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- EMDB-18903: CryoEM structure of wheat 40S ribosomal subunit, head domain -

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Basic information

Entry
Database: EMDB / ID: EMD-18903
TitleCryoEM structure of wheat 40S ribosomal subunit, head domain
Map data
Sample
  • Complex: Small ribosomal subunit from Triticum aestivum (common wheat)
    • Protein or peptide: x 15 types
    • RNA: x 1 types
  • Ligand: x 4 types
Keywordssmall ribosomal subunit / wheat / eukaryotes / 40S / RIBOSOME
Function / homology
Function and homology information


plastid / translation regulator activity / rescue of stalled ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein kinase C binding / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit ...plastid / translation regulator activity / rescue of stalled ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein kinase C binding / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome binding / small ribosomal subunit / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
: / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a ...: / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / 40S Ribosomal protein S10 / Ribosomal protein S28e conserved site / Ribosomal protein S28e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S28e / Ribosomal protein S28e signature. / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ribosomal protein S3, conserved site / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ubiquitin family / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S14 / Type-2 KH domain profile. / Ribosomal protein S13/S18 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ubiquitin homologues / Ribosomal protein S14p/S29e / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / Ribosomal protein S9, conserved site / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S13 signature. / Ubiquitin-like domain / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S13 family profile. / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ribosomal protein S7p/S5e / Ribosomal protein S9/S16 / Ubiquitin domain profile. / Ribosomal protein S9 signature. / Zinc-binding ribosomal protein / Ribosomal protein S5 domain 2-type fold, subgroup / G-protein beta WD-40 repeat / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Ribosomal protein S5 domain 2-type fold / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
40S ribosomal protein S17 / 40S ribosomal protein S15 / Small ribosomal subunit protein uS14 / Putative ribosomal protein S18 / Ribosomal protein S20 / Ubiquitin-like domain-containing protein / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS7c / Uncharacterized protein / 40S ribosomal protein S16 ...40S ribosomal protein S17 / 40S ribosomal protein S15 / Small ribosomal subunit protein uS14 / Putative ribosomal protein S18 / Ribosomal protein S20 / Ubiquitin-like domain-containing protein / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS7c / Uncharacterized protein / 40S ribosomal protein S16 / 40S ribosomal protein S28 / 40S ribosomal protein S25 / 40S ribosomal protein S12 / 40S ribosomal protein S19 / 30S ribosomal protein S3, chloroplastic
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsKravchenko OV / Baymukhametov TN / Afonina ZA / Vasilenko KS
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20186 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit.
Authors: Olesya V Kravchenko / Timur N Baymukhametov / Zhanna A Afonina / Konstantin S Vassilenko /
Abstract: Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has ...Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has been resolved to date; it especially concerns plant ribosomes and ribosomal subunits. Here, we report a high-resolution cryo-electron microscopy reconstruction of the small subunit of the (common wheat) cytoplasmic ribosome. A detailed atomic model was built that includes the majority of the rRNA and some of the protein modifications. The analysis of the obtained data revealed structural peculiarities of the 40S subunit in the monocot plant ribosome. We applied the 3D Flexible Refinement approach to analyze the internal mobility of the 40S subunit and succeeded in decomposing it into four major motions, describing rotations of the head domain and a shift in the massive rRNA expansion segment. It was shown that these motions are almost uncorrelated and that the 40S subunit is flexible enough to spontaneously adopt any conformation it takes as a part of a translating ribosome or ribosomal complex. Here, we introduce the first high-resolution structure of an isolated plant 40S subunit and the first quantitative analysis of the flexibility of small ribosomal subunits, hoping that it will help in studying various aspects of ribosome functioning.
History
DepositionNov 16, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18903.png

Downloads & links

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Map

FileDownload / File: emd_18903.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-5.601671 - 9.427519
Average (Standard dev.)0.0029629015 (±0.08703385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 412.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharp

Fileemd_18903_additional_1.map
Annotationsharp
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18903_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18903_half_map_2.map
Projections & Slices
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Sample components

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Entire : Small ribosomal subunit from Triticum aestivum (common wheat)

EntireName: Small ribosomal subunit from Triticum aestivum (common wheat)
Components
  • Complex: Small ribosomal subunit from Triticum aestivum (common wheat)
    • Protein or peptide: Plectin/eS10 N-terminal domain-containing protein
    • Protein or peptide: 40S ribosomal protein S12
    • Protein or peptide: 40S ribosomal protein S3
    • Protein or peptide: Small ribosomal subunit protein uS7c
    • Protein or peptide: 40S ribosomal protein S16
    • Protein or peptide: Ribosomal protein S20
    • Protein or peptide: 40S ribosomal protein S19
    • Protein or peptide: 40S ribosomal protein S25
    • Protein or peptide: 40S ribosomal protein S28
    • Protein or peptide: Small ribosomal subunit protein uS14
    • Protein or peptide: Ribosomal protein RACK1 subfamily. WD repeat G protein beta familyRibosome
    • Protein or peptide: Putative ribosomal protein S18
    • Protein or peptide: 40S ribosomal protein S15
    • Protein or peptide: 40S ribosomal protein S17
    • RNA: RNA (458-MER)
    • Protein or peptide: Ubiquitin-like domain-containing protein
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: POTASSIUM IONPotassium
  • Ligand: water

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Supramolecule #1: Small ribosomal subunit from Triticum aestivum (common wheat)

SupramoleculeName: Small ribosomal subunit from Triticum aestivum (common wheat)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Triticum aestivum (bread wheat) / Strain: Moskovskaya / Organ: seed / Tissue: germ / Location in cell: cytoplasm

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Macromolecule #1: Plectin/eS10 N-terminal domain-containing protein

MacromoleculeName: Plectin/eS10 N-terminal domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 20.463965 KDa
SequenceString:
MIISKKNRNE ICKYLFQEGV LYAKKDYNLA KHPQIDVPNL QVIKLMQSFK SKEYVRETFS WQHYYWYLTN DGIEFLRNFL NLPSEIVPA TLKKSARPPG RPLGSGPPGD RPRGPPRFEG DRPRYGDRDG YRGGPRGAPG DFGGEKGGAP AEFQPSFRSS G GGGFGRGG GGGFGRGGGG GGGFGASPME

UniProtKB: Plectin/eS10 N-terminal domain-containing protein

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Macromolecule #2: 40S ribosomal protein S12

MacromoleculeName: 40S ribosomal protein S12 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 15.364775 KDa
SequenceString:
MAEENAPVEV AAPVAAPTPV LGEPMDLMTA LQLVMKKSSA HDGLVKGLRE AAKAIEKHAA QICVLAEDCD QPDYVKLVKA LCAEHNVHL VTVPSAKTLG EWAGLCKIDS EGKARKVVGC SCVVVKDYGE DSEGLHIVQE YVKSH

UniProtKB: 40S ribosomal protein S12

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Macromolecule #3: 40S ribosomal protein S3

MacromoleculeName: 40S ribosomal protein S3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 25.39873 KDa
SequenceString: MATQISKKKK FVSDGVFYAE LNEMLTRELA EDGYSGVEVR VTPMRTEIII RATRTQNVLG EKGRRIRELT SVVQKRFNFP ENGVELYAE KVVNRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFVMES GAKGCEVIVS GKLRAQRAKS MKFKDGYMIS S GQPVNEYI ...String:
MATQISKKKK FVSDGVFYAE LNEMLTRELA EDGYSGVEVR VTPMRTEIII RATRTQNVLG EKGRRIRELT SVVQKRFNFP ENGVELYAE KVVNRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFVMES GAKGCEVIVS GKLRAQRAKS MKFKDGYMIS S GQPVNEYI DAAVRHVLLR QGVLGIKVKI MLDWDPKGKL GPTTPLPDLV TIHPPKEEDE LRPPALVEV

UniProtKB: 30S ribosomal protein S3, chloroplastic

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Macromolecule #4: Small ribosomal subunit protein uS7c

MacromoleculeName: Small ribosomal subunit protein uS7c / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 22.350879 KDa
SequenceString: MAVVEPVPGG DVKLFNRWTF EDVQVSDISL NDYLAVTSMK HYTFLPHSAG RYSAKRFRKA QCPIIERLTN SLMMHGRNNG KKIMAVRII KHTMEIIHLL TDANPIQIIV DAIINSGPRE DATRIGSAGV VRRQAVDISP LRRVNQAIYL LTTGARESAF R NVKTIAEC ...String:
MAVVEPVPGG DVKLFNRWTF EDVQVSDISL NDYLAVTSMK HYTFLPHSAG RYSAKRFRKA QCPIIERLTN SLMMHGRNNG KKIMAVRII KHTMEIIHLL TDANPIQIIV DAIINSGPRE DATRIGSAGV VRRQAVDISP LRRVNQAIYL LTTGARESAF R NVKTIAEC LADELINAAK GSSNSYAIKK KDEIERVAKA NR

UniProtKB: Small ribosomal subunit protein uS7c

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Macromolecule #5: 40S ribosomal protein S16

MacromoleculeName: 40S ribosomal protein S16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 16.856967 KDa
SequenceString:
MAAVLTRPTP GTVQCFGRKK TAVAVAYCKP GRGLIKVNGA PIELIRPEML RLKAFEPILL AGRSRFKDID MRIRVRGGGK TSQIYSIRQ AIAKSLVAYY QKYVDEAAKK EVKEIFGRYD RTLLVADPRR CEPKKFGGRG ARARFQKSYR

UniProtKB: 40S ribosomal protein S16

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Macromolecule #6: Ribosomal protein S20

MacromoleculeName: Ribosomal protein S20 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 14.128448 KDa
SequenceString:
MATELAYAPP MKSGKLGFEG TQEVQHRIRI TLSSKSVKNL EKVCSDLVKG AKEKQLKVKG PVRMPTKVLN ITTRKSPCGE GTNTWDRFE MRVHKRVIDL VSSPDVVKQI TSITIEPGVE VEVTISDQ

UniProtKB: Ribosomal protein S20

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Macromolecule #7: 40S ribosomal protein S19

MacromoleculeName: 40S ribosomal protein S19 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 17.097604 KDa
SequenceString:
MATVPAPAAE TAASTARTVK DVNPHEFVKA YSAHLKRSGK MELPEWVDIV KTARFKELPP SDADWYYIRA ASMARKIYLR QGIGIGGFQ KIYGGRQRNG SRPPHFCKSS GAVSRNILQE LQKMGIIDVD PKGGRLITSQ GRRDLDQVAG TVPAEF

UniProtKB: 40S ribosomal protein S19

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Macromolecule #8: 40S ribosomal protein S25

MacromoleculeName: 40S ribosomal protein S25 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 12.094188 KDa
SequenceString:
MAPKKEKAPA ASSKPAKSGG GKQKKKKWSK GKQKEKVNNA VLFDQATYDK LLTEVPKYKQ ITPSVLSERL RINGSLARRA IKDLMERGL IRMVSIHSSQ QIFTRATNT

UniProtKB: 40S ribosomal protein S25

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Macromolecule #9: 40S ribosomal protein S28

MacromoleculeName: 40S ribosomal protein S28 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 7.477787 KDa
SequenceString:
MDTQVKLAVV VKVMGRTGSR GQVTQVRVKF LDDQNRLIMR NVKGPVREGD ILTLLESERE ARRLR

UniProtKB: 40S ribosomal protein S28

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Macromolecule #10: Small ribosomal subunit protein uS14

MacromoleculeName: Small ribosomal subunit protein uS14 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 6.39244 KDa
SequenceString:
MGHSNVWNSH PKNYGAGSRV CRVCGNSHGL IRKYGLMCCR QCFRSDAKDI GFIKYR

UniProtKB: Small ribosomal subunit protein uS14

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Macromolecule #11: Ribosomal protein RACK1 subfamily. WD repeat G protein beta family

MacromoleculeName: Ribosomal protein RACK1 subfamily. WD repeat G protein beta family
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 36.200527 KDa
SequenceString: MAGAQESLVY AGVMRGHNDV VTAIATPIDN SPFIVSSSRD KSLLVWDLTN PIQATQDSSS EYGVPFRRLT GHGHFVQDVV LSSDGQFAL SGSWDGELRL WDLSTGVTTR RFVGHEKDVL SVAFSIDNRQ IVSASRDRTI KLWNTLGECK YTIGGDLGGG E GHTGWVSC ...String:
MAGAQESLVY AGVMRGHNDV VTAIATPIDN SPFIVSSSRD KSLLVWDLTN PIQATQDSSS EYGVPFRRLT GHGHFVQDVV LSSDGQFAL SGSWDGELRL WDLSTGVTTR RFVGHEKDVL SVAFSIDNRQ IVSASRDRTI KLWNTLGECK YTIGGDLGGG E GHTGWVSC VRFSPNNFAP TIVSGSWDRS VKVWNLTNCK LRCTLDGHGG YVSAVAVSPD GSLCASGGKD GVTLLWDLTE GK RLYSLDA GSIINSLCFS PNRYWLCAAT QDSIKIWDLE SKHIVQDLRP EVPVSTKQML YCTCLSWSAD GSTLYAGYTD GTI RIYKIS GFSYSS

UniProtKB: Uncharacterized protein

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Macromolecule #12: Putative ribosomal protein S18

MacromoleculeName: Putative ribosomal protein S18 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 17.702686 KDa
SequenceString:
MSLIAGEEFQ HILRVLNTNV DGKQKIMFAL TSIKGVGRRF SNIVCKKADI DMNKRAGELS AEEMDRLMAV VHNPRQFKVP DWFLNRKKD YKDGRFSQVV SNAVDMKLRD DLERLKKIRN HRGLRHYWGV RVRGQHTKTT GRRGKTVGVS KKR

UniProtKB: Putative ribosomal protein S18

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Macromolecule #13: 40S ribosomal protein S15

MacromoleculeName: 40S ribosomal protein S15 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 17.295375 KDa
SequenceString:
MADVDVDPEV AAAGPKKRTF RKFSYRGVDL DALLDMSTED LVQLFPARPR RRFSRGLKRK PMALVKKLRK AKSEAPAGEK PEQVRTHLR NMIIMPEMIG SVVGIYNGKC FNQVEIKPEM IGHYLAEFSL SYKPVKHGRP GIGATHSSRF IPLK

UniProtKB: 40S ribosomal protein S15

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Macromolecule #14: 40S ribosomal protein S17

MacromoleculeName: 40S ribosomal protein S17 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 16.47909 KDa
SequenceString:
MGRVRTKTVK KTSRQVIEKY YSRMTLDFHT NKKVLEEVSI LQSKRLRNKV AGFTTHLMRR IQRGPVRGIS LKLQEEERER RMDFVPEKS ALEVDEIRVD KETMDMLAFL GMADLPGVER APEATSAAAP YRQPFNGPRG GNRA

UniProtKB: 40S ribosomal protein S17

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Macromolecule #16: Ubiquitin-like domain-containing protein

MacromoleculeName: Ubiquitin-like domain-containing protein / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 17.692639 KDa
SequenceString:
MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLADYN IQKESTLHLV LRLRGGAKKR KKKTYTKPK KQKHKHKKVK LAVLQFYKVD DATGKVTRLR KECPNADCGA GTFMANHFDR HYCGKCGLTY VYNQKA

UniProtKB: Ubiquitin-like domain-containing protein

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Macromolecule #15: RNA (458-MER)

MacromoleculeName: RNA (458-MER) / type: rna / ID: 15 / Number of copies: 1
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 584.382812 KDa
SequenceString: UACCUGGUUG AUCCUGCCAG UAGUCAU(A2M)UG CUUG(PSU)CU(OMC)AA AGAUUAAGCC AUGCAUGUGC AAGUAUGA A CCAAUUUGAA CUGUGAAACU GCGAAUGGCU CAU(PSU)AAAUCA G(PSU)UAUAGUUU G(PSU)U(OMU)GAUGGU ACG UGCUAC ...String:
UACCUGGUUG AUCCUGCCAG UAGUCAU(A2M)UG CUUG(PSU)CU(OMC)AA AGAUUAAGCC AUGCAUGUGC AAGUAUGA A CCAAUUUGAA CUGUGAAACU GCGAAUGGCU CAU(PSU)AAAUCA G(PSU)UAUAGUUU G(PSU)U(OMU)GAUGGU ACG UGCUAC UCGGAUAACC GUAGUAAUUC UAG(A2M)GCUAA(OMU) ACGUGCAACA AACCCCGACU UCUGGGAGGG GCGCAU UUA (PSU)UAGAUAAAA GGCUGACGCG GGCUCUGCUC GCUGAUCC(OMG)A UGAUUCA(PSU)GA (PSU)AACUCGACG G AUCGCACG GCCUUCGUGC CGGCGACGCA UCA(PSU)UCAAA(PSU) U(PSU)CUGCCCUA UCAACUUUCG AUGGUAGGAU AGGGGCCUA CCAUGGUGGU GACGGG(PSU)GAC GGAGAAUUAG GGUUCGAUUC CGGAGA(OMG)GGA GCCUGAGAAA CGG CUACCA CAU(OMC)CAAGG(A2M) AGGCAGCAG(OMG) CGCGC(A2M)AAUU ACCCAAUCCU GACACGGGGA GGU(A2M) GUGAC AAUAAAUAAC AAUACCGGGC GCAUUAGUGU CUGGUAAUUG GAAUGAGUAC AAUCUAAAUC CCUUAACGAG G (A2M)UCCAUUG GAGGGCAAGU CUGGUGCCAG CAGCCGCGGU AAUUCCAGCU CCAAUA(OMG)CGU A(UY1)A(PSU) (PSU)UAAG UUG(OMU)UGCAGU U(A2M)AAAAGCUC GUAG(PSU)UGGAC CUUGGGCCGG GUCGGCCGGU CCGCCUCAC GGCGAGCACC GACCUACUCG ACCCUUCGGC CGGCAUCGCG CUCCUAGCCU UAAUUGGCCG GGUCGUGUUU CCGGCAUCGU UACUUUGAA GAAA(PSU)(PSU)AGAG UGCUCAAAGC AAGCCAUCGC UCUGGAUACA UU(A2M)GCA(PSU)GGG A (PSU)AACAUCA UAGGAUUCCG GUCCUAUUGU GUUGGCCUUC GGGAUCGGAG UAAUGAUUAA UAGGGACAGU CGGGGGCA U UCGUAUUUCA UAGUCAGAGG UGAAAUUCUU GGAUUUAUGA AAGACGAACA ACUGCGAAAG CAUUUGCCAA GGAUGUUUU CAUUAAUCAA GA(A2M)CGAAAGU UGGGGGCUCG AAGACGA(PSU)CA GAUACCG(OMU)CC UAGUCUCAAC CAUAAACG A UGCCGACCAG GGAUCGGCGG AUGUUGCUUA UAGGACUCCG CCGGCACC(PSU)U AUGAGAAAUC AAAG(PSU)CUUUG G G(PSU)UCCGGG GGGAGUA(PSU)GG UCGCAA(OMG)GCU GAAACUUAAA GGAAUUGACG GAAGGCACCA CCAGGCGUGG AGCC(PSU)GCGG CUUAAUU(PSU)GA CUCAACACGG GGAAACUUAC CAGG(PSU)(OMC)CAGA CAUAGCAAGG A (OMU)UGACAGA CUGAGAGCUC UUUCUUGAUU C(OMU)A(OMU)GGGUGG (OMU)G(OMG)UGCAUGG C(4AC)GUUCUU A GU(PSU)GGUG(OMG)AG CGA(PSU)UUG(PSU)CU GG(PSU)UAAUUCC GUUAACGA(A2M)C GAGA(OMC)CUCAG C CUGCUAAC UAGCUAUGCG GAGCCAUCC(OMC) (PSU)CCGCAGCUA GCU(OMU)CUUAGA GGGACUAUCG CCGUU(PSU) AGG CGACGGAAGU UUGAGGCAAU AACA(OMG)GUCUG (PSU)GAUGCCC(OMU)U AGAUGUUCUG GGCCGCACGC GCGCU ACAC (PSU)GAUGUAUUC AACGAGUAUA UAGCCUUGGC CGACAGGCCC GGGUAAUCUU GGGAAA(PSU)U(PSU)C AUCG UGAUG GGGAUAGAUC AUUGCAAUUG U(PSU)GGUCUUCA ACG(A2M)G(7MG)AAUG CCUAGUAAGC GCGAGUCA(PSU) CAGC(PSU)CGCGU (PSU)GACUACGUC CCUGCCCUU(PSU) GUACACACCG (OMC)CCGUCGCUC CUACCGAUUG AAUG GUCCG GUGAAGUGUU CGGAUCGCGG CGACGGGGGC GGUUCGCCGC CCCCGACGUC GCGAGAAGUC CAUUGAACCU UAUCA UUUA GAGGA(A2M)GGAG AAGUCGUA(6MZ)C AAGGUUUC(4AC)G UAGGUG(MA6)(MA6)CC UGCGGAAGGA UCAUUG

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Macromolecule #17: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 17 / Number of copies: 20 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #18: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #19: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 19 / Number of copies: 6 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #20: water

MacromoleculeName: water / type: ligand / ID: 20 / Number of copies: 357 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridSupport film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 10
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.1 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 0-32 / Number grids imaged: 1 / Number real images: 6201 / Average exposure time: 1.6 sec. / Average electron dose: 84.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 982063
Startup modelType of model: OTHER
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 256000
FSC plot (resolution estimation)

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