[English] 日本語
Yorodumi
- EMDB-64695: Cryo- EM structure of small subunit (body) of 75S ribosome with P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64695
TitleCryo- EM structure of small subunit (body) of 75S ribosome with P- tRNA from Entamoeba histolytica
Map data
Sample
  • Complex: Entamoeba histolytica SSU body with P-tRNA from 75S ribosome
    • Protein or peptide: x 17 types
    • RNA: x 3 types
KeywordsSSU-body / Entamoeba histolytica / Ribosome
Function / homology
Function and homology information


endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / cytosol
Similarity search - Function
PUA domain profile. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal ...PUA domain profile. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / : / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / : / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / Ribosomal protein S11 / RNA-binding S4 domain superfamily / Ribosomal protein S11 / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Ribosomal protein L23/L15e core domain superfamily / Zinc-binding ribosomal protein / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
40S ribosomal protein S13, putative / Ribosomal protein S14, putative / 40S ribosomal protein S21 / 40S ribosomal protein S15a, putative / 40S ribosomal protein S6 / 40S ribosomal protein S4, putative / 40S ribosomal protein S24, putative / Small ribosomal subunit protein uS2 / 40S ribosomal protein S23, putative / Small ribosomal subunit protein eS1 ...40S ribosomal protein S13, putative / Ribosomal protein S14, putative / 40S ribosomal protein S21 / 40S ribosomal protein S15a, putative / 40S ribosomal protein S6 / 40S ribosomal protein S4, putative / 40S ribosomal protein S24, putative / Small ribosomal subunit protein uS2 / 40S ribosomal protein S23, putative / Small ribosomal subunit protein eS1 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS5 / 40S ribosomal protein S8 / 40S ribosomal protein S11, putative / 40S ribosomal protein S7 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS27
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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

-
Structure visualization

Supplemental images

emd_64695.png

Downloads & links

-
Map

FileDownload / File: emd_64695.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 270 pix.
= 288.9 Å		1.07 Å/pix.
x 270 pix.
= 288.9 Å		1.07 Å/pix.
x 270 pix.
= 288.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5
Minimum - Maximum-4.36523 - 15.439314
Average (Standard dev.)0.000000000008893 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 288.90002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_64695_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64695_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Entamoeba histolytica SSU body with P-tRNA from 75S ribosome

EntireName: Entamoeba histolytica SSU body with P-tRNA from 75S ribosome
Components
  • Complex: Entamoeba histolytica SSU body with P-tRNA from 75S ribosome
    • Protein or peptide: 40S ribosomal protein S26
    • Protein or peptide: Small ribosomal subunit protein eS27
    • RNA: P-tRNA
    • RNA: mRNA
    • RNA: 17S rRNA
    • Protein or peptide: Small ribosomal subunit protein uS2
    • Protein or peptide: Small ribosomal subunit protein uS5
    • Protein or peptide: Small ribosomal subunit protein eS1
    • Protein or peptide: 40S ribosomal protein S4, putative
    • Protein or peptide: 40S ribosomal protein S6
    • Protein or peptide: 40S ribosomal protein S7
    • Protein or peptide: 40S ribosomal protein S8
    • Protein or peptide: Small ribosomal subunit protein uS4
    • Protein or peptide: 40S ribosomal protein S11, putative
    • Protein or peptide: 40S ribosomal protein S13, putative
    • Protein or peptide: Ribosomal protein S14, putative
    • Protein or peptide: 40S ribosomal protein S15a, putative
    • Protein or peptide: 40S ribosomal protein S21
    • Protein or peptide: 40S ribosomal protein S23, putative
    • Protein or peptide: 40S ribosomal protein S24, putative

+
Supramolecule #1: Entamoeba histolytica SSU body with P-tRNA from 75S ribosome

SupramoleculeName: Entamoeba histolytica SSU body with P-tRNA from 75S ribosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote) / Organelle: Ribosome / Location in cell: cytoplasmic

+
Macromolecule #1: 40S ribosomal protein S26

MacromoleculeName: 40S ribosomal protein S26 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 16.455373 KDa
SequenceString:
MTSKRRNNGR SKKGRGHTQN VRCSHCGRCV PKDKAIKRYQ IKNIVEAAAV RDISDNSALT KYKLPKTYMK LEYCVSCGIH GRVVRVRSR TDRRNRLPPK RVVKKTNKQQ AVKPSTEAVK VEIPADVVTA PKVAAQKERP FKYLQ

UniProtKB: 40S ribosomal protein S26

+
Macromolecule #2: Small ribosomal subunit protein eS27

MacromoleculeName: Small ribosomal subunit protein eS27 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 9.338131 KDa
SequenceString:
MPLIEVDLLN PTAASEAKAH KMKRLVPTPN SYFLEIKCPK CGATTTTFSH AHRQILCQKC GQPLGQPTGG KLKLTQQCKF RIKK

UniProtKB: Small ribosomal subunit protein eS27

+
Macromolecule #6: Small ribosomal subunit protein uS2

MacromoleculeName: Small ribosomal subunit protein uS2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 28.633951 KDa
SequenceString: MSKNVKTNFP DILKPSAEDI KMMVACRVHI GATNLNFAME EYVYERGNNN ECIFNLMKTW EKLSLAARVI AGISNETPSD VVAVAGREM AHRASLKFMK YTGCTAVAGR FTPGSFTNQI QKKFMEPRLI IVSDPSVDHQ ALRESGYINV PTIAFCNSDN S LKNVDIAI ...String:
MSKNVKTNFP DILKPSAEDI KMMVACRVHI GATNLNFAME EYVYERGNNN ECIFNLMKTW EKLSLAARVI AGISNETPSD VVAVAGREM AHRASLKFMK YTGCTAVAGR FTPGSFTNQI QKKFMEPRLI IVSDPSVDHQ ALRESGYINV PTIAFCNSDN S LKNVDIAI PCNNRSRLSI GLMWWMLTRE ILRYQGKLAR DEKWDVMVDL FLHRELDAKK DAPVIAGEEK VAKVEDKKAA SD ATVASTE WDDQKKN

UniProtKB: Small ribosomal subunit protein uS2

+
Macromolecule #7: Small ribosomal subunit protein uS5

MacromoleculeName: Small ribosomal subunit protein uS5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 27.737283 KDa
SequenceString: MDAKQQRGEK RQFGNRRGGR GAPRGRGARK DGASDGWTPV TKLGRLVKDG KVKSIDQIFE FGIKIKEYQI VDHLLPGLKE EVMTMQSVQ KQTSAGQRTR LKAYVAIGDH NGHAGLGVKC AKEVAEAIKG AMIQAKLAMV PVRRGYWGAT IGEVHTVPCK L TGACGSVR ...String:
MDAKQQRGEK RQFGNRRGGR GAPRGRGARK DGASDGWTPV TKLGRLVKDG KVKSIDQIFE FGIKIKEYQI VDHLLPGLKE EVMTMQSVQ KQTSAGQRTR LKAYVAIGDH NGHAGLGVKC AKEVAEAIKG AMIQAKLAMV PVRRGYWGAT IGEVHTVPCK L TGACGSVR VRLVPAPRGT GIVAAPTPKK FLILAGIEDV FTQTTGHTKT LGNFVKATYD AVRQSYGFQT KDLWKVGGVK QS PMDKYAK ILAESKKN

UniProtKB: Small ribosomal subunit protein uS5

+
Macromolecule #8: Small ribosomal subunit protein eS1

MacromoleculeName: Small ribosomal subunit protein eS1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 29.094215 KDa
SequenceString: MATGKNKKYK AGNVKKGSKR KIAEPFSKKE WYNVKVPKNF KRRTVGQIVV NKTAGTRIAS EQLKGRVVEV NLADLMENEK FGAYNYKFK CEDVNGKDCL MIFHGLKLTT DKLRSIVKKW CTLIETSVDV KTTDGHLIRI FCIGFTSRKS NQIKKTSYAK S AQIKKIRK ...String:
MATGKNKKYK AGNVKKGSKR KIAEPFSKKE WYNVKVPKNF KRRTVGQIVV NKTAGTRIAS EQLKGRVVEV NLADLMENEK FGAYNYKFK CEDVNGKDCL MIFHGLKLTT DKLRSIVKKW CTLIETSVDV KTTDGHLIRI FCIGFTSRKS NQIKKTSYAK S AQIKKIRK IMNNLITKEA ASRELTQFVD YLRENKLPKE IVAKCSKVFS MDNVYIRKVK ILKAGKIDSL KLLDQHQDTS AP VEAAPVA EEKGEVVEA

UniProtKB: Small ribosomal subunit protein eS1

+
Macromolecule #9: 40S ribosomal protein S4, putative

MacromoleculeName: 40S ribosomal protein S4, putative / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 36.830812 KDa
SequenceString: MARGPRHHLK RLNAPHHWML SKLGGTFAPK PSHGPHGMKE CLPLILILRN RLNYALNGRE VTMIVKNRTI KIDGKIRTDT RYPVGFMDV LSIPRTKENF RLMYNTKRRF CLVPLTAEQA KFKLCKIEKR VLGTGAIPYI VTHDGRTIRY PHPELQANDT I KLNLETGK ...String:
MARGPRHHLK RLNAPHHWML SKLGGTFAPK PSHGPHGMKE CLPLILILRN RLNYALNGRE VTMIVKNRTI KIDGKIRTDT RYPVGFMDV LSIPRTKENF RLMYNTKRRF CLVPLTAEQA KFKLCKIEKR VLGTGAIPYI VTHDGRTIRY PHPELQANDT I KLNLETGK IVDFVKFDIG NTAMMIGGNG MGRVGVIVKR EVHPGSFEIV HIKDAKGNTF TTRLNNVFVI GKGTETLVNL PL DKGIKKP LLQQVNETIK KNKMQKAGIQ KASKKSKTTT EKKVTPKAAV EKKEEQVEKI YKKYPKKQAA PKKSKGNKKV VPG KKIGKK

UniProtKB: 40S ribosomal protein S4, putative

+
Macromolecule #10: 40S ribosomal protein S6

MacromoleculeName: 40S ribosomal protein S6 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 29.822223 KDa
SequenceString: MKINVANPAT GRIKKFDFEE EKNYRPFLDK RIGQEVDASS LGDEFKGYIL KITGGCDKDG FPMMTGVATN NRVRLLLDGR NGCYKPLRN GERRRKTVRG AIVAGDISVL NTIVVKKGEG EIEGVTNDAL PMRAGPKRAS HIRKLFNLSQ KDDVKKFVIR R EVAKKHPK ...String:
MKINVANPAT GRIKKFDFEE EKNYRPFLDK RIGQEVDASS LGDEFKGYIL KITGGCDKDG FPMMTGVATN NRVRLLLDGR NGCYKPLRN GERRRKTVRG AIVAGDISVL NTIVVKKGEG EIEGVTNDAL PMRAGPKRAS HIRKLFNLSQ KDDVKKFVIR R EVAKKHPK EGKSTKRSKA PKIQRLVTPR RLQHKAQKLE AKKLHKIAML KEAKRYAAIL NRYKVLKAHG MKVVSFADTD AV FKQNKAG SKKAASKGKK VGSKKTGKK

UniProtKB: 40S ribosomal protein S6

+
Macromolecule #11: 40S ribosomal protein S7

MacromoleculeName: 40S ribosomal protein S7 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 21.999256 KDa
SequenceString: MSGKMTAAKS AARAQVSTEV VVKKPGFDAY SKLVKEAVAG IPELKGVKVI SAKKVTISKD KKATVIFIPL RMMRICRASF EKVIEALEK KLNGPVFIIG KRVVAHTKKV GQSGKTDYKP RSRTSKAVHE AYLNEMLYPV EVAGQRVHAT LVHKKVANSK T VFVAVDDA ...String:
MSGKMTAAKS AARAQVSTEV VVKKPGFDAY SKLVKEAVAG IPELKGVKVI SAKKVTISKD KKATVIFIPL RMMRICRASF EKVIEALEK KLNGPVFIIG KRVVAHTKKV GQSGKTDYKP RSRTSKAVHE AYLNEMLYPV EVAGQRVHAT LVHKKVANSK T VFVAVDDA KLKNSVKAKL PIYSAVYKNI TGEKVKFAFP VVA

UniProtKB: 40S ribosomal protein S7

+
Macromolecule #12: 40S ribosomal protein S8

MacromoleculeName: 40S ribosomal protein S8 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 27.017352 KDa
SequenceString: MGITRDSRHK RRATGGKKNS MQKKKKNTMG RQPANTRLGA IRVHDVRCRY GIIKRRALRL ENGNFSWASQ SITKGTKILN VVYNASDND FVRTNTLVKG AIIEIDPAPF RLWFLKFYGK DIASTDYYKS LESATFKTEK KVVVPKEEEN KEKTIAQQIA E TQVALMNP ...String:
MGITRDSRHK RRATGGKKNS MQKKKKNTMG RQPANTRLGA IRVHDVRCRY GIIKRRALRL ENGNFSWASQ SITKGTKILN VVYNASDND FVRTNTLVKG AIIEIDPAPF RLWFLKFYGK DIASTDYYKS LESATFKTEK KVVVPKEEEN KEKTIAQQIA E TQVALMNP SKTMQKKYAK KLEVLKNMKF DEALLEGFQS GRVLACISSR PGQTGSVEGY ILEGKELDFY SKKISDKKK

UniProtKB: 40S ribosomal protein S8

+
Macromolecule #13: Small ribosomal subunit protein uS4

MacromoleculeName: Small ribosomal subunit protein uS4 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 21.54848 KDa
SequenceString:
MGRCLRNHSI TYKTPKVPYE RERFDAELKL VGQFGLKNKK EIQRVHYMLG HMRTIAKVML MKDAKDPKRL LEGAALLRRL HNLGILPRD QNKLEFVLAL KEENLLERRL QTLVYRKGFA KSIHHARVLI RGKMIKVGKQ VVDVPSFLVR VESEPLIQLA D NTPLTNPE INGRRKRKNN HAGKEDN

UniProtKB: Small ribosomal subunit protein uS4

+
Macromolecule #14: 40S ribosomal protein S11, putative

MacromoleculeName: 40S ribosomal protein S11, putative / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 18.248143 KDa
SequenceString:
MAEQTERAYQ KQVFHHHSRN EKGEIDFGNV KRYHKQIGMG FVTPAEAIKG TYIDKKCPFT SDVSIRGRTL SGIVKSCHMK RTIIVRRDY FHYVSKYQRY EKRHKNIAVH CSPAFRQLKE GDHVVIGQCR PLSKTVRFNV LKFTSRGTGD KKQFAIF

UniProtKB: 40S ribosomal protein S11, putative

+
Macromolecule #15: 40S ribosomal protein S13, putative

MacromoleculeName: 40S ribosomal protein S13, putative / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 17.038281 KDa
SequenceString:
MGRMYNPGRG ISRRCIPYRR SAPSWLKTST LEVIDEMCKL AKKGIAPSQI GAIMRDTHGV GLVKSVTGSK VLRILKLAGL APKIPEDLY FLMKRAVSVR KHLEKNKKDK DAKYHLILIE SKIHRLTRYY KSAKVLEASF KYDANTASAI VS

UniProtKB: 40S ribosomal protein S13, putative

+
Macromolecule #16: Ribosomal protein S14, putative

MacromoleculeName: Ribosomal protein S14, putative / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 15.67012 KDa
SequenceString:
MSKKVAAKSN VPEVIPGSTK DAFGVAHIYA TFNDTFVHVT DISGKETIIR ITGGMRVKAD RDESSPYAAM TAAQDVAKRC KDLGVTSLH IKMRGEGGVY SKTPGPGAQA ALRALARANM KIGRIEDVTP IPTDCTKRKG GRRGRRL

UniProtKB: Ribosomal protein S14, putative

+
Macromolecule #17: 40S ribosomal protein S15a, putative

MacromoleculeName: 40S ribosomal protein S15a, putative / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 14.692098 KDa
SequenceString:
MVRVNVLADA LKSITNAEKQ GKRQVMIRPA SKVICEFLNV MMKHQYITDY TVVDTHRSGK IVVNLNGRLN KCAVISPRFN VTLSEFDKW EANLLPSRHF GALVLTTSYG ILDNTEARAK HTGGRILGFF Y

UniProtKB: 40S ribosomal protein S15a, putative

+
Macromolecule #18: 40S ribosomal protein S21

MacromoleculeName: 40S ribosomal protein S21 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 9.582097 KDa
SequenceString:
MASNKKIELY IPRHCSVTHT LIAADDHAAV QILVPHVNEN GVILPESTVY TVKGSVRKDG ISDHSLNRQF QKDGFLKTVV PKNMMI

UniProtKB: 40S ribosomal protein S21

+
Macromolecule #19: 40S ribosomal protein S23, putative

MacromoleculeName: 40S ribosomal protein S23, putative / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 15.745536 KDa
SequenceString:
MARGLHAARK MLAQRRANKW ADKEWKKGKL VTRYKCNPLG TASHAKGLVQ EKLGIETKQP NSGIRKCVRV RLLKNGKKIT AFVPRDGSL NYVNENDEVL ISGFGRRGHA VGDIPGVRFK VVCVAGVSLW GLWTNKKQKP HA

UniProtKB: 40S ribosomal protein S23, putative

+
Macromolecule #20: 40S ribosomal protein S24, putative

MacromoleculeName: 40S ribosomal protein S24, putative / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 16.302694 KDa
SequenceString:
MATQKSEVTI RTRNLIVNPL LCRKQVVVDI YHPGIVQPKF TEIKEKLAKM YKVKDVQTIV LNGFVTKYGG GKTSGFALIY DTLSALKKF VPKHQLIRAG LDKKTKAPRK ARKEHKKKWR MCHSFKDYKK KEMKKASRKK K

UniProtKB: 40S ribosomal protein S24, putative

+
Macromolecule #3: P-tRNA

MacromoleculeName: P-tRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 24.362412 KDa
SequenceString:
GACCUUAUAG CUCAGUCGGU AGAGCACGGG AUUUAUAAUC CCGGUGUCAU CGGUUCGAUU CCGAUUAAGG UCACCA

+
Macromolecule #4: mRNA

MacromoleculeName: mRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 1.861157 KDa
SequenceString:
UUAAUA

+
Macromolecule #5: 17S rRNA

MacromoleculeName: 17S rRNA / type: rna / ID: 5 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
Image processing

Particle selectionNumber selected: 142247
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.4) / Number images used: 53764
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)

-
Atomic model buiding 1

Initial model
PDB IDChain

5xxb

source_name: PDB, initial_model_type: experimental model

4ug0

source_name: PDB, initial_model_type: experimental model
SoftwareName: Coot
Detailsphenix.real_space_refinement
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 76.07
Output model

PDB-9v1j:
Cryo- EM structure of small subunit (body) of 75S ribosome with P- tRNA from Entamoeba histolytica

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more