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- PDB-3j7r: Structure of the translating mammalian ribosome-Sec61 complex -

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Basic information

Entry
Database: PDB / ID: 3j7r
TitleStructure of the translating mammalian ribosome-Sec61 complex
Components
  • (Ribosomal protein ...) x 76
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • A/P tRNA
  • Messenger RNA
  • P/E tRNA
  • Sec61 alpha subunit
  • Sec61 beta subunit
  • Sec61 gamma subunit
KeywordsRIBOSOME / mammalian / Sec61 / translocation / translation
Function / homology
Function and homology information


Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RMTs methylate histone arginines / Protein methylation / TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / : ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RMTs methylate histone arginines / Protein methylation / TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / : / regulation of cell cycle => GO:0051726 / regulation of cell cycle => GO:0051726 / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / malate dehydrogenase / protein-transporting ATPase activity / L-malate dehydrogenase (NAD+) activity / embryonic brain development / protein tyrosine kinase inhibitor activity / translation at presynapse / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / negative regulation of RNA splicing / carboxylic acid metabolic process / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / RHO GTPases Activate Formins / regulation of establishment of cell polarity / negative regulation of phagocytosis / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / alpha-beta T cell differentiation / 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 / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / regulation of cell division / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / organelle membrane / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein targeting / cellular response to interleukin-4 / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / signaling adaptor activity / negative regulation of smoothened signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / laminin binding / rough endoplasmic reticulum / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gastrulation / tricarboxylic acid cycle / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / negative regulation of ubiquitin-dependent protein catabolic process / rescue of stalled ribosome / SH2 domain binding / cyclin binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of GTPase activity / ribosomal large subunit biogenesis / maturation of SSU-rRNA / mRNA 3'-UTR binding / neural tube closure / positive regulation of translation / cellular response to glucose stimulus / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / positive regulation of protein-containing complex assembly / negative regulation of cell growth / cellular response to gamma radiation / receptor tyrosine kinase binding / cellular response to growth factor stimulus
Similarity search - Function
: / : / Malate dehydrogenase, type 3 / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. ...: / : / Malate dehydrogenase, type 3 / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / L-lactate/malate dehydrogenase / 40S ribosomal protein SA / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / metallochaperone-like domain / Ribosomal protein S12e / TRASH domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L1, conserved site / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L1 signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L1 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S27e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L15 / 40S ribosomal protein S7 / Large ribosomal subunit protein uL4 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L15 / 40S ribosomal protein S7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / 40S ribosomal protein S27 / 40S ribosomal protein S6 / 40S ribosomal protein S10 / 40S ribosomal protein S15a / 60S ribosomal protein L35a / 60S ribosomal protein L23a / 60S ribosomal protein L3 isoform a / 60S ribosomal protein L13a isoform 1 / 60S ribosomal protein L36a / Ribosomal protein / 60S ribosomal protein L8 / 40S ribosomal protein S9 isoform a / 60S ribosomal protein L36 / 40S ribosomal protein S11 / Ribosomal protein L37 / 40S ribosomal protein S25 / Ribosomal protein L19 / 60S ribosomal protein L23 / 60S ribosomal protein L7 / 40S ribosomal protein S30 / Protein transport protein Sec61 subunit gamma / 60S ribosomal protein L37a / Malate dehydrogenase / 60S ribosomal protein L28 isoform 2 / 40S ribosomal protein S19 / Large ribosomal subunit protein eL24 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL15 / 60S ribosomal protein L13 / Plug_translocon domain-containing protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL39 / 40S ribosomal protein S4 / Ribosomal protein L18 / 40S ribosomal protein S27a / 60S ribosomal protein L7a / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38 / Ribosomal protein S5 / 40S ribosomal protein S13 / 40S ribosomal protein S2 / Large ribosomal subunit protein uL6 / 40S ribosomal protein S12 / Small ribosomal subunit protein eS26 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL31 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL6 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL29
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsVoorhees, R.M. / Fernandez, I.S. / Scheres, S.H.W. / Hegde, R.S.
CitationJournal: Cell / Year: 2014
Title: Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution.
Authors: Rebecca M Voorhees / Israel S Fernández / Sjors H W Scheres / Ramanujan S Hegde /
Abstract: Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either ...Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 Å resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionSep 3, 2014ID: 3J73, 4W26, 4W27, 4W28
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4W26, 4W27, 4W28
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Dec 17, 2014Group: Other
Revision 1.3Apr 15, 2015Group: Non-polymer description
Revision 1.4Jul 18, 2018Group: Advisory / Data collection
Category: em_image_scans / em_software / pdbx_database_PDB_obs_spr
Item: _em_software.image_processing_id / _em_software.name / _pdbx_database_PDB_obs_spr.replace_pdb_id
Revision 2.0Oct 30, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity.pdbx_ec / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _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.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

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Assembly

Deposited unit
5: 28S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
A: Ribosomal protein uL2
B: Ribosomal protein uL3
C: Ribosomal protein uL4
D: Ribosomal protein uL18
E: Ribosomal protein eL6
F: Ribosomal protein uL30
G: Ribosomal protein eL8
H: Ribosomal protein uL6
I: Ribosomal protein uL16
J: Ribosomal protein uL5
L: Ribosomal protein eL13
M: Ribosomal protein eL14
N: Ribosomal protein eL15
O: Ribosomal protein uL13
P: Ribosomal protein uL22
Q: Ribosomal protein eL18
R: Ribosomal protein eL19
S: Ribosomal protein eL20
T: Ribosomal protein eL21
U: Ribosomal protein eL22
V: Ribosomal protein uL14
W: Ribosomal protein eL24
X: Ribosomal protein uL23
Y: Ribosomal protein uL24
Z: Ribosomal protein eL27
a: Ribosomal protein uL15
b: Ribosomal protein eL29
c: Ribosomal protein eL30
d: Ribosomal protein eL31
e: Ribosomal protein eL32
f: Ribosomal protein eL33
g: Ribosomal protein eL34
h: Ribosomal protein uL29
i: Ribosomal protein eL36
j: Ribosomal protein eL37
k: Ribosomal protein eL38
l: Ribosomal protein eL39
m: Ribosomal protein eL40
n: Ribosomal protein eL41
o: Ribosomal protein eL42
p: Ribosomal protein eL43
r: Ribosomal protein eL28
z: Ribosomal protein uL1
1: Sec61 alpha subunit
2: Sec61 gamma subunit
3: Sec61 beta subunit
S2: 18S ribosomal RNA
SA: Ribosomal protein uS2
SB: Ribosomal protein eS1
SC: Ribosomal protein uS5
SD: Ribosomal protein uS3
SE: Ribosomal protein eS4
SF: Ribosomal protein uS7
SG: Ribosomal protein eS6
SH: Ribosomal protein eS7
SI: Ribosomal protein eS8
SJ: Ribosomal protein uS4
SK: Ribosomal protein eS10
SL: Ribosomal protein uS17
SM: Ribosomal protein eS12
SN: Ribosomal protein uS15
SO: Ribosomal protein uS11
SP: Ribosomal protein uS19
SQ: Ribosomal protein uS9
SR: Ribosomal protein eS17
SS: Ribosomal protein uS13
ST: Ribosomal protein eS19
SU: Ribosomal protein uS10
SV: Ribosomal protein eS21
SW: Ribosomal protein uS8
SX: Ribosomal protein uS12
SY: Ribosomal protein eS24
SZ: Ribosomal protein es25
Sa: Ribosomal protein eS26
Sb: Ribosomal protein eS27
Sc: Ribosomal protein eS28
Sd: Ribosomal protein uS14
Se: Ribosomal protein eS30
Sf: Ribosomal protein eS31
Sg: Ribosomal protein RACK1
S4: Messenger RNA
S5: A/P tRNA
S6: P/E tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,421,331256
Polymers3,417,03586
Non-polymers4,296170
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 7 types, 7 molecules 578S2S4S5S6

#1: RNA chain 28S ribosomal RNA


Mass: 1206101.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#2: RNA chain 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: GenBank: 371913672
#3: RNA chain 5.8S ribosomal RNA


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: GenBank: 115552481
#50: RNA chain 18S ribosomal RNA


Mass: 561958.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: GenBank: 37956930
#84: RNA chain Messenger RNA


Mass: 3039.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#85: RNA chain A/P tRNA


Mass: 23874.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#86: RNA chain P/E tRNA


Mass: 24484.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas

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Ribosomal protein ... , 76 types, 76 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#4: Protein Ribosomal protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480Q387
#5: Protein Ribosomal protein uL3


Mass: 44759.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480L253
#6: Protein Ribosomal protein uL4


Mass: 41635.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A287AE76, UniProt: F1SJJ5*PLUS
#7: Protein Ribosomal protein uL18


Mass: 34417.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A287ASD0
#8: Protein Ribosomal protein eL6


Mass: 27052.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q2YGT9
#9: Protein Ribosomal protein uL30


Mass: 26590.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480W0U3
#10: Protein Ribosomal protein eL8


Mass: 30166.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1W808
#11: Protein Ribosomal protein uL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3LP78
#12: Protein Ribosomal protein uL16 / Protein QM homolog / Ribosomal protein L10


Mass: 24465.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q29195
#13: Protein Ribosomal protein uL5


Mass: 20248.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q29205
#14: Protein Ribosomal protein eL13


Mass: 24365.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1TBV3
#15: Protein Ribosomal protein eL14


Mass: 23383.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A1XQU3
#16: Protein Ribosomal protein eL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A286ZL65
#17: Protein Ribosomal protein uL13


Mass: 23435.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480L469
#18: Protein Ribosomal protein uL22


Mass: 17757.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A287B386
#19: Protein Ribosomal protein eL18


Mass: 21588.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1W0N5
#20: Protein Ribosomal protein eL19


Mass: 23567.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480VXS3
#21: Protein Ribosomal protein eL20


Mass: 26103.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A287APR1
#22: Protein Ribosomal protein eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P49666
#23: Protein Ribosomal protein eL22 / Heparin-binding protein HBp15


Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P67985
#24: Protein Ribosomal protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480VZZ1
#25: Protein Ribosomal protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1SH42
#26: Protein Ribosomal protein uL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480KZ98
#27: Protein Ribosomal protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1V977
#28: Protein Ribosomal protein eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A1XQU5
#29: Protein Ribosomal protein uL15


Mass: 16631.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1SN08
#30: Protein Ribosomal protein eL29


Mass: 17545.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q95281
#31: Protein Ribosomal protein eL30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1TXJ8
#32: Protein Ribosomal protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P62901
#33: Protein Ribosomal protein eL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6QAT0
#34: Protein Ribosomal protein eL33


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480KUB2
#35: Protein Ribosomal protein eL34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q29223
#36: Protein Ribosomal protein uL29


Mass: 14591.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q29361
#37: Protein Ribosomal protein eL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480QBP0
#38: Protein Ribosomal protein eL37


Mass: 10102.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480UVT3
#39: Protein Ribosomal protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z568
#40: Protein Ribosomal protein eL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1VIM4
#41: Protein Ribosomal protein eL40 / CEP52 / 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) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P63053
#42: Protein/peptide Ribosomal protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#43: Protein Ribosomal protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480LCM6
#44: Protein Ribosomal protein eL43


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480WPS5
#45: Protein Ribosomal protein eL28


Mass: 14301.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480YX24
#46: Protein Ribosomal protein uL1


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480NYW2
#51: Protein Ribosomal protein uS2 / 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 / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 32958.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q4GWZ2
#52: Protein Ribosomal protein eS1


Mass: 29931.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: B6V8C8
#53: Protein Ribosomal protein uS5


Mass: 24091.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3LJ87
#54: Protein Ribosomal protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
References: UniProt: Q0Z8U2, DNA-(apurinic or apyrimidinic site) lyase
#55: Protein Ribosomal protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1W0I3
#56: Protein Ribosomal protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z5E6
#57: Protein Ribosomal protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480E3J4
#58: Protein Ribosomal protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A287A9Y6
#59: Protein Ribosomal protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480YST6
#60: Protein Ribosomal protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480Q6G1
#61: Protein Ribosomal protein eS10


Mass: 18967.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480EHW2
#62: Protein Ribosomal protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480QMH2
#63: Protein Ribosomal protein eS12


Mass: 13776.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P46405
#64: Protein Ribosomal protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F6Q5P0
#65: Protein Ribosomal protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#66: Protein Ribosomal protein uS19 / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P62844
#67: Protein Ribosomal protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q29201
#68: Protein Ribosomal protein eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6QAP7
#69: Protein Ribosomal protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P62272
#70: Protein Ribosomal protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1SDD8
#71: Protein Ribosomal protein uS10


Mass: 13357.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A1XQU9
#72: Protein Ribosomal protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P63221
#73: Protein Ribosomal protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480KS86
#74: Protein Ribosomal protein uS12


Mass: 15854.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6SA96
#75: Protein Ribosomal protein eS24


Mass: 15366.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1SJK8
#76: Protein Ribosomal protein es25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480V055
#77: Protein Ribosomal protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P49171
#78: Protein Ribosomal protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A287BF06
#79: Protein Ribosomal protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6QAT1
#80: Protein Ribosomal protein uS14


Mass: 6612.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6QAP6
#81: Protein Ribosomal protein eS30


Mass: 14411.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480W155
#82: Protein Ribosomal protein eS31


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1W6H9
#83: Protein Ribosomal protein RACK1 / Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor for activated C kinase / ...Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor for activated C kinase / Receptor of activated protein kinase C 1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P63246

-
Protein , 2 types, 2 molecules 12

#47: Protein Sec61 alpha subunit


Mass: 43496.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1TV07
#48: Protein Sec61 gamma subunit


Mass: 7752.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480WFL1

-
Protein/peptide , 1 types, 1 molecules 3

#49: Protein/peptide Sec61 beta subunit


Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas

-
Non-polymers , 2 types, 170 molecules

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


Mass: 24.305 Da / Num. of mol.: 166 / Source method: obtained synthetically / Formula: Mg
#88: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: The 80S-Sec61 complex purified from porcine pancreas / Type: RIBOSOME
Buffer solutionName: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin
pH: 7.5
Details: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 400 mesh copper grids
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 120 K
Details: 3 uL sample was incubated on the grid for 30 seconds and blotted for 9 seconds before being plunged into liquid ethane (FEI VITROBOT MARK IV).

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Apr 7, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 70 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Details: Back-thinned
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1REFMACmodel fitting
2RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Single particle / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14723 / Nominal pixel size: 1.34 Å / Symmetry type: POINT
Atomic model buildingB value: 37 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor and FSC / Details: METHOD--Maximum likelihood
Atomic model building
IDPDB-ID 3D fitting-ID
13J3A

3j3a
PDB Unreleased entry

1
23J3B

3j3b
PDB Unreleased entry

1
33J3D

3j3d
PDB Unreleased entry

1
43J3F

3j3f
PDB Unreleased entry

1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms96256 125910 170 0 222336

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