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- EMDB-62893: State G of archaeal pre-50S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-62893
TitleState G of archaeal pre-50S ribosome
Map dataState G_halfA
Sample
  • Complex: State G of archaeal pre-50S ribosome
    • RNA: x 2 types
    • Protein or peptide: x 23 types
  • Protein or peptide: x 6 types
  • Ligand: x 5 types
KeywordsState G of archaeal pre-50S ribosome / RIBOSOME
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / nucleotide binding / DNA repair / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
: / Ribosomal protein L40e, archaeal / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L19e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal ...: / Ribosomal protein L40e, archaeal / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L19e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, archaeal / : / : / Ribosomal protein L7Ae, archaea / DNA repair Rad51/transcription factor NusA, alpha-helical / SAM-like Helix-hairpin-helix tandem / : / Ribosomal L15/L27a, N-terminal / : / Ribosomal protein L23 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L2, archaeal-type / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L10e / Ribosomal L40e family / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L44e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L44 / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L19 / Ribosomal protein L13, eukaryotic/archaeal / : / Ribosomal protein L18e / : / : / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal_L15e / Ribosomal protein L32e / Ribosomal protein L37ae/L37e / Ribosomal protein L32e superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 ...Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL18
Similarity search - Component
Biological speciesHaloferax mediterranei ATCC 33500 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.07 Å
AuthorsLi ZQ / Yang XY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32301015 China
CitationJournal: To Be Published
Title: State G of archaeal pre-50S ribosome
Authors: Li ZQ / Yang XY
History
DepositionDec 29, 2024-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62893.png

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Map

FileReleased
AnnotationState G_halfA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 640 pix.
= 427.52 Å		0.67 Å/pix.
x 640 pix.
= 427.52 Å		0.67 Å/pix.
x 640 pix.
= 427.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-2.481007 - 5.534702
Average (Standard dev.)-0.0029830823 (±0.13455734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 427.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: State G halfA

Fileemd_62893_half_map_1.map
AnnotationState G_halfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: State G halfB

Fileemd_62893_half_map_2.map
AnnotationState G_halfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : State G of archaeal pre-50S ribosome

EntireName: State G of archaeal pre-50S ribosome
Components
  • Complex: State G of archaeal pre-50S ribosome
    • RNA: 23S RNA
    • RNA: 5S RNA
    • Protein or peptide: Large ribosomal subunit protein uL15
    • Protein or peptide: Large ribosomal subunit protein eL8
    • Protein or peptide: Large ribosomal subunit protein uL16
    • Protein or peptide: Large ribosomal subunit protein eL15
    • Protein or peptide: Large ribosomal subunit protein eL18
    • Protein or peptide: Large ribosomal subunit protein uL18
    • Protein or peptide: Large ribosomal subunit protein eL19
    • Protein or peptide: Large ribosomal subunit protein eL21
    • Protein or peptide: Large ribosomal subunit protein uL22
    • Protein or peptide: Large ribosomal subunit protein eL24
    • Protein or peptide: Large ribosomal subunit protein uL24
    • Protein or peptide: Large ribosomal subunit protein uL30
    • Protein or peptide: Large ribosomal subunit protein eL31
    • Protein or peptide: Large ribosomal subunit protein eL32
    • Protein or peptide: Large ribosomal subunit protein eL43
    • Protein or peptide: Large ribosomal subunit protein eL37
    • Protein or peptide: Large ribosomal subunit protein eL42
    • Protein or peptide: Large ribosomal subunit protein uL2
    • Protein or peptide: Large ribosomal subunit protein uL3
    • Protein or peptide: Large ribosomal subunit protein uL4
    • Protein or peptide: Large ribosomal subunit protein uL5
    • Protein or peptide: Large ribosomal subunit protein uL6
    • Protein or peptide: Large ribosomal subunit protein uL13
  • Protein or peptide: Large ribosomal subunit protein eL40
  • Protein or peptide: Large ribosomal subunit protein uL23
  • Protein or peptide: Large ribosomal subunit protein uL29
  • Protein or peptide: Large ribosomal subunit protein uL14
  • Protein or peptide: Large ribosomal subunit protein eL20
  • Protein or peptide: Large ribosomal subunit protein eL39
  • Ligand: beta-D-glucopyranose
  • Ligand: SPERMIDINE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: State G of archaeal pre-50S ribosome

SupramoleculeName: State G of archaeal pre-50S ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)

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Macromolecule #1: 23S RNA

MacromoleculeName: 23S RNA / type: rna / ID: 1
Details: PSU, UR3, 1MA and 6MZ are chemically modified rRNA residues.
Number of copies: 1
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 944.122375 KDa
SequenceString: UAUAUCAACU GGCUACUGUG CCAGCUGGUG GAUAGC(PSU)CGG CUCGAGAGCC GAUGACGGAC GUGCCAAGCU GCGA (UR3)AAGC CUCAGGGACC CGCAUGGAGG GAAAGAACUG AGGAUCUCCG AAUGGGAAUC CCCACAGCAA UUGCCUAGCG C AAUGGGGA ...String:
UAUAUCAACU GGCUACUGUG CCAGCUGGUG GAUAGC(PSU)CGG CUCGAGAGCC GAUGACGGAC GUGCCAAGCU GCGA (UR3)AAGC CUCAGGGACC CGCAUGGAGG GAAAGAACUG AGGAUCUCCG AAUGGGAAUC CCCACAGCAA UUGCCUAGCG C AAUGGGGA ACGUUCCGAA UUGAAACAUC UUAGUAGGAA CAGGAAAAGA AAGCAAUCCG CGAUGUCGUU AGUAACGGCG AG UGAACGC GAUACAGUCC AAACCGAAGC CUUCGGGCAA UGUGGUGUAC GGACUACCCA UAACGGACCU GGAAUUCACA CGA AGUCUC CUGGAACGGA GCGUGAUACA GGGUGAAAAC CCCGUAGUGU GAAGGAAAGA UCCCGGGGUU GUUCCAGAAU AGCG GGGGU UGGAUAUCCC UCGUGAAUUA CGCAGGCAUC AACUGCGAAG ACUAAACACU CCUCGAGACC GAUAGCGAAC AAGUA GCGU GAGCGAACGC UGAAAAGCAC CCCGAAAAGG GCGGUGCAAU AGGGCUUGAA AUCAGUUGGC GAUAGAGCGA UAUAGC AUA CAAGGUCGUC UGACGAAUGA CCUAGAAGCG AUUCUACAGU AAGACUCAGA CGAAGCCGAU GUUAUAUCGU ACGUUUU G(1MA) AAAACGAACC AUGGAGUGCA UCUGACUGGC GAGUCUAAGG GGAGAACCCC CGGAGGCAUA GGGAA(6MZ)CCGA UACGGCCGC AGUCUUUGAC CAGGGCCACC GUCUUCAAGG GCGGGGAGCC AACCGGAUGC GACCCGAAAC CAAGUGAUCU A CGCCGGAG CAGGGCGAAG CGUGGCGAAA GCUGCGUGGA GGCCCGUUAG AGUUGGUGUC CUACAAUACC CUCUCGUGAC UC UGGUGUA GGGGUGAAAG GCCCAUCGAA CUUGGCAACA GCUGGUUCCA ACCGAAACAU GUCGAAGCAU GACC(PSU)CUGA UGAGAUAGUC CGUGAGGUAG AGCGACCGAU UGGGAAUCCG GCCUCCGAGA GGAGUUCGCU UCCCUGUCAA ACUCCAAACU UACGGACAU CGUAGACUCA GGGAGUCCGG UGUGCGGGGU AAGCUUGUGC ACCGUGAGGG AGACAACCCA GAGCCAGGUU A AGGACCCA AAGUGUGGAU UAAGUGUGAU CGAAGAUUGU CUCGAGCCCU AAACAGCCGG GAGGUGAGCU UAGAAGCAGC UA CCCUCUA AGAAUAGCGU AACAGCUUAC CGGCCGAGGU UCGAGGCGUC GAAAAUGAUC GGGACUCAAA UCCACCUCCG AGA CCUGGC GGCGUGCUAU UUAGCACGAU UCCGUAGGUU GGCAUACUGC AUGGACGGAA GUACGGGUGA GAACUCGUAU GGAC CGUGC AGCAACGAAA AUCAUGGUCU CAGUAGCAGC GAGAGUCGGG UGUGAACCCC GACGACCUUA CGCGCAAGGG UUCCU CGGC ACUGUCAAUC AGCCGAGGGU UAGUCGAUCC UAAGUCUAUC CGUAAUUCGA AAUAGAUGAA AGGGAAACUG GUUAAU AUU CCAGUACCUU CUUGCAAUAA AAGUCGACGC UUUAGGAAAC ACCGAGCGGG GCCUUCGCCC CGUCGAAUCA CCGAACU UC GUGGAAGCCG UAAUGGCACG AAGCGAAAGA AUGGUGAGAU AGGGAAACUC GGCGGUACCU AGAGCCCGUG AAAAGACA A GCAAGAAGCU CGUACCGAGA UCCGACACAG GUGCGCUGGC AGAGUAAGCC AAGGUCUGUC GGGAUCAACC GACGUUAGG GAAUUCGGCA AGUUAGUCCC GUAAGUUCGC GAUAAGGGAU ACCUGCUCUU GAUAGAGCAG GUCGCAGUGA CUCGGACGCU CCGACUGUC UAGUAACAAC AUAGGUGACC GCAAAUCCGC AAGGACUCGU ACGGUCACUG AAUCCUGCCC AGUGCGGGUA U CUGAACAC CCAUUACAAU GGGACGAAGG ACCCGUCAAC GGCGGGGGUA ACUAUGACCC UCUUAAGGUA GCGUAGUACC UU GCCGCUU CAGUAGCGGC UUGCAUGAAU GGAUCAACGA GAGCGUCACU GUCCCAACGU UGGGCCCGGU GAACAGUACG UUC CAGUGC GGAGUCUGGA GACCCCCAAG GGGAAGCGAA GACCCUAUAG AGCUUUACUG CAGGCUGUCG CUGAGACGUG GUCG CUAAU GUGCAGCAUA GGUAGGAGCC GUUACACAGG UACCCGCGCC AGCGGGCCAC CGAGGCAGCA UUGAAAUACU ACCCG UUAG UGACUGCGAC UCUCACUCCU GGCGGAGGAC ACCGGUAGCC GGGCAGUUUG ACUGGGGCGG UACGCGCUCG AAAAGA UAU CGAGCGCGCC CAAAGAUUUC CUCACGCGAG UCGGGAACUC GUGGAAGAGC GCAAGAGCAA ACGGAAGUCU GACAGUG AC AUUCCCAACG AGUGUCGCUG ACGCGAAAGC GUGGUCUAGC GAACCUACGA GGUUCAUUCA UGGGACCCGU AGAUGACA G AAAAGCUACC UUAGGGAUAA CAGAGUCGUC ACCCGCAAGA GCACAUAUCG ACCGGGUGGC UUGCUACCUC GAUGUCGGU UCCCUCCAUC CUGCCUGUGC AGAAGCAGGC AAGGGUGAGG UUGUUCGCCU AUUAAAGGAG G(PSU)CGUGAGCU GGG (UR3)UUAGA CCGUCGUGAG ACAGGUCGGC UGCUAUCUAU UGGGGGUGCU AAGGAACUUG ACGUGAACGU UCGUAUAGUA CGAGAGGAA CUACGAAUGG GUGCCACUGG UGUACCGGU(PSU) GUCCGAGAGG GCAGUUGCCG GGCAGCUACG CACCGCA GG GUAAGAGCUG AAAGCAUCUA AGCUCGAAAC CUACACGGAA AAGAAGUUCC ACUGAGGUCA CUCGUAGAAG ACGAGUUC G AUAGACUCGG GGUGUACGUG UCGAGGCAAC GAGACAUUAA GCCCGCGAGC ACUAACAGAC CAAGCCACAU UC

GENBANK: GENBANK: CP001868.2

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Macromolecule #2: 5S RNA

MacromoleculeName: 5S RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 39.188254 KDa
SequenceString:
UACGGCGGCC AGAGCGGUGA GGUUCCACCC GUACCCAUCC CGAACACGGA AGUUAAGCUC GCCUGCGUUC UGGUCAGUAC UGGAGUGAG CGAUCCUCUG GGAAAUCCAG UUCGCCGCCC CUA

GENBANK: GENBANK: CP007551.1

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Macromolecule #3: Large ribosomal subunit protein uL15

MacromoleculeName: Large ribosomal subunit protein uL15 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 18.16452 KDa
SequenceString:
MTSKKRRQRG SRTHSGGTHK NRRGAGHRGG RGRAGRDKHE YHHYEPRGKH GFKRPDSLQD TVAEVKIQKL DEDAALLAAD GVAEKDGDA YTIDARDVAE DGWDVDVVKV IGGGQVRNEL NVVADAFTAG AVELIEEAGG SADLSERAEE AAEAEAEEAE A DADEDDEE

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #4: Large ribosomal subunit protein eL8

MacromoleculeName: Large ribosomal subunit protein eL8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 12.659957 KDa
SequenceString:
MAVYVDFDVP ADLADSAVEA LEVARDTGIV KKGTNETTKS IERGNAQLVL IAEDVSPEEI VMHLPELADE KGIPFLFVET QDDIGHAAG LEVGSAAAAI VDAGEASDDV EDIATKVEDL R

UniProtKB: Large ribosomal subunit protein eL8

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Macromolecule #5: Large ribosomal subunit protein uL16

MacromoleculeName: Large ribosomal subunit protein uL16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 19.814604 KDa
SequenceString:
MSDKPASMYR EIKNPAYTRR EYITGIPGSK IAQHNMGDLQ ADPEDYPVEI SLEVEEDVQI RHGSLESARL SANRLMLKNA GEKQYKMIL RKFPHHVIRE NKQATGAGAD RVSDGMRQSF GKVVGTAARI PKGETVFTIY CDVEDAEIAK DAFRRAYNKM S PPCRIVVE RGEELLVA

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #6: Large ribosomal subunit protein eL15

MacromoleculeName: Large ribosomal subunit protein eL15 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 22.703906 KDa
SequenceString: MARSFYSHIK EAWKTPKEGK LAELQWQRKQ EWRNQGAIER IERPTRLDKA RELGYKAKQG IVVVRVSVRK GGARKQRHKA GRRTKRQGV NRIGRRKSIP RIAEERASRK YPNMRVLNSY GVGQDGSQKW QEVILVDPNH PAIQNDDDLN WICNDDHDGR A FRGLTNAG ...String:
MARSFYSHIK EAWKTPKEGK LAELQWQRKQ EWRNQGAIER IERPTRLDKA RELGYKAKQG IVVVRVSVRK GGARKQRHKA GRRTKRQGV NRIGRRKSIP RIAEERASRK YPNMRVLNSY GVGQDGSQKW QEVILVDPNH PAIQNDDDLN WICNDDHDGR A FRGLTNAG KRGRGLQNRG KGTEHIRPSL SSSRRRGK

UniProtKB: Large ribosomal subunit protein eL15

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Macromolecule #7: Large ribosomal subunit protein eL18

MacromoleculeName: Large ribosomal subunit protein eL18 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 12.754392 KDa
SequenceString:
MSKTNPRLKS LIAELKAVSR ESGANVWQDV ADRLEKPRRT HAEVNLGRIE RYAQEDETVV VPGKVLGSGV LQKNVTVAAV DFSSTARTK IEQVGDVVTL EQLAEQNPDG SNVRVIR

UniProtKB: Large ribosomal subunit protein eL18

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Macromolecule #8: Large ribosomal subunit protein uL18

MacromoleculeName: Large ribosomal subunit protein uL18 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 20.208398 KDa
SequenceString:
MATGPRYKVP MRRRREVRTD YHQRLRLLKS GKPRLVARVS NKHVRAQLVT PGPQGDETHA AATSADLDEY GWEAPTGNLP SAYLTGYLA GIRALAAGVE EAVLDIGLNT ATPGNKVFAV QEGAIDAGLE IPHNDAVLAD WDRNRGVHIA EYAEQLDEPL Y SGDFDATN LPEHFDEVLG NLQEDE

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #9: Large ribosomal subunit protein eL19

MacromoleculeName: Large ribosomal subunit protein eL19 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 17.291387 KDa
SequenceString:
MTDLKAQKRM AADVLDVGKG RVWFDPEAQS DIAEAITRED IRELVDEGTI RAKNAKGNSK GRARERAAKR SYGHRKGAGS RKGRSGARQ NKKDAWVSRI RAQRRRLKEL REDGTLDRTQ YRTLYNKASG GEFDSVDRLE AYIQNNYQVE IQ

UniProtKB: Large ribosomal subunit protein eL19

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Macromolecule #10: Large ribosomal subunit protein eL21

MacromoleculeName: Large ribosomal subunit protein eL21 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 10.606102 KDa
SequenceString:
MPSSNGPMKG TRGKLSNKPR ERGTSPPQRA IAEFEEGQKV HLNLDPSVRD GRFHPRFNGL TGEVVGKQGR AFKVQINDGG KEKMVIARP AHLRAQQ

UniProtKB: Large ribosomal subunit protein eL21

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Macromolecule #11: Large ribosomal subunit protein uL22

MacromoleculeName: Large ribosomal subunit protein uL22 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 16.975057 KDa
SequenceString:
MGINYSVEAD PDTTAKGMLR DRPISLKHSK AISRAIKGMP VADAEEYLEA VIDGERSVPF KQHNSGVGHR SDIEGWDAGR YPEKASKAF LELLENVRNN ATEQGFDGPA MEIKHIAAHK VGERPGRKPR AFGRADPWNT PICDVELIIE EVEE

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #12: Large ribosomal subunit protein eL24

MacromoleculeName: Large ribosomal subunit protein eL24 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 7.658405 KDa
SequenceString:
MVEKRTCDYS GEEIEPGTGT MYVKTDGTIL HFKNSKAEKN YFLGREARDL EWTEAGRRAS GRAEEDN

UniProtKB: Large ribosomal subunit protein eL24

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Macromolecule #13: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 13.361635 KDa
SequenceString:
MTRQPRKQRT QTRDAPLHER QKQVRAPLSA DLREEYGSRN VRVNAGDTVE VLRGDFAGEE GEVTEVDLTD AVIFVEDVTV AKADGEEVP RPLQASNVRV TELDLEDDVR EARLKEDNE

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #14: Large ribosomal subunit protein uL30

MacromoleculeName: Large ribosomal subunit protein uL30 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 17.112893 KDa
SequenceString:
MQAIVQLRGE VNISQDVRDT LSMLNIHRVN HATFVPENDA YRGMITKVND FVAHGTPSVD VVETLVRTRA EPESGDGDIS DEWVSENTD YDDVAALAQA LVDEETTLRE QGVSPVLRLH PPRGGHRGQK HVTKEGGQLG KHDTEQIDEL LEAMR

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #15: Large ribosomal subunit protein eL31

MacromoleculeName: Large ribosomal subunit protein eL31 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 10.593835 KDa
SequenceString:
MSANDFEERV VTVPLRDVKA VPSHERAGRS MKIIREHLAK HFKVDAENVR LDPQINEDIW EHGRQSPPSK FRVRAARFDE DGESIVEAE PAE

UniProtKB: Large ribosomal subunit protein eL31

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Macromolecule #16: Large ribosomal subunit protein eL32

MacromoleculeName: Large ribosomal subunit protein eL32 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 25.889312 KDa
SequenceString: MSEEITELED ISGVGPSKAD ALREAGFESV DDVQAASQSE LAEVDGIGNA LAARIKADVG GLEVSEEAEA EVEDESEAEV EEPAEDVET ELRPRGHADK KPQLDDETAE ALAQKRREGK PQFNRQDYHK KKRTPTSWRR PRGGLSKQRR GVKGKGPKVE A GYRTPKAA ...String:
MSEEITELED ISGVGPSKAD ALREAGFESV DDVQAASQSE LAEVDGIGNA LAARIKADVG GLEVSEEAEA EVEDESEAEV EEPAEDVET ELRPRGHADK KPQLDDETAE ALAQKRREGK PQFNRQDYHK KKRTPTSWRR PRGGLSKQRR GVKGKGPKVE A GYRTPKAA RDLHPSGFEE VRVFNTDDLE GVDGDTQAVR IASSVGARKR ERIEEVCEDR EIRVLNPTYV EVEVDN

UniProtKB: Large ribosomal subunit protein eL32

+
Macromolecule #17: Large ribosomal subunit protein eL43

MacromoleculeName: Large ribosomal subunit protein eL43 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 9.832003 KDa
SequenceString:
MAEKKARSVG SAGRFGARYG RVARRRVKEI EAEMRNAKVD GDNVTRVETG IWKNEETGEI FTGGTYRPET PAGKQVSRSI RAALTGENE

UniProtKB: Large ribosomal subunit protein eL43

+
Macromolecule #18: Large ribosomal subunit protein eL37

MacromoleculeName: Large ribosomal subunit protein eL37 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 6.442465 KDa
SequenceString:
MTGAGTPSQG KKNKTTHVKC RRCGEKSYHV KKKVCSSCGF GKSKKRRSYA WQSKSGDN

UniProtKB: Large ribosomal subunit protein eL37

+
Macromolecule #19: Large ribosomal subunit protein eL42

MacromoleculeName: Large ribosomal subunit protein eL42 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 10.698334 KDa
SequenceString:
MQMPRRFNTY CPNCKGHHEH EVEKVRSGRP TGMKWDARAQ KRGKSTIGNA GRFSKVPGGD KPTKKTHLKY ICSDCGKAHM REGWRAGRL EFQE

UniProtKB: Large ribosomal subunit protein eL42

+
Macromolecule #20: Large ribosomal subunit protein uL2

MacromoleculeName: Large ribosomal subunit protein uL2 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 25.707346 KDa
SequenceString: MGRRIQGQRR GRGSSTFRAP SHRYKAELSH KKSEEKDTIT GTVVGIEHDP ARSAPIALVE FEDEQRMILA PEGISVGEEL QIGVSAEIK PGNTLPLAEI PEGVPVCNVE HQPGDGGKFA RASGVSAQLL SHDREVAIVK LPSGEVKRLN PNCRATIGVV A GGGRTEKP ...String:
MGRRIQGQRR GRGSSTFRAP SHRYKAELSH KKSEEKDTIT GTVVGIEHDP ARSAPIALVE FEDEQRMILA PEGISVGEEL QIGVSAEIK PGNTLPLAEI PEGVPVCNVE HQPGDGGKFA RASGVSAQLL SHDREVAIVK LPSGEVKRLN PNCRATIGVV A GGGRTEKP FVKAGKKYHK MKARGIKWPR VRGVAMNAVD HPFGGGGRQH PGQPKSVSRD APPGRKVGDI ASKRTGRGGK GG N

UniProtKB: Large ribosomal subunit protein uL2

+
Macromolecule #21: Large ribosomal subunit protein uL3

MacromoleculeName: Large ribosomal subunit protein uL3 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 37.409047 KDa
SequenceString: MPQPSRPRKG SMGFSPRKRA VKEVPRIKSW PDDDGSPALQ GFAGYKAGMT HVMMVNDEAD SPREGMEESV PVTVVETPPM RAVALRAYE QTPYGMKPKT EVWASEFHDE LDRVLDLPAE DTFESDADAL REAVEAGEVD DLRVITHTVP AELKNVPKKK P DVMETRVG ...String:
MPQPSRPRKG SMGFSPRKRA VKEVPRIKSW PDDDGSPALQ GFAGYKAGMT HVMMVNDEAD SPREGMEESV PVTVVETPPM RAVALRAYE QTPYGMKPKT EVWASEFHDE LDRVLDLPAE DTFESDADAL REAVEAGEVD DLRVITHTVP AELKNVPKKK P DVMETRVG GGSMVERADF ALDLVEEGGE HEMSDVFRAG EYLDAAGVTK GKGTQGPVKR WGVQKRKGKH ARQGWRRRIG NL GPWNPSR VRSTVPQLGQ TGYHQRTELN KRLIDLGEGD DASVEGGFVN YGEVDGSYAL IKGSLPGPNK RLLRFRPAIR PND QPRLDP EVRFVSTASN QG

UniProtKB: Large ribosomal subunit protein uL3

+
Macromolecule #22: Large ribosomal subunit protein uL4

MacromoleculeName: Large ribosomal subunit protein uL4 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 27.023252 KDa
SequenceString: MQATIRDLNG DDAGSIDLPE VFETAYRPDL IKRAVIAAQA NRKQPYGADP YAGLRTPAES MGSGRGMSHD PRQNGVARRV PHAVSGRRA HPPKAEKDQG KEINTKERKL AVRSALAATT DSELVAERGH RFDDDLELPL VVSDDFEDLV KTKEVVDLLQ T LGVYDDIE ...String:
MQATIRDLNG DDAGSIDLPE VFETAYRPDL IKRAVIAAQA NRKQPYGADP YAGLRTPAES MGSGRGMSHD PRQNGVARRV PHAVSGRRA HPPKAEKDQG KEINTKERKL AVRSALAATT DSELVAERGH RFDDDLELPL VVSDDFEDLV KTKEVVDLLQ T LGVYDDIE RSEDNKKVKG GQGKLRGRKY TRPKSILFVT AEEPSKAARN LAGVDVATAA NVSAEDLAPG THAGRLTLFT ES AIEEVAE R

UniProtKB: Large ribosomal subunit protein uL4

+
Macromolecule #23: Large ribosomal subunit protein uL5

MacromoleculeName: Large ribosomal subunit protein uL5 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 19.145168 KDa
SequenceString:
MSEAEFHEMR DPRIEKVVVH MGVGEGGREL AKSEDILEEI TGQESVRTIS GRASQDFGVR QGEPVGAKVT LRGESAVEFL ETALPITDL SASSFDETGN FGFGVEEHTE FPSQEYDPQI GIYGLDVTVN IVRPGYRVKK RDKRSRQIPS SHRMTVEDAV A FIESTFDV EVEE

UniProtKB: Large ribosomal subunit protein uL5

+
Macromolecule #24: Large ribosomal subunit protein uL6

MacromoleculeName: Large ribosomal subunit protein uL6 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 19.543463 KDa
SequenceString:
MSRIEIEIPD EVSAEVSNLE LTIEGPNGSV TKRLWYPNVS VSAEDGAIAI ESDVENAKTN ATIGTFESHV NNMLHGATEG WEYQMEVHY AHFPMQVSVE GDDVVIKNFL GEKSPRRAAI RGDTDVQVDG EEVTLTGPDK EDVGQTAADI EQLTRVKDKD T RVFTDGVY ITQKPKTGDA

UniProtKB: Large ribosomal subunit protein uL6

+
Macromolecule #25: Large ribosomal subunit protein uL13

MacromoleculeName: Large ribosomal subunit protein uL13 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 16.199331 KDa
SequenceString:
MSFAEFDADV VVNARNCIMG RVSSEVAQRV LAGETVAVVN AEDTVITGSE EDVMGKFRKR VEVGSDQGPY YPKRPDRIFK RAIRGMLPY KKPRGREALS NVRVYVGNPY DEDGEMLEDT SLDRLSNIKF ISLGEVSEKL GANVTW

UniProtKB: Large ribosomal subunit protein uL13

+
Macromolecule #26: Large ribosomal subunit protein eL40

MacromoleculeName: Large ribosomal subunit protein eL40 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 5.579713 KDa
SequenceString:
MASDAATKRT LEKQICMRCN ARNPKKAKQC RKCGYKHLRP KSKERRAA

UniProtKB: Large ribosomal subunit protein eL40

+
Macromolecule #27: Large ribosomal subunit protein uL23

MacromoleculeName: Large ribosomal subunit protein uL23 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 9.441704 KDa
SequenceString:
MSIIEHPLVT EKAMNQMDFQ NKLQFIVHVD SSKADVKDEV ESRYDVTVEK VNTQVTMKGK KKATVRLSED DDAQEVASRI GVF

UniProtKB: Large ribosomal subunit protein uL23

+
Macromolecule #28: Large ribosomal subunit protein uL29

MacromoleculeName: Large ribosomal subunit protein uL29 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 7.690576 KDa
SequenceString:
MAILYTEEIR DMTPAERVAE LEELETELLN AKAVQAAGGA PENPGRVSEL KKTIARIKTI QGEEGDLDEE

UniProtKB: Large ribosomal subunit protein uL29

+
Macromolecule #29: Large ribosomal subunit protein uL14

MacromoleculeName: Large ribosomal subunit protein uL14 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 14.272468 KDa
SequenceString:
MEALKADITK GVARGSLVTC ADNTGARELK IISVAGYSGT KNRHPKAGIG DKVTVSVTKG TPEMRRQVLE AVIVRQRKSI RRPDGTRVK FEDNAAVIID EMEEPRGTEI KGPIAREVAE RFGSIASTAT MIV

UniProtKB: Large ribosomal subunit protein uL14

+
Macromolecule #30: Large ribosomal subunit protein eL20

MacromoleculeName: Large ribosomal subunit protein eL20 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 6.308004 KDa
SequenceString:
MSQFTITGSF TSRGVVHEFT KTVEAPNENV AEERAYSLIG SEHGIKRTKV TLSEVSAA

UniProtKB: Large ribosomal subunit protein eL20

+
Macromolecule #31: Large ribosomal subunit protein eL39

MacromoleculeName: Large ribosomal subunit protein eL39 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Molecular weightTheoretical: 6.058146 KDa
SequenceString:
MGKKSKAKKK RLAKLERQNS RVPAWVMLKT DMEVSRNPKR RNWRRSNTDE

UniProtKB: Large ribosomal subunit protein eL39

+
Macromolecule #32: beta-D-glucopyranose

MacromoleculeName: beta-D-glucopyranose / type: ligand / ID: 32 / Number of copies: 2 / Formula: BGC
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BGC:
beta-D-glucopyranose

+
Macromolecule #33: SPERMIDINE

MacromoleculeName: SPERMIDINE / type: ligand / ID: 33 / Number of copies: 4 / Formula: SPD
Molecular weightTheoretical: 145.246 Da
Chemical component information

ChemComp-SPD:
SPERMIDINE

+
Macromolecule #34: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 34 / Number of copies: 317 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #35: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 35 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #36: water

MacromoleculeName: water / type: ligand / ID: 36 / Number of copies: 6727 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3g6e

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 918876
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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