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- EMDB-10535: Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23... -

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Basic information

Entry
Database: EMDB / ID: EMD-10535
TitleMini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA
Map dataMini-RNase III (Mini-III) bound to 50S ribosome with pre-23S rRNA
Sample
  • Complex: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
    • Complex: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
      • Protein or peptide: x 27 types
      • RNA: x 2 types
    • Complex: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
      • Protein or peptide: x 1 types
  • Ligand: x 2 types
KeywordsMini-RNase III / Mini-III / complex / ribosome / 50S / RNA maturation / RNA processing / precursor 23S rRNA / pre-23S rRNA / 23S rRNA / L3 / Ribosomal protein / RNase III-like fold / RNase
Function / homology
Function and homology information


ribonuclease III activity / positive regulation of rRNA processing / nucleoid / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA nuclease activity / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly ...ribonuclease III activity / positive regulation of rRNA processing / nucleoid / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA nuclease activity / rRNA processing / 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 / mRNA binding / DNA binding / RNA binding / cytoplasm
Similarity search - Function
Mini-ribonuclease 3 family / Ribonuclease III domain / Ribonuclease III family / Ribonuclease III domain / Ribonuclease III, endonuclease domain superfamily / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : ...Mini-ribonuclease 3 family / Ribonuclease III domain / Ribonuclease III family / Ribonuclease III domain / Ribonuclease III, endonuclease domain superfamily / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L21 / Ribosomal protein L19 superfamily / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L2, conserved site / : / Ribosomal protein L5, N-terminal
Similarity search - Domain/homology
Mini-ribonuclease 3 / Large ribosomal subunit protein bL19 / 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 uL16 ...Mini-ribonuclease 3 / Large ribosomal subunit protein bL19 / 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 uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria) / Bacillus subtilis subsp. subtilis str. 168 / Bacillus subtilis subsp. subtilis str. 168
Methodsingle particle reconstruction / Resolution: 3.07 Å
AuthorsOerum S / Dendooven T
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Mol Cell / Year: 2020
Title: Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs.
Authors: Stephanie Oerum / Tom Dendooven / Marjorie Catala / Laetitia Gilet / Clément Dégut / Aude Trinquier / Maxime Bourguet / Pierre Barraud / Sarah Cianferani / Ben F Luisi / Ciarán Condon / Carine Tisné /
Abstract: The pathways for ribosomal RNA (rRNA) maturation diverge greatly among the domains of life. In the Gram-positive model bacterium, Bacillus subtilis, the final maturation steps of the two large ...The pathways for ribosomal RNA (rRNA) maturation diverge greatly among the domains of life. In the Gram-positive model bacterium, Bacillus subtilis, the final maturation steps of the two large ribosomal subunit (50S) rRNAs, 23S and 5S pre-rRNAs, are catalyzed by the double-strand specific ribonucleases (RNases) Mini-RNase III and RNase M5, respectively. Here we present a protocol that allowed us to solve the 3.0 and 3.1 Å resolution cryoelectron microscopy structures of these RNases poised to cleave their pre-rRNA substrates within the B. subtilis 50S particle. These data provide the first structural insights into rRNA maturation in bacteria by revealing how these RNases recognize and process double-stranded pre-rRNA. Our structures further uncover how specific ribosomal proteins act as chaperones to correctly fold the pre-rRNA substrates and, for Mini-III, anchor the RNase to the ribosome. These r-proteins thereby serve a quality-control function in the process from accurate ribosome assembly to rRNA processing.
History
DepositionDec 9, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseSep 30, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tnn
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10535.png

Downloads & links

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Map

FileDownload / File: emd_10535.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMini-RNase III (Mini-III) bound to 50S ribosome with pre-23S rRNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 360 pix.
= 406.8 Å		1.13 Å/pix.
x 360 pix.
= 406.8 Å		1.13 Å/pix.
x 360 pix.
= 406.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-5.441321 - 9.780046
Average (Standard dev.)0.014125716 (±0.21950085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 406.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.131.131.13
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z406.800406.800406.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-5.4419.7800.014

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Supplemental data

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Sample components

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Entire : Mini-RNase III bound to 50S ribosome with precursor 23S rRNA

EntireName: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
Components
  • Complex: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
    • Complex: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
      • Protein or peptide: 50S ribosomal protein L10
      • RNA: pre-23S rRNA
      • RNA: 5S rRNA
      • 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 L16
      • 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 L32
      • Protein or peptide: 50S ribosomal protein L33 1
      • Protein or peptide: 50S ribosomal protein L34
      • Protein or peptide: 50S ribosomal protein L35
      • Protein or peptide: 50S ribosomal protein L36
      • Protein or peptide: 50S ribosomal protein L28
      • Protein or peptide: 50S ribosomal protein L29
      • Protein or peptide: 50S ribosomal protein L30
    • Complex: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
      • Protein or peptide: Mini-ribonuclease 3
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA

SupramoleculeName: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30

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Supramolecule #2: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA

SupramoleculeName: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3-#30
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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Supramolecule #3: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA

SupramoleculeName: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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Macromolecule #1: 50S ribosomal protein L10

MacromoleculeName: 50S ribosomal protein L10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 18.101748 KDa
SequenceString:
MSSAIETKKV VVEEIASKLK ESKSTIIVDY RGLNVSEVTE LRKQLREANV EFKVYKNTMT RRAVEQAELN GLNDFLTGPN AIAFSTEDV VAPAKVLNDF AKNHEALEIK AGVIEGKVST VEEVKALAEL PSREGLLSML LSVLQAPVRN LALAAKAVAE Q KEEQGA

UniProtKB: Large ribosomal subunit protein uL10

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Macromolecule #2: Mini-ribonuclease 3

MacromoleculeName: Mini-ribonuclease 3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 16.251371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLEFDTIKDS KQLNGLALAY IGNAIFEVYV RHHLLKQGFT KPNDLHKKSS RIVSAKSQAE ILFFLQNQSF FTEEEEAVLK RGRNAKSGT TPKNTDVQTY RYSTAFEALL GYLFLEKKEE RLSQLVAEAI QFGTSGRKTN ESAT

UniProtKB: Mini-ribonuclease 3

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Macromolecule #5: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #6: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #7: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #8: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #9: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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: Large ribosomal subunit protein uL6

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Macromolecule #10: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #11: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #12: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #13: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 16.223049 KDa
SequenceString:
MLLPKRVKYR REHRGKMRGR AKGGTEVHFG EFGIQALEAS WITNRQIEAA RIAMTRYMKR GGKVWIKIFP SKPYTAKPLE VRMGSGKGA PEGWVAVVKP GKVLFEISGV SEEVAREALR LASHKLPIKT KFVKREEIGG ESNES

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #14: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #15: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #16: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #17: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 13.669189 KDa
SequenceString:
MPRVKGGTVT RKRRKKVLKL AKGYFGSKHT LYKVANQQVM KSGNYAFRDR RQKKRDFRKL WITRINAAAR MNGLSYSRLM HGLKLSGIE VNRKMLADLA VNDLTAFNQL ADAAKAQLNK

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #18: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #19: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #20: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #21: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #22: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
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 #23: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 6.745073 KDa
SequenceString:
MAVPFRRTSK MKKRLRRTHF KLNVPGMTEC PSCGEMKLSH RVCKACGSYN GKDINVKSN

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #24: 50S ribosomal protein L33 1

MacromoleculeName: 50S ribosomal protein L33 1 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 5.915875 KDa
SequenceString:
MRVNITLACT ECGERNYISK KNKRNNPDRV EFKKYCPRDK KSTLHRETK

UniProtKB: Large ribosomal subunit protein bL33A

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Macromolecule #25: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 5.271332 KDa
SequenceString:
MKRTFQPNNR KRSKVHGFRS RMSSKNGRLV LARRRRKGRK VLSA

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #26: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 7.581128 KDa
SequenceString:
MPKMKTHRGS AKRFKKTGSG KLKRSHAYTS HLFANKSQKQ KRKLRKSAVV SAGDFKRIKQ MLANIK

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #27: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 4.318422 KDa
SequenceString:
MKVRPSVKPI CEKCKVIRRK GKVMVICENP KHKQKQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #28: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 6.826144 KDa
SequenceString:
MARKCVITGK KTTAGNNRSH AMNASKRTWG ANLQKVRILV NGKPKKVYVS ARALKSGKVE RV

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #29: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 7.728029 KDa
SequenceString:
MKANEIRDLT TAEIEQKVKS LKEELFNLRF QLATGQLENT ARIREVRKAI ARMKTVIRER EIAANK

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #30: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168
Molecular weightTheoretical: 6.650795 KDa
SequenceString:
MAKLEITLKR SVIGRPEDQR VTVRTLGLKK TNQTVVHEDN AAIRGMINKV SHLVSVKEQ

UniProtKB: Large ribosomal subunit protein uL30

+
Macromolecule #3: pre-23S rRNA

MacromoleculeName: pre-23S rRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 950.280812 KDa
SequenceString: ACGGUUAAGU UAGAAAGGGC GCACGGUGGA UGCCUUGGCA CUAGGAGCCG AUGAAGGACG GGACGAACAC CGAUAUGCUU CGGGGAGCU GUAAGCAAGC UUUGAUCCGG AGAUUUCCGA AUGGGGAAAC CCACCACUCG UAAUGGAGUG GUAUCCAUAU C UGAAUUCA ...String:
ACGGUUAAGU UAGAAAGGGC GCACGGUGGA UGCCUUGGCA CUAGGAGCCG AUGAAGGACG GGACGAACAC CGAUAUGCUU CGGGGAGCU GUAAGCAAGC UUUGAUCCGG AGAUUUCCGA AUGGGGAAAC CCACCACUCG UAAUGGAGUG GUAUCCAUAU C UGAAUUCA UAGGAUAUGA GAAGGCAGAC CCGGGGAACU GAAACAUCUA AGUACCCGGA GGAAGAGAAA GCAAAUGCGA UU CCCUGAG UAGCGGCGAG CGAAACGGGA UCAGCCCAAA CCAAGAGGCU UGCCUCUUGG GGUUGUAGGA CACUCUGUAC GGA GUUACA AAGGAACGAG GUAGAUGAAG AGGUCUGGAA AGGCCCGCCA UAGGAGGUAA CAGCCCUGUA GUCAAAACUU CGUU CUCUC CUGAGUGGAU CCUGAGUACG GCGGAACACG UGAAAUUCCG UCGGAAUCCG GGAGGACCAU CUCCCAAGGC UAAAU ACUC CCUAGUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGU GAAAAGCACC CCGGAAGGGG AGUGAAAGAG AUCCUG AAA CCGUGUGCCU ACAAGUAGUC AGAGCCCGUU AACGGGUGAU GGCGUGCCUU UUGUAGAAUG AACCGGCGAG UUACGAU CC CGUGCAAGGU UAAGCAGAAG AUGCGGAGCC GCAGCGAAAG CGAGUCUGAA UAGGGCGCAU GAGUACGUGG UCGUAGAC C CGAAACCAGG UGAUCUACCC AUGUCCAGGG UGAAGUUCAG GUAACACUGA AUGGAGGCCC GAACCCACGC ACGUUGAAA AGUGCGGGGA UGAGGUGUGG GUAGGGGUGA AAUGCCAAUC GAACCUGGAG AUAGCUGGUU CUCUCCGAAA UAGCUUUAGG GCUAGCCUC AAGGUAAGAG UCUUGGAGGU AGAGCACUGA UUGGACUAGG GGCCCCUACC GGGUUACCGA AUUCAGUCAA A CUCCGAAU GCCAAUGACU UAUCCUUGGG AGUCAGACUG CGAGUGAUAA GAUCCGUAGU CGAAAGGGAA ACAGCCCAGA CC GCCAGCU AAGGUCCCAA AGUAUACGUU AAGUGGAAAA GGAUGUGGAG UUGCUUAGAC AACCAGGAUG UUGGCUUAGA AGC AGCCAC CAUUUAAAGA GUGCGUAAUA GCUCACUGGU CGAGUGACUC UGCGCCGAAA AUGUACCGGG GCUAAACGUA UCAC CGAAG CUGCGGACUG UUCUUCGAAC AGUGGUAGGA GAGCGUUCUA AGGGCUGUGA AGCCAGACCG GAAGGACUGG UGGAG CGCU UAGAAGUGAG AAUGCCGGUA UGAGUAGCGA AAGAGGGGUG AGAAUCCCCU CCACCGAAUG CCUAAGGUUU CCUGAG GAA GGCUCGUCCG CUCAGGGUUA GUCGGGACCU AAGCCGAGGC CGAAAGGCGU AGGCGAUGGA CAACAGGUUG AUAUUCC UG UACCACCUCC UCACCAUUUG AGCAAUGGGG GGACGCAGGA GGAUAGGGUA AGCGCGGUAU UGGAUAUCCG CGUCCAAG C AGUUAGGCUG GGAAAUAGGC AAAUCCGUUU CCCAUAAGGC UGAGCUGUGA UGGCGAGCGA AAUAUAGUAG CGAAGUUCC UGAUUCCACA CUGCCAAGAA AAGCCUCUAG CGAGGUGAGA GGUGCCCGUA CCGCAAACCG ACACAGGUAG GCGAGGAGAG AAUCCUAAG GUGAUCGAGA GAACUCUCGU UAAGGAACUC GGCAAAAUGA CCCCGUAACU UCGGGAGAAG GGGUGCUCUG U UAGGGUGC AAGCCCGAGA GAGCCGCAGU GAAUAGGCCC AGGCGACUGU UUAGCAAAAA CACAGGUCUC UGCGAAGCCG UA AGGCGAA GUAUAGGGGC UGACGCCUGC CCGGUGCUGG AAGGUUAAGA GGAGCGCUUA GCGUAAGCGA AGGUGCGAAU UGA AGCCCC AGUAAACGGC GGCCGUAACU AUAACGGUCC UAAGGUAGCG AAAUUCCUUG UCGGGUAAGU UCCGACCCGC ACGA AAGGC GCAACGAUCU GGGCACUGUC UCAACGAGAG ACUCGGUGAA AUUAUAGUAC CUGUGAAGAU GCAGGUUACC CGCGA CAGG ACGGAAAGAC CCCGUGGAGC UUUACUGCAG CCUGAUAUUG AAUGUUGGUA CAGCUUGUAC AGGAUAGGUA GGAGCC UUG GAAACCGGAG CGCCAGCUUU GGUGGAGGCA UCGGUGGGAU ACUACCCUGG CUGUAUUGAC CUUCUAACCC GCCGCCC UU AUCGGGCGGG GAGACAGUGU CAGGUGGGCA GUUUGACUGG GGCGGUCGCC UCCUAAAAGG UAACGGAGGC GCCCAAAG G UUCCCUCAGA AUGGUUGGAA AUCAUUCGCA GAGUGUAAAG GCACAAGGGA GCUUGACUGC GAGACCUACA AGUCGAGCA GGGACGAAAG UCGGGCUUAG UGAUCCGGUG GUUCCGCAUG GAAGGGCCAU CGCUCAACGG AUAAAAGCUA CCCCGGGGAU AACAGGCUU AUCUCCCCCA AGAGUCCACA UCGACGGGGA GGUUUGGCAC CUCGAUGUCG GCUCAUCGCA UCCUGGGGCU G UAGUCGGU CCCAAGGGUU GGGCUGUUCG CCCAUUAAAG CGGUACGCGA GCUGGGUUCA GAACGUCGUG AGACAGUUCG GU CCCUAUC CGUCGCGGGC GCAGGAAAUU UGAGAGGAGC UGUCCUUAGU ACGAGAGGAC CGGGAUGGAC GCACCGCUGG UGU ACCAGU UGUUCUGCCA AGGGCAUCGC UGGGUAGCUA UGUGCGGACG GGAUAAGUGC UGAAAGCAUC UAAGCAUGAA GCCC CCCUC AAGAUGAGAU UUCCCAUUCC GCAAGGAAGU AAGAUCCCUG AAAGAUGAUC AGGUUGAUAG GUCUGAGGUG GAAGU GUGG CGACACAUGG AGCUGACAGA UACUAAUCGA UCGAGGACUU AACCAU

GENBANK: GENBANK: D26185.1

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Macromolecule #4: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 37.420242 KDa
SequenceString:
UUUGGUGGCG AUAGCGAAGA GGUCACACCC GUUCCCAUAC CGAACACGGA AGUUAAGCUC UUCAGCGCCG AUGGUAGUCG GGGGUUUCC CCCUGUGAGA GUAGGACGCC GCCAAGC

GENBANK: GENBANK: CP019662.1

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Macromolecule #31: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 31 / Number of copies: 221 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #32: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 32 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 23.94 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57683
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

3j3v


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6tnn:
Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA

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