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- EMDB-10772: Structure of a human 48S translational initiation complex - head -

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Basic information

Entry
Database: EMDB / ID: EMD-10772
TitleStructure of a human 48S translational initiation complex - head
Map data
Sample48S initiation complex
  • (Eukaryotic translation initiation factor 3 subunit ...) x 2
  • Receptor of activated protein C kinase 1
  • (40S ribosomal protein ...) x 13
  • Ubiquitin-40S ribosomal protein S27a
  • nucleic-acidNucleic acid
  • (ligand) x 2
Function / homology
Function and homology information


mRNA cap binding / cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / positive regulation of mRNA binding / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / response to TNF agonist ...mRNA cap binding / cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / positive regulation of mRNA binding / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of DNA repair / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / eukaryotic 43S preinitiation complex / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / response to extracellular stimulus / NF-kappaB complex / positive regulation of Golgi to plasma membrane protein transport / IRE1-RACK1-PP2A complex / eukaryotic 48S preinitiation complex / cytoplasmic side of rough endoplasmic reticulum membrane / formation of cytoplasmic translation initiation complex / positive regulation of endodeoxyribonuclease activity / oxidized purine DNA binding / regulation of cell division / protein kinase A binding / negative regulation of endoplasmic reticulum unfolded protein response / supercoiled DNA binding / negative regulation of hydrogen peroxide-induced neuron death / positive regulation of ceramide biosynthetic process / signaling adaptor activity / erythrocyte homeostasis / negative regulation of phagocytosis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of Wnt signaling pathway / pigmentation / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of T cell receptor signaling pathway / positive regulation of mitochondrial depolarization / phagocytic cup / rescue of stalled ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of activated T cell proliferation / positive regulation of cellular component movement / fibroblast growth factor binding / iron-sulfur cluster binding / ion channel inhibitor activity / positive regulation of apoptotic signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / positive regulation of interleukin-2 production / monocyte chemotaxis / BH3 domain binding / positive regulation of cyclic-nucleotide phosphodiesterase activity / spindle assembly / ribosomal small subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane / regulation of translational fidelity / maturation of SSU-rRNA / negative regulation of protein kinase B signaling / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of JUN kinase activity / gastrulation / negative regulation of respiratory burst involved in inflammatory response / polysome / positive regulation of microtubule polymerization / ribosomal small subunit biogenesis / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / viral transcription / positive regulation of DNA repair / molecular adaptor activity / Hsp70 protein binding / erythrocyte differentiation / tubulin binding / translation initiation factor activity / translational initiation / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of protein ubiquitination / endodeoxyribonuclease activity / MyD88-independent toll-like receptor signaling pathway / polysomal ribosome / osteoblast differentiation / nucleotide-binding oligomerization domain containing signaling pathway / nucleotide-excision repair, DNA gap filling / SH2 domain binding / nucleotide-excision repair, DNA damage recognition / cyclin binding / nucleotide-excision repair, DNA duplex unwinding / TRIF-dependent toll-like receptor signaling pathway / DNA-(apurinic or apyrimidinic site) endonuclease activity / mitotic spindle / global genome nucleotide-excision repair / small ribosomal subunit rRNA binding / chromosome segregation / host cell
Ribosomal protein S27a / Ribosomal protein S13, conserved site / K homology domain-like, alpha/beta / Eukaryotic translation initiation factor 3 subunit G / WD40-repeat-containing domain / Ribosomal protein S17e / Ribosomal protein S14 / Ribosomal protein S9 / Ribosomal protein S10, conserved site / Ubiquitin-like domain ...Ribosomal protein S27a / Ribosomal protein S13, conserved site / K homology domain-like, alpha/beta / Eukaryotic translation initiation factor 3 subunit G / WD40-repeat-containing domain / Ribosomal protein S17e / Ribosomal protein S14 / Ribosomal protein S9 / Ribosomal protein S10, conserved site / Ubiquitin-like domain / Ribosomal protein S19e / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S3, conserved site / WD40 repeat, conserved site / Ubiquitin conserved site / Ribosomal protein S12e / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / G-protein beta WD-40 repeat / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S19/S15 / Ribosomal protein S13 / Ribosomal protein S10 / Ribosomal protein S3, C-terminal / Eukaryotic translation initiation factor 3 subunit D / K homology domain superfamily, prokaryotic type / WD40 repeat / Ribosomal protein S13-like, H2TH / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Nucleotide-binding alpha-beta plait domain superfamily / Ubiquitin domain / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S25 / Ribosomal protein S28e / Ribosomal protein S14/S29 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / S27a-like superfamily / Ribosomal protein S19e domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S9, conserved site / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein S5/S7 / Winged helix DNA-binding domain superfamily / RNA recognition motif domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S19, superfamily / RNA-binding domain superfamily / Eukaryotic translation initiation factor 3 subunit G, N-terminal / Ribosomal protein S7 domain / K Homology domain, type 2 / 50S ribosomal protein L30e-like / Ribosomal protein S10 domain / Ribosomal protein S28e conserved site / eIF3G, RNA recognition motif / Ubiquitin-like domain superfamily
40S ribosomal protein S16 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S28 / 40S ribosomal protein S25 / 40S ribosomal protein S15 / 40S ribosomal protein S29 / 40S ribosomal protein S18 / Eukaryotic translation initiation factor 3 subunit G / 40S ribosomal protein S20 / 40S ribosomal protein S10 ...40S ribosomal protein S16 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S28 / 40S ribosomal protein S25 / 40S ribosomal protein S15 / 40S ribosomal protein S29 / 40S ribosomal protein S18 / Eukaryotic translation initiation factor 3 subunit G / 40S ribosomal protein S20 / 40S ribosomal protein S10 / 40S ribosomal protein S5 / 40S ribosomal protein S19 / 40S ribosomal protein S12 / 40S ribosomal protein S3 / 40S ribosomal protein S17 / Eukaryotic translation initiation factor 3 subunit D / Receptor of activated protein C kinase 1
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBrito Querido J / Sokabe M / Kraatz S / Gordiyenko Y / Skehel M / Fraser C / Ramakrishnan V
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Wellcome TrustWTY096570 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM092927 United States
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
CitationJournal: Science / Year: 2020
Title: Structure of a human 48 translational initiation complex.
Authors: Jailson Brito Querido / Masaaki Sokabe / Sebastian Kraatz / Yuliya Gordiyenko / J Mark Skehel / Christopher S Fraser / V Ramakrishnan /
Abstract: A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to ...A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 initiation complex (i.e., the 48). The 48 then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 subunit during scanning.
Validation ReportPDB-ID: 6ybs

SummaryFull reportAbout validation report
History
DepositionMar 17, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateSep 16, 2020-
Current statusSep 16, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ybs
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ybs
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10772.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 500 pix.
= 537. Å
1.07 Å/pix.
x 500 pix.
= 537. Å
1.07 Å/pix.
x 500 pix.
= 537. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.033
Minimum - Maximum-0.20110273 - 0.40833396
Average (Standard dev.)0.00013005463 (±0.004569401)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 537.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z537.000537.000537.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.2010.4080.000

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Supplemental data

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Segmentation: #1

Fileemd_10772_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: #1

Fileemd_10772_additional_1.map
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Additional map: #2

Fileemd_10772_additional_2.map
Projections & Slices
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Half map: #1

Fileemd_10772_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_10772_half_map_2.map
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Sample components

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Entire 48S initiation complex

EntireName: 48S initiation complex / Number of components: 21

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Component #1: protein, 48S initiation complex

ProteinName: 48S initiation complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Eukaryotic translation initiation factor 3 subunit D

ProteinName: Eukaryotic translation initiation factor 3 subunit D / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 64.060758 kDa
SourceSpecies: Human (human)

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Component #3: protein, Receptor of activated protein C kinase 1

ProteinName: Receptor of activated protein C kinase 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.115652 kDa
SourceSpecies: Human (human)

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Component #4: protein, 40S ribosomal protein S28

ProteinName: 40S ribosomal protein S28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.855052 kDa
SourceSpecies: Human (human)

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Component #5: protein, 40S ribosomal protein S17

ProteinName: 40S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.578156 kDa
SourceSpecies: Human (human)

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Component #6: protein, 40S ribosomal protein S20

ProteinName: 40S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.398763 kDa
SourceSpecies: Human (human)

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Component #7: protein, Eukaryotic translation initiation factor 3 subunit G

ProteinName: Eukaryotic translation initiation factor 3 subunit G / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.662016 kDa
SourceSpecies: Human (human)

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Component #8: protein, 40S ribosomal protein S10

ProteinName: 40S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.933846 kDa
SourceSpecies: Human (human)

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Component #9: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.538987 kDa
SourceSpecies: Human (human)

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Component #10: protein, 40S ribosomal protein S29

ProteinName: 40S ribosomal protein S29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.690821 kDa
SourceSpecies: Human (human)

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Component #11: protein, 40S ribosomal protein S15

ProteinName: 40S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.076207 kDa
SourceSpecies: Human (human)

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Component #12: protein, 40S ribosomal protein S3

ProteinName: 40S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.729369 kDa
SourceSpecies: Human (human)

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Component #13: protein, 40S ribosomal protein S19

ProteinName: 40S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.091562 kDa
SourceSpecies: Human (human)

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Component #14: protein, 40S ribosomal protein S25

ProteinName: 40S ribosomal protein S25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.776224 kDa
SourceSpecies: Human (human)

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Component #15: protein, 40S ribosomal protein S18

ProteinName: 40S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.759777 kDa
SourceSpecies: Human (human)

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Component #16: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.913453 kDa
SourceSpecies: Human (human)

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Component #17: protein, Ubiquitin-40S ribosomal protein S27a

ProteinName: Ubiquitin-40S ribosomal protein S27a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.004041 kDa
SourceSpecies: Human (human)

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Component #18: protein, 40S ribosomal protein S16

ProteinName: 40S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.477377 kDa
SourceSpecies: Human (human)

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Component #19: nucleic-acid, 18S rRNA

nucleic acidName: 18S rRNA18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UACCUGGUUG AUCCUGCCAG UAGCAU(A2M)UGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUG AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGU(OMU)CC(PSU)U (OMU)GGUCGCUCG CUCCUCUCCU ACUUGGAUAA ...Sequence:
UACCUGGUUG AUCCUGCCAG UAGCAU(A2M)UGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUG AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGU(OMU)CC(PSU)U (OMU)GGUCGCUCG CUCCUCUCCU ACUUGGAUAA CUGUGGUA(A2M)U UCUAG(A2M)GCUA AUA(O)(N)CAUGC CGACGGGCGC UGACCCCCUU CGCGGGGGGG AUGCGUGCAU UUAUCAGAUC AAAACCAACC CGGUCAGCCC CUCUCCGGCC CCGGCCGGGG GGCGGGCGCC GGCGGCUUUG GUGACUCUAG AUAACCUCGG GCCGAUCGCA CGCCCCCCGU GGCGGCGACG ACCCAUUCGA ACGUCUGCCC UAUCAACUUU CGAUGGUAGU CGCCGUGCCU ACCAUGGUGA CCACGGGUGA CGGGGAAUCA GGGUUCGAUU CCGGAGAGGG AGCCUGAGAA ACGGCUACCA CAUCCAAGGA AGGCAGCAGG CGCGC(A2M)AAUU ACCCACUCCC GACCCGGGGA (OMG)GUAGUGA(OMC)G AAAAAUAACA AUACAGGACU CUUUCGAGGC CCUGUAAUUG GAAUGAGUCC ACUUUAAAUC CUUUAACGAG GAUCCAUUGG AGGGCAAGUC UGG(P)(N)UGCCA GCAGCCGCGG UAAUUCCAGC UCCAAUA(O)(N)G CGUAUAUUAA AGUUGCUGCA GUU(A2M)AAAAGC UCGUAGUU(OMG)G AUCUUGGGAG CGGGCGGGCG GUCCGCCGCG AGGCGAGCCA CCGCCCGUCC CCGCCCCUUG CCUCUCGGCG CCCCCUCGAU GCUCUUAGCU GAGUGUCCCG CGGGGCCCGA AGCGUUUACU UUGAAAAAA(N) UUAGAGUG(PSU)(PSU) CAAAGCAGGC CCGAGCCGCC UGGAUACCGC AGCUAGGAAU AAUGGAAUAG GACCGCGGUU CUAUUUUGUU GGUUUUCGGA ACUGAGGCCA UGAUUAAGAG GGACGGCCGG GGGCAUUCGU AUUGCGCCGC UAGAGGUGAA AUUCUUGGAC CGGCGCAAGA CGGACCAGAG CGAAAGCAUU UGCCAAGAAU GUUUUCAUUA AUCAAGA(A2M)CG AAAGUCGGAG GUUCGAAGAC GAUCAGAUAC CGUCGUAGUU CCGACCA(PSU)AA ACGAUGCCGA CCGGCGAUGC GGCGGCGUUA UUCCCAUGAC CCGCCGGGCA GCUUCCGGGA AACCAAAGUC UUUGGGUUCC GGGGGGAGUA UGGUUGCAAA GCUGAAACUU AAAGGAAUUG ACGGAAGGGC ACCAC(JMH)AGGA GUGGAGCCUG CGGCUUAAU(PSU) UGACUCAACA CGGGAAACCU CACCCGGCCC GGACACGGAC AGGAUUGACA GAUUGAUAGC UCUUUCUCGA UUCCGUGGGU GGUGGUGCAU GGCCGUUCUU AGUUGGUGGA GCGAUUUGUC UGGUUAAUUC (5MC)GAUAACGAA CGAGACUCUG GCAUGCUAAC UAGUUACGCG ACCCCCGAGC GGUCGGCGUC CCCCAACUUC UUAGAGGGAC AAGUGGCGUU CAGCCACCCG AGAUUGAGCA AUAACAGGUC UGUGAUGCCC UUAGAUGUCC GGGGCUGCAC GCGCGCUACA CUGACUGGCU CAGCGUGUGC CUACCCUACG CCGGCAGGCG CGGGUAACCC GUUGAACCCC AUUCGUGAUG GGGAUCGGGG AUUGCAAUUA UUCCCCAUGA ACGAGGAAUU CCCAGUAAGU GCGGGUCAUA AGCUUGCGUU GAUU(A2M)AGUCC CUGCCCUUUG UACACACCG(OMC) CCGUCGCUAC UACCGAUUGG AUGGUUUAGU GAGGCCCUCG GAUCGGCCCC GCCGGGGUCG GCCCACGGCC CUGGCGGAGC GCUGAGAAGA CGGUCGAACU UGACUAUCUA GAGGAAGUAA AAGUCG(UR3)A(6MZ)C AAGGUUUCCG UAGGUG(MA6)(MA6)CC UGCGGAAGGA UCAUUA
MassTheoretical: 604.237938 kDa
SourceSpecies: Homo sapiens (human)

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Component #20: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 29 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #21: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 107 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 144882
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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