
#47: Protein Large ribosomal subunit protein uL23 / 60S ribosomal protein L23a


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62751
#49: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26 / Silica-induced gene 20 protein / SIG-20


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61255
#51: Protein Large ribosomal subunit protein eL27 / 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61358
#53: Protein Large ribosomal subunit protein uL15 / 60S ribosomal protein L27a / L29


Mass: 16648.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14115
#55: Protein Large ribosomal subunit protein eL29 / 60S ribosomal protein L29


Mass: 17635.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47915
#56: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62889
#57: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62900
#58: Protein Large ribosomal subunit protein eL32 / 60S ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62911
#59: Protein Large ribosomal subunit protein eL33 / 60S ribosomal protein L35a


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O55142
#60: Protein Large ribosomal subunit protein eL34 / 60S ribosomal protein L34


Mass: 13325.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1R9
#61: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14595.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWV7
#62: Protein Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47964
#63: Protein Large ribosomal subunit protein eL37 / 60S ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D823
#64: Protein Large ribosomal subunit protein eL38 / 60S ribosomal protein L38


Mass: 8224.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9JJI8
#65: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62892
#68: Protein Large ribosomal subunit protein eL42 / 60S ribosomal protein L36a / 60S ribosomal protein L44


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P83882
#69: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61514
#70: Protein Large ribosomal subunit protein eL28 / 60S ribosomal protein L28


Mass: 15770.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P41105

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RNA chain , 6 types, 8 molecules A2B2BvBzn2BxC2m2

#2: RNA chain 28S ribosomal RNA


Mass: 1171994.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#5: RNA chain 5S ribosomal RNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#7: RNA chain transfer RNA


Mass: 24485.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 1843603821
#8: RNA chain messenger RNA


Mass: 3016.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#11: RNA chain 5.8S ribosomal RNA


Mass: 50157.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 1756494520
#83: RNA chain 18S ribosomal RNA


Mass: 528132.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Small ribosomal subunit protein ... , 30 types, 30 molecules A3B3C3D3E3F3G3H3I3J3K3L3M3N3O3P3Q3R3S3o2q2r2s2t2u2v2w2x2y2z2

#3: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18 / Ke-3 / Ke3


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62270
#6: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


Mass: 16117.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZX8
#12: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P60867
#15: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21


Mass: 9154.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQR2
#18: Protein Small ribosomal subunit protein uS12 / 40S ribosomal protein S23


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62267
#21: Protein Small ribosomal subunit protein eS26 / 40S ribosomal protein S26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62855
#24: Protein Small ribosomal subunit protein eS28 / 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62858
#27: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62274
#29: Protein Small ribosomal subunit protein RACK1 / 12-3 / Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor for activated C kinase / ...12-3 / Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor for activated C kinase / Receptor of activated protein C kinase 1 / Receptor of activated protein kinase C 1 / p205


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68040
#31: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3


Mass: 31283.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P25444
#33: Protein Small ribosomal subunit protein eS6 / 40S ribosomal protein S6 / Phosphoprotein NP33


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62754
#36: Protein Small ribosomal subunit protein uS4 / 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWN5
#38: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 14549.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63323
#40: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62301
#42: Protein Small ribosomal subunit protein uS11 / 40S ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62264
#44: Protein Small ribosomal subunit protein uS8 / 40S ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62245
#46: Protein Small ribosomal subunit protein eS24 / 40S ribosomal protein S24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62849
#48: Protein Small ribosomal subunit protein eS25 / 40S ribosomal protein S25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62852
#50: Protein Small ribosomal subunit protein eS27 / 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWU9
#71: Protein Small ribosomal subunit protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37 kDa oncofetal antigen / 37/67 kDa laminin receptor / ...37 kDa laminin receptor precursor / 37LRP / 37 kDa oncofetal antigen / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal protein SA / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / OFA/iLRP


Mass: 32867.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14206
#73: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P62908, DNA-(apurinic or apyrimidinic site) lyase
#74: Protein Small ribosomal subunit protein eS4 / 40S ribosomal protein S4 / X isoform


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62702
#75: Protein Small ribosomal subunit protein uS7 / 40S ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97461
#76: Protein Small ribosomal subunit protein eS7 / 40S ribosomal protein S7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62082
#77: Protein Small ribosomal subunit protein eS8 / 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62242
#78: Protein Small ribosomal subunit protein eS10 / 40S ribosomal protein S10


Mass: 18951.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63325
#79: Protein Small ribosomal subunit protein uS17 / 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62281
#80: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62843
#81: Protein Small ribosomal subunit protein uS9 / 40S ribosomal protein S16


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14131
#82: Protein Small ribosomal subunit protein eS17 / 40S ribosomal protein S17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63276

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Protein/peptide , 2 types, 2 molecules Byh2

#9: Protein/peptide Nascent protein chain


Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#67: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62947

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Protein , 2 types, 2 molecules T3p2

#52: Protein Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / FAU ubiquitin-like and ribosomal protein S30


Mass: 14441.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62862
#72: Protein 40S ribosomal protein S3a / Protein TU-11


Mass: 29942.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97351

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Ubiquitin-ribosomal protein ... , 2 types, 2 molecules U3g2

#54: Protein Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin carboxyl extension protein 80


Mass: 17990.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62983
#66: Protein Ubiquitin-ribosomal protein eL40 fusion protein / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62984

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Non-polymers , 3 types, 125 molecules

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


Mass: 24.305 Da / Num. of mol.: 118 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#86: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Elogating Ribosome in Classical PRE translocation state
Type: RIBOSOME
Details: de-novo peptide chain By is only visible in the Refine 3D map.
Entity ID: #1, #3-#6, #9, #7, #10-#26, #28-#65, #67-#68, #70-#82
Source: NATURAL
Molecular weightValue: 4.3 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Strain: Ba/F3
Buffer solutionpH: 7.5
Details: 20 mM Hepes pH 7.5, 150 mM NaCl, 10 mM MgCl2, 1 mM DTT
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMSodium chlorideNaCl1
310 mMMagnesium chlorideMgCl21
41 mMDithiothreitolC4H10O2S21
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: RNA concentration was measured by nanordrop
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 292 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 100000 X / Nominal defocus max: 2900 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7139

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2PHENIX1.21.2_5419:model refinement
5CTFFIND1.14CTF correction
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 691132
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9545 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Initial fitting was done using PDB ID 7LS1 in Chimera. Refmac and Phenix were used for Refine
Atomic model buildingPDB-ID: 7LS1

7ls1


Accession code: 7LS1 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00253500
ELECTRON MICROSCOPYf_angle_d0.57278011
ELECTRON MICROSCOPYf_dihedral_angle_d21.99221217
ELECTRON MICROSCOPYf_chiral_restr0.0359679
ELECTRON MICROSCOPYf_plane_restr0.0055514

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