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- EMDB-64720: Cryo- EM structure of small subunit (head) of 75S ribosome with A... -

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Basic information

Entry
Database: EMDB / ID: EMD-64720
TitleCryo- EM structure of small subunit (head) of 75S ribosome with A/P- & P/E- tRNAs from Entamoeba histolytica
Map data
Sample
  • Complex: Cryo-EM structure of SSU-head of 75S ribosome with A/P and P/E-tRNA from Entamoeba histolytica
    • Protein or peptide: x 12 types
    • RNA: x 1 types
KeywordsSSU-head of 75S Ribosome / A/P-tRNA / P/E-tRNA / Entamoeba histolytica / Ribosome
Function / homology
Function and homology information


inositol hexakisphosphate binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome ...inositol hexakisphosphate binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. ...Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S14/S29 / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / K homology domain-like, alpha/beta / Ribosomal protein S13-like, H2TH / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S5 domain 2-type fold, subgroup / Winged helix DNA-binding domain superfamily / Ribosomal protein S5 domain 2-type fold / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
40S ribosomal protein S3 / 40S ribosomal protein S10, putative / Ribosomal protein S29, putative / 40S ribosomal protein S28, putative / 40S ribosomal protein S17, putative / 40S ribosomal protein S16, putative / Small ribosomal subunit protein uS10 / 40S ribosomal protein S15, putative / 40S ribosomal protein S25 / Small ribosomal subunit protein uS7 ...40S ribosomal protein S3 / 40S ribosomal protein S10, putative / Ribosomal protein S29, putative / 40S ribosomal protein S28, putative / 40S ribosomal protein S17, putative / 40S ribosomal protein S16, putative / Small ribosomal subunit protein uS10 / 40S ribosomal protein S15, putative / 40S ribosomal protein S25 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS13
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSharma S / Mishra S / Gourinath S / Kaushal PS
Funding support India, 1 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR45101/DRUG/134/121/2022 India
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structure of ribosome from pathogenic protozoa Entamoeba histolytica reveals unique features of its architecture.
Authors: Shivani Sharma / Shalini Mishra / Samudrala Gourinath / Prem S Kaushal /
Abstract: Entamoeba histolytica, an anaerobic protozoan parasite, is the causative agent of amoebiasis, bloody diarrhea, and liver abscesses in humans. Amoebiasis is more predominant in tropical areas with ...Entamoeba histolytica, an anaerobic protozoan parasite, is the causative agent of amoebiasis, bloody diarrhea, and liver abscesses in humans. Amoebiasis is more predominant in tropical areas with poor sanitation conditions, and it remains the fourth leading cause of death due to a protozoan infection. E. histolytica life cycle spans between an infective 'cyst stage' and an active disease-causing 'trophozoite stage'. We have isolated ribosomes from the trophozoite stage of E. histolytica. Here, we report single particle cryo-EM structures of the 53S ribosome large subunit (LSU), and 75S associated ribosomes, with P-tRNA, A/P and P/E tRNAs, and with paromomycin antibiotic, at 2.8 Å to 3.4 Å resolution. The E. histolytica possesses a reduced ribosome with a conserved core, and the periphery evolved with species-specific unique features. The most notable features are the presence of the rRNA triple helix near the peptide exit tunnel, the expansion segment H88ES102 near the exit site on LSU, and unique insertions in r-proteins. Furthermore, the 75S ribosome paromomycin complex structure provides the atomic details of its interactions. These structures provide insights into the evolutionary adaptation of the E. histolytica translational machinery and may be explored further for amoebicidal therapeutic intervention.
History
DepositionMay 19, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64720.png

Downloads & links

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Map

FileDownload / File: emd_64720.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 210 pix.
= 224.7 Å		1.07 Å/pix.
x 210 pix.
= 224.7 Å		1.07 Å/pix.
x 210 pix.
= 224.7 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.6
Minimum - Maximum-4.5274568 - 15.011265
Average (Standard dev.)-0.000000000006664 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 224.70001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64720_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_64720_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of SSU-head of 75S ribosome with A/P and P/E-tR...

EntireName: Cryo-EM structure of SSU-head of 75S ribosome with A/P and P/E-tRNA from Entamoeba histolytica
Components
  • Complex: Cryo-EM structure of SSU-head of 75S ribosome with A/P and P/E-tRNA from Entamoeba histolytica
    • Protein or peptide: 40S ribosomal protein S25
    • Protein or peptide: 40S ribosomal protein S28, putative
    • Protein or peptide: Ribosomal protein S29, putative
    • RNA: 17S rRNA
    • Protein or peptide: 40S ribosomal protein S3
    • Protein or peptide: Small ribosomal subunit protein uS7
    • Protein or peptide: 40S ribosomal protein S10, putative
    • Protein or peptide: 40S ribosomal protein S15, putative
    • Protein or peptide: 40S ribosomal protein S16, putative
    • Protein or peptide: 40S ribosomal protein S17, putative
    • Protein or peptide: Small ribosomal subunit protein uS13
    • Protein or peptide: Small ribosomal subunit protein eS19
    • Protein or peptide: 40S ribosomal protein S20, putative

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Supramolecule #1: Cryo-EM structure of SSU-head of 75S ribosome with A/P and P/E-tR...

SupramoleculeName: Cryo-EM structure of SSU-head of 75S ribosome with A/P and P/E-tRNA from Entamoeba histolytica
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote) / Organelle: ribosome / Location in cell: cytoplasmic

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Macromolecule #1: 40S ribosomal protein S25

MacromoleculeName: 40S ribosomal protein S25 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 14.794739 KDa
SequenceString:
MPPKDAKGKG AASGKKGALT KPKKSSGGKA PKKSWSKTKV KEKLNNAVLF DKATLDKCTK EVPSMKVITP AVVADRMKIT CSLAKILLK DLEKKELIVP VKVDNHIWIY TRSAKHAAAA PTEAEKKPAK GSKKQVKA

UniProtKB: 40S ribosomal protein S25

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Macromolecule #2: 40S ribosomal protein S28, putative

MacromoleculeName: 40S ribosomal protein S28, putative / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 7.745989 KDa
SequenceString:
MSTQVTETPV IYAQVTEILG RTGSRGGVLQ VRCDIMGENR QILRNVKGPI RVGDILTLLE AEREARRLR

UniProtKB: 40S ribosomal protein S28, putative

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Macromolecule #3: Ribosomal protein S29, putative

MacromoleculeName: Ribosomal protein S29, putative / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 6.472543 KDa
SequenceString:
MGSYSIYNAH PRNYGNGSRT CRKCGARKGL IRKYGLDLCR RCFREKAVEI GFQKLD

UniProtKB: Ribosomal protein S29, putative

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Macromolecule #5: 40S ribosomal protein S3

MacromoleculeName: 40S ribosomal protein S3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 26.97765 KDa
SequenceString: MFCLTKTKAL NVDVLKTNIS RKHKFVADGV FYAELNELLQ RELSADGYSG VEVRKNGSKF QIIIRATRTT NIIGDKGRRI HELTNLLIA RFGFPKDKIE LYVEKVLARG LCPVSQAESI KYKIAEGLPV RRAVGSVMRL IMDSGAKGCE VSISGKLRGQ R AQGMVFKE ...String:
MFCLTKTKAL NVDVLKTNIS RKHKFVADGV FYAELNELLQ RELSADGYSG VEVRKNGSKF QIIIRATRTT NIIGDKGRRI HELTNLLIA RFGFPKDKIE LYVEKVLARG LCPVSQAESI KYKIAEGLPV RRAVGSVMRL IMDSGAKGCE VSISGKLRGQ R AQGMVFKE GYMIKSGNAT RQFYSSAVRC VLLRMGIIGI KVTIMLDTDP SGKNGPAARI PDVVEIKTPK DESTTVKTEV IP ANKQ

UniProtKB: 40S ribosomal protein S3

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Macromolecule #6: Small ribosomal subunit protein uS7

MacromoleculeName: Small ribosomal subunit protein uS7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 23.07292 KDa
SequenceString: MAEAVAQPVE TVAHTFAPKL FNKWSYDVTV SDISLKELLA INSKLKYQVF LPHTAGRYQI KPFRKIQCPI VERLVCCMMQ HGKNSGKKL LAMRVVEESF EIIHLLTEKN PIQVLVDAII NASPREDSTR VGTGGNAKRQ AVDVSPLRRI NQALYLMTMG C RSAAFRNS ...String:
MAEAVAQPVE TVAHTFAPKL FNKWSYDVTV SDISLKELLA INSKLKYQVF LPHTAGRYQI KPFRKIQCPI VERLVCCMMQ HGKNSGKKL LAMRVVEESF EIIHLLTEKN PIQVLVDAII NASPREDSTR VGTGGNAKRQ AVDVSPLRRI NQALYLMTMG C RSAAFRNS KTLAECLADE IVNASKSNTA SFAIKKKEDM ERVAKSNR

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #7: 40S ribosomal protein S10, putative

MacromoleculeName: 40S ribosomal protein S10, putative / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 14.575251 KDa
SequenceString:
MRIATKDIIA IYKQLFNDGC IVCHKDFVCL HPVFGIPNLQ VFMLMKGLAT KKCVKETCNW RCLYWTLNDE GIAYLRQKLA LPEDAVPST LKQSIHTAVH DEAKQIQGER KLKKDFNAGK KPEMKKAE

UniProtKB: 40S ribosomal protein S10, putative

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Macromolecule #8: 40S ribosomal protein S15, putative

MacromoleculeName: 40S ribosomal protein S15, putative / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 16.405531 KDa
SequenceString:
MSETVAKKRT FKKFELQGKS LEEITAMPEA DFVKMLDARA RRSYRRSPKL KHERLVKKLL KIKKATKEGE KPKLVKTHCR DKIILPNMI GSVIGVYNGK SFTTVEIKPE MLGHYLGEFS ITYKPVTHGR PGVGATHSSK FVPLK

UniProtKB: 40S ribosomal protein S15, putative

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Macromolecule #9: 40S ribosomal protein S16, putative

MacromoleculeName: 40S ribosomal protein S16, putative / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 17.547773 KDa
SequenceString:
MSATVKATGK TQKKHTEALK SVQVFGKKKT AIAVCLCKEG KGMIRVNGVP LDLINPPVLR IKVFEPLFIV GKENYAKLDL KIRVTGGGQ VAQAYAIRQA IAKALIAYNQ KFVDETTKNE LKAKFLEYDR TLLVADPRRC EAKKFGGPGA RAKYQKSYR

UniProtKB: 40S ribosomal protein S16, putative

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Macromolecule #10: 40S ribosomal protein S17, putative

MacromoleculeName: 40S ribosomal protein S17, putative / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 13.61797 KDa
SequenceString:
MGGVRTKTVK RAARNIIEKY YPLLTLDFHT NKRVVDEVAV VETKRLRNKI AGFITHLMRR IQKGPVRGIS FKLQEEERER RDNYVPEKS EVNIDKITAD PVTLKMLESI GMPINKKN

UniProtKB: 40S ribosomal protein S17, putative

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Macromolecule #11: Small ribosomal subunit protein uS13

MacromoleculeName: Small ribosomal subunit protein uS13 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 17.698568 KDa
SequenceString:
MATVTSESEF QHMLRVCNTN LDGRRKVPYA LTGIKGCGRR YAYLVCKRAG IDVNKRAGLM TPAEIEKIVD ILNNPLNYKI PVWFLNRQK DNKDGKDSQL IANAVETRLR EDIEALKKMR AHRGLRHYWG LRVRGQHTKT TGRRGRTVGV SRTKGA

UniProtKB: Small ribosomal subunit protein uS13

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Macromolecule #12: Small ribosomal subunit protein eS19

MacromoleculeName: Small ribosomal subunit protein eS19 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 17.776846 KDa
SequenceString:
MHHFSNIKDV VAIDFIKAYA EHLKKSGKLE IPEWVDTVKT GMCKELAPLN PDWIYIRAAA IARKVYLNNG IGVMALRRAY GDQYNKHYN PSHRTLGSGK VNRYILQQLE KMGIVAKIQS GRSLTKEGRK DMDKIAFQVY KEHEAKVTPM ILMPMN

UniProtKB: Small ribosomal subunit protein eS19

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Macromolecule #13: 40S ribosomal protein S20, putative

MacromoleculeName: 40S ribosomal protein S20, putative / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 13.258735 KDa
SequenceString:
MANIKKDIKA PVTPKVYKNI TITITSTKVK AVESLCAEVK ENGKKKGVQV KGPVRIPTKT LRITTRKTPC GEGSKTWDHY QMRIYKRVL SMKTTPETVK EITSLKVEPG VELEVAMFD

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #4: 17S rRNA

MacromoleculeName: 17S rRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 628.40175 KDa
SequenceString: UAUCUGGUUG AUCCUGCCAG UAUUAUAUGC UGAUGUUAAA GAUUAAGCCA UGCAUGUGUA AGUAUAAAGA CCAAGUAGGA UGAAACUGC GGACGGCUCA UUAUAACAGU AAUAGUUUCU UUGGUUAGUA AAAUACAAGG AUAGCUUUGU GAAUGAUAAA G AUAAUACU ...String:
UAUCUGGUUG AUCCUGCCAG UAUUAUAUGC UGAUGUUAAA GAUUAAGCCA UGCAUGUGUA AGUAUAAAGA CCAAGUAGGA UGAAACUGC GGACGGCUCA UUAUAACAGU AAUAGUUUCU UUGGUUAGUA AAAUACAAGG AUAGCUUUGU GAAUGAUAAA G AUAAUACU UGAGACGAUC CAGUUUGUAU UAGUACAAAA UGGCCAAUUC AUUCAAUGAA UUGAGAAAUG ACAUUCUAAG UG AGUUAGG AUGCCACGAC AAUUGUAGAA CACACAGUGU UUAACAAGUA ACCAAUGAGA AUUUCUGAUC UAUCAAUCAG UUG GUAGUA UCGAGGACUA CCAAGAUUAU AACGGAUAAC GAGGAAUUGG GGUUCGACAU CGGAGAGGGA GCUUUACAGA UGGC UACCA CUUCUAAGGA AGGCAGCAGG CGCGUAAAUU ACCCACUUUC GAAUUGAAGA GGUAGUGACG ACACAUAACU CUAGA GUUG AGUAAAAUCA AUUCUUGAAG GAAUGAGUAG GAGGUAAAUU CUCCUACGAA AUCAAUUGGA GGGCAAGUCU GGUGCC AGC AGCCGCGGUA AUUCCAGCUC CAAUAGUGUA UAUUAAAGUU GCUGUGAUUA AAACGCUCGU AGUUGAAUUA AAAUGUG GU UUUAUACAUU UUGAAGACUU UAUGUAAGUA AAGUUUCUAG AAAUGUUAAA UUAAAAUCAA AGAAGGAAAC AAUUCAAG U AAUUGAGUUG UUAUUACUUU GAAUAAAAUA AGGUGUUUAA AGCAAAACAU UAUGUUAAUG AAUAUUCAAG CAUGGGACA AUGCUGAGGG GAUGUCAAUA AGACAUUUCG AGAGAAGGAU UAAAAGGAAC AAUUGGGGUG AUUCAGAAAA UAACGGGAGA GGUGAAAAU CCAUGAUCGC UAUAAGAUGC ACGAGAGCGA AAGCAUUUCA CUCAACUGUG UCCAUUAAUC AAGAACGAAA G UUAGGGGA UCGAAGACGA UCAGAUACCG UCGUAGUCCU AACUAUAAAC GAUGUCAACC AAGGAUUGGA UGAAAUUCAG AU GUACAAA GAUAGAGAAG CAUUGUUUCU AGAUCUGAGU AUAUCAAUAU UACCUUGUUC AGAACUUAAA GAGAAAUCUU GAG UUUAUG GACUUCAGGG GGAGUAUGGU CACAAGGCUG AAACUUAAAG GAAUUGACGG AAGGGCACAC CAGGAGUGGA GCCU GCGGC UUAAUUUGAC UCAACACGGG AAAACUUACC AAGACCGAAC AGUAGAAGGA AUGACAGAUU AAGAGUUCUU UCAUG AUUU AUUGGGUAGU GGUGCAUGGC CGUUCUUAGU UGGUGGAGUG AUUUGUCAGG UUAAUUCCGG UAACGAACGA GACUGA AAC CUAUUAAUUA GUUUUCUGCC UAUAAGACAG AAAUGUUCGC AAGAACAGGU GCGUAAGUAC CACUUCUUAA AGGGACA CA UUUCAAUUGU CCUAUUUUAA UUGUAGUUAU CUAAUUUCGG UUAGACCUCU UUUAACGUGG GAAAAAGAAA AAGGAAGC A UUCAGCAAUA ACAGGUCUGU GAUGCCCUUA GACAUCUUGG GCCGCACGCG CGCUACAAUG GAGUUACUAG AGAGUAUUU UAUCAUUUAC ACCUUAUUUA UUAGGCUUUG UCUAAUAAUU AAGGAUAGUA AGUGGUGUAC CGAGAUUGAA AUAGUUAAGG AAAACUCAA AAGAACGUAC AUGACAGGGA UAAAUGAUUG GAAUUAUUUG UUUUGAACGA GGAAUUCCUU GUAAUAUCGA G UCAUUAAC UCGAGAUGAA UACGUCCCUG CCCUUUGUAC ACACCGCCCG UCGCUCCUAC CGAUUGAAUA AAGAGGUGAA AU UCUAGGA UUCUGUCUUA UAGAUAGAAA AAUGGAUUUA AAUCUCCUUA UUUAGAGGAA GGAGAAGUCG UAACAAGGUU UCC GUAGGU GAACCUGCGG AAGGAUCAUU A

GENBANK: GENBANK: BDEQ01000001.1

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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

Concentration1 mg/mL
BufferpH: 7.4
Details: 20nM HEPES-sodium salt buffer pH 7.4, 100mM Potassium acetate, 10mM Magnesium acetate, 10mm Ammonium acetate, 3mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 290 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 11840 / Average exposure time: 2.0 sec. / Average electron dose: 1.106 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 142247
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

2660

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.4) / Number images used: 39958
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.4)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
source_name: Other, initial_model_type: otherthe coordinates of 75S with P-tRNA was used
source_name: Other, initial_model_type: otherthe coordinates of 75S with P-tRNA was used
SoftwareName: Coot
Detailsphenix.real_space_refinement
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 56.93
Output model

PDB-9v28:
Cryo- EM structure of small subunit (head) of 75S ribosome with A/P- & P/E- tRNAs from Entamoeba histolytica

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