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- EMDB-20441: RbgA+45SRbgA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20441
TitleRbgA+45SRbgA complex
Map dataRbgA 45SRbgA complex
Sample
  • Complex: RbgA + 45SRbgA ribosomal assembly intermediate complex
    • RNA: x 2 types
    • Protein or peptide: x 21 types
  • Protein or peptide: x 1 types
  • Ligand: x 1 types
KeywordsRibosome assembly / 50S subunit / RbgA / YlqF / RIBOSOME
Function / homology
Function and homology information


positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity ...positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / GTPase activity / GTP binding / DNA binding / RNA binding / cytoplasm
Similarity search - Function
GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / GTP-binding protein, orthogonal bundle domain superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : ...GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / GTP-binding protein, orthogonal bundle domain superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L17 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L29 signature. / Ribosomal protein L5 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / ribosomal L5P family C-terminus / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L6 / Ribosomal protein L2, domain 3 / Ribosomal protein L14P, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L22/L17, conserved site / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / Ribosomal protein L13, conserved site / Ribosomal protein L13 signature. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ribosomal protein L14 signature. / Ribosomal protein L22 signature. / Ribosomal protein L15 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L25/L23
Similarity search - Domain/homology
Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL15 ...Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL21 / Ribosome biogenesis GTPase A / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL19 / Ribosome biogenesis GTPase A / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL13
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsOrtega J / Seffouh A
Funding support Canada, United States, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-153044 Canada
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01GM110248 United States
CitationJournal: Nucleic Acids Res / Year: 2019
Title: Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate.
Authors: Amal Seffouh / Nikhil Jain / Dushyant Jahagirdar / Kaustuv Basu / Aida Razi / Xiaodan Ni / Alba Guarné / Robert A Britton / Joaquin Ortega /
Abstract: Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most ...Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most bacteria. Homologs of this protein are also implicated in the assembly of the large subunit of the mitochondrial and eukaryotic ribosome. We present here the cryo-electron microscopy structure of RbgA bound to a Bacillus subtilis 50S subunit assembly intermediate (45SRbgA particle) that accumulates in cells upon RbgA depletion. Binding of RbgA at the P site of the immature particle stabilizes functionally important rRNA helices in the A and P-sites, prior to the completion of the maturation process of the subunit. The structure also reveals the location of the highly conserved N-terminal end of RbgA containing the catalytic residue Histidine 9. The derived model supports a mechanism of GTP hydrolysis, and it shows that upon interaction of RbgA with the 45SRbgA particle, Histidine 9 positions itself near the nucleotide potentially acting as the catalytic residue with minimal rearrangements. This structure represents the first visualization of the conformational changes induced by an assembly factor in a bacterial subunit intermediate.
History
DepositionJul 7, 2019-
Header (metadata) releaseAug 21, 2019-
Map releaseSep 18, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ppk
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20441.png

Downloads & links

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Map

FileDownload / File: emd_20441.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRbgA 45SRbgA complex
Voxel sizeX=Y=Z: 1.45 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.046727907 - 0.1023259
Average (Standard dev.)0.0008374617 (±0.004920296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z348.000348.000348.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0470.1020.001

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Supplemental data

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Sample components

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Entire : RbgA + 45SRbgA ribosomal assembly intermediate complex

EntireName: RbgA + 45SRbgA ribosomal assembly intermediate complex
Components
  • Complex: RbgA + 45SRbgA ribosomal assembly intermediate complex
    • RNA: 23S rRNA23S ribosomal RNA
    • RNA: 5S rRNA5S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L34
  • Protein or peptide: Ribosome biogenesis GTPase A
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

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Supramolecule #1: RbgA + 45SRbgA ribosomal assembly intermediate complex

SupramoleculeName: RbgA + 45SRbgA ribosomal assembly intermediate complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#23
Details: 50S subunit assembly intermediate generated by RbgA depletion in cells in complex with RbgA protein
Source (natural)Organism: Bacillus subtilis (bacteria) / Strain: JH642

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Macromolecule #1: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 949.340125 KDa
SequenceString: GGUUAAGUUA GAAAGGGCGC ACGGUGGAUG CCUUGGCACU AGGAGCCGAU GAAGGACGGG ACGAACACCG AUAUGCUUCG GGGAGCUGU AAGCAAGCUU UGAUCCGGAG AUUUCCGAAU GGGGAAACCC ACCACUCGUA AUGGAGUGGU AUCCAUAUCU G AAUUCAUA ...String:
GGUUAAGUUA GAAAGGGCGC ACGGUGGAUG CCUUGGCACU AGGAGCCGAU GAAGGACGGG ACGAACACCG AUAUGCUUCG GGGAGCUGU AAGCAAGCUU UGAUCCGGAG AUUUCCGAAU GGGGAAACCC ACCACUCGUA AUGGAGUGGU AUCCAUAUCU G AAUUCAUA GGAUAUGAGA AGGCAGACCC GGGGAACUGA AACAUCUAAG UACCCGGAGG AAGAGAAAGC AAAUGCGAUU CC CUGAGUA GCGGCGAGCG AAACGGGAUC AGCCCAAACC AAGAGGCUUG CCUCUUGGGG UUGUAGGACA CUCUGUACGG AGU UACAAA GGAACGAGGU AGAUGAAGAG GUCUGGAAAG GCCCGCCAUA GGAGGUAACA GCCCUGUAGU CAAAACUUCG UUCU CUCCU GAGUGGAUCC UGAGUACGGC GGAACACGUG AAAUUCCGUC GGAAUCCGGG AGGACCAUCU CCCAAGGCUA AAUAC UCCC UAGUGACCGA UAGUGAACCA GUACCGUGAG GGAAAGGUGA AAAGCACCCC GGAAGGGGAG UGAAAGAGAU CCUGAA ACC GUGUGCCUAC AAGUAGUCAG AGCCCGUUAA CGGGUGAUGG CGUGCCUUUU GUAGAAUGAA CCGGCGAGUU ACGAUCU CG UGCAAGGUUA AGCAGAAGAU GCGGAGCCGC AGCGAAAGCG AGUCUGAAUA GGGCGCAUGA GUACGUGGUC GUAGACCC G AAACCAGGUG AUCUACCCAU GUCCAGGGUG AAGUUCAGGU AACACUGAAU GGAGGCCCGA ACCCACGCAC GUUGAAAAG UGCGGGGAUG AGGUGUGGGU AGGGGUGAAA UGCCAAUCGA ACCUGGAGAU AGCUGGUUCU CUCCGAAAUA GCUUUAGGGC UAGCCUCAA GGUAAGAGUC UUGGAGGUAG AGCACUGAUU GGACUAGGGG CCCCUACCGG GUUACCGAAU UCAGUCAAAC U CCGAAUGC CAAUGACUUA UCCUUGGGAG UCAGACUGCG AGUGAUAAGA UCCGUAGUCG AAAGGGAAAC AGCCCAGACC GC CAGCUAA GGUCCCAAAG UAUACGUUAA GUGGAAAAGG AUGUGGAGUU GCUUAGACAA CCAGGAUGUU GGCUUAGAAG CAG CCACCA UUUAAAGAGU GCGUAAUAGC UCACUGGUCG AGUGACUCUG CGCCGAAAAU GUACCGGGGC UAAACGUAUC ACCG AAGCU GCGGACUGUU CUUCGAACAG UGGUAGGAGA GCGUUCUAAG GGCUGUGAAG CCAGACCGGA AGGACUGGUG GAGCG CUUA GAAGUGAGAA UGCCGGUAUG AGUAGCGAAA GAGGGGUGAG AAUCCCCUCC ACCGAAUGCC UAAGGUUUCC UGAGGA AGG CUCGUCCGCU CAGGGUUAGU CGGGACCUAA GCCGAGGCCG AAAGGCGUAG GCGAUGGACA ACAGGUUGAU AUUCCUG UA CCACCUCCUC ACCAUUUGAG CAAUGGGGGG ACGCAGGAGG AUAGGGUAAG CGCGGUAUUG GAUAUCCGCG UCCAAGCA G UUAGGCUGGG AAAUAGGCAA AUCCGUUUCC CAUAAGGCUG AGCUGUGAUG GCGAGCGAAA UAUAGUAGCG AAGUUCCUG AUUCCACACU GCCAAGAAAA GCCUCUAGCG AGGUGAGAGG UGCCCGUACC GCAAACCGAC ACAGGUAGGC GAGGAGAGAA UCCUAAGGU GAUCGAGAGA ACUCUCGUUA AGGAACUCGG CAAAAUGACC CCGUAACUUC GGGAGAAGGG GUGCUCUGUU A GGGUGCAA GCCCGAGAGA GCCGCAGUGA AUAGGCCCAG GCGACUGUUU AGCAAAAACA CAGGUCUCUG CGAAGCCGUA AG GCGAAGU AUAGGGGCUG ACGCCUGCCC GGUGCUGGAA GGUUAAGAGG AGCGCUUAGC GUAAGCGAAG GUGCGAAUUG AAG CCCCAG UAAACGGCGG CCGUAACUAU AACGGUCCUA AGGUAGCGAA AUUCCUUGUC GGGUAAGUUC CGACCCGCAC GAAA GGCGC AACGAUCUGG GCACUGUCUC AACGAGAGAC UCGGUGAAAU UAUAGUACCU GUGAAGAUGC AGGUUACCCG CGACA GGAC GGAAAGACCC CGUGGAGCUU UACUGCAGCC UGAUAUUGAA UGUUGGUACA GCUUGUACAG GAUAGGUAGG AGCCUU GGA AACCGGAGCG CCAGCUUCGG UGGAGGCAUC GGUGGGAUAC UACCCUGGCU GUAUUGACCU UCUAACCCGC CGCCCUU AU CGGGCGGGGA GACAGUGUCA GGUGGGCAGU UUGACUGGGG CGGUCGCCUC CUAAAAGGUA ACGGAGGCGC CCAAAGGU U CCCUCAGAAU GGUUGGAAAU CAUUCGCAGA GUGUAAAGGC ACAAGGGAGC UUGACUGCGA GACCUACAAG UCGAGCAGG GACGAAAGUC GGGCUUAGUG AUCCGGUGGU UCCGCAUGGA AGGGCCAUCG CUCAACGGAU AAAAGCUACC CCGGGGAUAA CAGGCUUAU CUCCCCCAAG AGUCCACAUC GACGGGGAGG UUUGGCACCU CGAUGUCGGC UCAUCGCAUC CUGGGGCUGU A GUCGGUCC CAAGGGUUGG GCUGUUCGCC CAUUAAAGCG GUACGCGAGC UGGGUUCAGA ACGUCGUGAG ACAGUUCGGU CC CUAUCCG UCGCGGGCGC AGGAAAUUUG AGAGGAGCUG UCCUUAGUAC GAGAGGACCG GGAUGGACGC ACCGCUGGUG UAC CAGUUG UUCUGCCAAG GGCAUCGCUG GGUAGCUAUG UGCGGACGGG AUAAGUGCUG AAAGCAUCUA AGCAUGAAGC CCCC CUCAA GAUGAGAUUU CCCAUUCCGC AAGGAAGUAA GAUCCCUGAA AGAUGAUCAG GUUGAUAGGU CUGAGGUGGA AGUGU GGCG ACACAUGGAG CUGACAGAUA CUAAUCGAUC GAGGACUUAA CCA

GENBANK: GENBANK: LN649259.1

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Macromolecule #2: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 38.423863 KDa
SequenceString:
UUUGGUGGCG AUAGCGAAGA GGUCACACCC GUUCCCAUAC CGAACACGGA AGUUAAGCUC UUCAGCGCCG AUGGUAGUCG GGGGUUUCC CCCUGUGAGA GUAGGACGCC GCCAAGCAAG

GENBANK: GENBANK: CP015004.1

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Macromolecule #3: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 30.335125 KDa
SequenceString: MAIKKYKPTS NGRRGMTTSD FAEITTDKPE KSLLAPLHKK GGRNNQGKLT VRHQGGGHKR QYRVIDFKRD KDGIPGRVAT VEYDPNRSA NIALINYADG EKRYILAPKG IQVGTEIMSG PEADIKVGNA LPLINIPVGT VVHNIELKPG KGGQLVRSAG T SAQVLGKE ...String:
MAIKKYKPTS NGRRGMTTSD FAEITTDKPE KSLLAPLHKK GGRNNQGKLT VRHQGGGHKR QYRVIDFKRD KDGIPGRVAT VEYDPNRSA NIALINYADG EKRYILAPKG IQVGTEIMSG PEADIKVGNA LPLINIPVGT VVHNIELKPG KGGQLVRSAG T SAQVLGKE GKYVLVRLNS GEVRMILSAC RASIGQVGNE QHELINIGKA GRSRWKGIRP TVRGSVMNPN DHPHGGGEGR AP IGRKSPM SPWGKPTLGF KTRKKKNKSD KFIVRRRKNK

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #4: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 22.723348 KDa
SequenceString: MTKGILGRKI GMTQVFAENG DLIPVTVIEA APNVVLQKKT AENDGYEAIQ LGFDDKREKL SNKPEKGHVA KAETAPKRFV KELRGVEMD AYEVGQEVKV EIFSAGEIVD VTGVSKGKGF QGAIKRHGQS RGPMSHGSRY HRRPGSMGPV DPNRVFKGKL L PGRMGGEQ ...String:
MTKGILGRKI GMTQVFAENG DLIPVTVIEA APNVVLQKKT AENDGYEAIQ LGFDDKREKL SNKPEKGHVA KAETAPKRFV KELRGVEMD AYEVGQEVKV EIFSAGEIVD VTGVSKGKGF QGAIKRHGQS RGPMSHGSRY HRRPGSMGPV DPNRVFKGKL L PGRMGGEQ ITVQNLEIVK VDAERNLLLI KGNVPGAKKS LITVKSAVKS K

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #5: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 22.424951 KDa
SequenceString: MPKVALYNQN GSTAGDIELN ASVFGIEPNE SVVFDAILMQ RASLRQGTHK VKNRSEVRGG GRKPWRQKGT GRARQGSIRS PQWRGGGVV FGPTPRSYSY KLPKKVRRLA IKSVLSSKVI DNNIIVLEDL TLDTAKTKEM AAILKGLSVE KKALIVTADA N EAVALSAR ...String:
MPKVALYNQN GSTAGDIELN ASVFGIEPNE SVVFDAILMQ RASLRQGTHK VKNRSEVRGG GRKPWRQKGT GRARQGSIRS PQWRGGGVV FGPTPRSYSY KLPKKVRRLA IKSVLSSKVI DNNIIVLEDL TLDTAKTKEM AAILKGLSVE KKALIVTADA N EAVALSAR NIPGVTVVEA NGINVLDVVN HEKLLITKAA VEKVEEVLA

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #6: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 20.177564 KDa
SequenceString:
MNRLKEKYNK EIAPALMTKF NYDSVMQVPK IEKIVINMGV GDAVQNAKAI DSAVEELTFI AGQKPVVTRA KKSIAGFRLR EGMPIGAKV TLRGERMYDF LDKLISVSLP RVRDFRGVSK KSFDGRGNYT LGIKEQLIFP EIDYDKVTKV RGMDIVIVTT A NTDEEARE LLTQVGMPFQ K

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #7: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 19.543389 KDa
SequenceString:
MSRVGKKLLE IPSDVTVTLN DNNTVAVKGP KGELTRTFHP DMEIKVEDNV LTVARPSDQK EHRALHGTTR SLLGNMVEGV SKGFERGLE LVGVGYRASK SGNKLVLNVG YSHPVEIVPE EGIEIEVPSQ TKVVVKGTDK ERVGAIAANI RAVRSPEPYK G KGIRYEGE VVRRKEGKSA K

UniProtKB: 50S ribosomal protein L6

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Macromolecule #8: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 16.407104 KDa
SequenceString:
MRTTPMANAS TIERKWLVVD AAGKTLGRLS SEVAAILRGK HKPTYTPHVD TGDHVIIINA EKIELTGKKL TDKIYYRHTQ HPGGLKSRT ALEMRTNYPE KMLELAIKGM LPKGSLGRQM FKKLNVYRGS EHPHEAQKPE VYELRG

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #9: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 13.175288 KDa
SequenceString:
MIQQETRLKV ADNSGAREVL TIKVLGGSGR KTANIGDVIV CTVKQATPGG VVKKGEVVKA VIVRTKSGAR RSDGSYISFD ENACVIIRD DKSPRGTRIF GPVARELREN NFMKIVSLAP EVI

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #10: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 15.410694 KDa
SequenceString:
MKLHELKPSE GSRKTRNRVG RGIGSGNGKT AGKGHKGQNA RSGGGVRPGF EGGQMPLFQR LPKRGFTNIN RKEYAVVNLD KLNGFAEGT EVTPELLLET GVISKLNAGV KILGNGKLEK KLTVKANKFS ASAKEAVEAA GGTAEVI

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #11: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 13.774806 KDa
SequenceString:
MSYRKLGRTS AQRKAMLRDL TTDLIINERI ETTETRAKEL RSVVEKMITL GKRGDLHARR QAAAYIRNEV ANEENNQDAL QKLFSDIAT RYEERQGGYT RIMKLGPRRG DGAPMAIIEL V

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #12: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 12.993829 KDa
SequenceString:
MITKTSKNAA RLKRHARVRA KLSGTAERPR LNVFRSNKHI YAQIIDDVNG VTLASASTLD KDLNVESTGD TSAATKVGEL VAKRAAEKG ISDVVFDRGG YLYHGRVKAL ADAAREAGLK F

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #13: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 13.416853 KDa
SequenceString:
MQKLIEDITK EQLRTDLPAF RPGDTLRVHV KVVEGNRERI QIFEGVVIKR RGGGISETFT VRKISYGVGV ERTFPVHTPK IAKIEVVRY GKVRRAKLYY LRELRGKAAR IKEIRR

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #14: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 13.537993 KDa
SequenceString:
PRVKGGTVTR KRRKKVLKLA KGYFGSKHTL YKVANQQVMK SGNYAFRDRR QKKRDFRKLW ITRINAAARM NGLSYSRLMH GLKLSGIEV NRKMLADLAV NDLTAFNQLA DAAKAQLNK

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #15: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 11.296081 KDa
SequenceString:
MYAIIKTGGK QIKVEEGQTV YIEKLAAEAG ETVTFEDVLF VGGDNVKVGN PTVEGATVTA KVEKQGRAKK ITVFRYKPKK NVHKKQGHR QPYTKVTIEK INA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #16: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 12.481608 KDa
SequenceString:
MQAKAVARTV RIAPRKARLV MDLIRGKQVG EAVSILNLTP RAASPIIEKV LKSAIANAEH NYEMDANNLV ISQAFVDEGP TLKRFRPRA MGRASQINKR TSHITIVVSE KKEG

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #17: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 10.978813 KDa
SequenceString:
MKDPRDVLKR PVITERSADL MTEKKYTFEV DVRANKTEVK DAVESIFGVK VDKVNIMNYK GKSKRVGRYT GMTSRRRKAI VKLTADSKE IEIFEA

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #18: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 11.16612 KDa
SequenceString:
MHVKKGDKVM VISGKDKGKQ GTILAAFPKK DRVLVEGVNM VKKHSKPTQA NPQGGISNQE APIHVSNVMP LDPKTGEVTR VGYKVEDGK KVRVAKKSGQ VLDK

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #19: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 10.391855 KDa
SequenceString:
MLRLDLQFFA SKKGVGSTKN GRDSEAKRLG AKRADGQFVT GGSILYRQRG TKIYPGENVG RGGDDTLFAK IDGTVKFERF GRDRKKVSV YPVAQ

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #20: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 6.650795 KDa
SequenceString:
MAKLEITLKR SVIGRPEDQR VTVRTLGLKK TNQTVVHEDN AAIRGMINKV SHLVSVKEQ

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #21: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 6.745073 KDa
SequenceString:
MAVPFRRTSK MKKRLRRTHF KLNVPGMTEC PSCGEMKLSH RVCKACGSYN GKDINVKSN

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #22: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 7.728029 KDa
SequenceString:
MKANEIRDLT TAEIEQKVKS LKEELFNLRF QLATGQLENT ARIREVRKAI ARMKTVIRER EIAANK

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #23: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 5.271332 KDa
SequenceString:
MKRTFQPNNR KRSKVHGFRS RMSSKNGRLV LARRRRKGRK VLSA

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #24: Ribosome biogenesis GTPase A

MacromoleculeName: Ribosome biogenesis GTPase A / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 32.033236 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MTIQWFPGHM AKARREVTEK LKLIDIVYEL VDARIPMSSR NPMIEDILKN KPRIMLLNKA DKADAAVTQQ WKEHFENQGI RSLSINSVN GQGLNQIVPA SKEILQEKFD RMRAKGVKPR AIRALIIGIP NVGKSTLINR LAKKNIAKTG DRPGITTSQQ W VKVGKELE ...String:
MTIQWFPGHM AKARREVTEK LKLIDIVYEL VDARIPMSSR NPMIEDILKN KPRIMLLNKA DKADAAVTQQ WKEHFENQGI RSLSINSVN GQGLNQIVPA SKEILQEKFD RMRAKGVKPR AIRALIIGIP NVGKSTLINR LAKKNIAKTG DRPGITTSQQ W VKVGKELE LLDTPGILWP KFEDELVGLR LAVTGAIKDS IINLQDVAVF GLRFLEEHYP ERLKERYGLD EIPEDIAELF DA IGEKRGC LMSGGLINYD KTTEVIIRDI RTEKFGRLSF EQPTM

UniProtKB: Ribosome biogenesis GTPase A

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Macromolecule #25: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 25 / Number of copies: 1 / Formula: GNP
Molecular weightTheoretical: 522.196 Da
Chemical component information

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM / 5'-Guanylyl imidodiphosphate

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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
Details: 20mM Tris-HCl pH 7.5, 10mM MgCl2, 50mM NH4Cl, 1mM DTT
GridSupport film - Material: CARBON / Support film - topology: HOLEY ARRAY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Details: Cryo-EM grids were prepared by applying a 3.6 microliters volume of the diluted samples to holey carbon grids (c-flat CF-2/2-2C-T) with a freshly applied additional layer of continuous thin ...Details: Cryo-EM grids were prepared by applying a 3.6 microliters volume of the diluted samples to holey carbon grids (c-flat CF-2/2-2C-T) with a freshly applied additional layer of continuous thin carbon (5-10nm). Grids were blotted for 3 seconds and with a blot force +1.

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1228 / Average exposure time: 15.0 sec. / Average electron dose: 43.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 169095
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3j9w

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 81392
FSC plot (resolution estimation)

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