EMDB-33599: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth

Basic information

Entry

Database: EMDB / ID: EMD-33599

• Title: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth
• Map data: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth

Sample

• Complex: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth
  • Protein or peptide: x 31 types
  • RNA: x 2 types
• Ligand: x 2 types

• Keywords: Mycobacterium 50S subunit / Domain IV of 23S rRNA / Log Phase / RIBOSOME

Function / homology

Function:

large ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / metal ion binding / cytoplasm

Domain/homology:

Ribosomal protein L25, long-form / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / : / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 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 L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L21 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / 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 L32p

Component:

Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Uncharacterized protein / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34

• Biological species: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Method: single particle reconstruction / cryo EM / Resolution: 4.1 Å
• Authors: Sengupta J / Baid P

Funding support

India, 2 items

Organization	Grant number	Country
Science and Engineering Research Board (SERB)	CRG/2019/001788	India
Council of Scientific & Industrial Research (CSIR)	MLP-139	India

• Citation: Journal: Int J Biol Macromol / Year: 2023; Title: Cryo-EM captures a unique conformational rearrangement in 23S rRNA helices of the Mycobacterium 50S subunit.; Authors: Priya Baid / Jayati Sengupta / ; Abstract: Structural investigations of the ribosomes isolated from pathogenic and non-pathogenic Mycobacterium species have identified several mycobacteria-specific structural features of ribosomal RNA and proteins. Here, we report structural evidence of a hitherto unknown conformational switch of mycobacterium 23S rRNA helices (H54a and H67-H71). Cryo-electron microscopy (cryo-EM) structures (~3-4 Å) of the M. smegmatis (Msm) log-phase 50S ribosomal subunit revealed conformational variability in H67-H71 region of the 23S rRNA, and manifested that, while H68 possesses the usual stretched conformation in one class of the maps, another one exhibits a bulge-out, fused density of H68-H69 at the inter-subunit surface, indicating an intrinsic dynamics of these rRNA helices. Remarkably, altered conformation of H68 forming a more prominent bulge-out structure at the inter-subunit surface of the 50S subunit due to the conformational rearrangements of 23S rRNA H67-H71 region was clearly visualized in a 3 Å cryo-EM map of the 50S subunit obtained from the stationary phase ribosome dataset. The Msm50S subunit having such bulge-out conformation at the intersubunit surface would be incompatible for associating with the 30S subunit due to its inability to form major inter-subunit bridges. Evidently, availability of active 70S ribosome pool can be modulated by stabilizing either one of the H68 conformation.

History

Deposition	Jun 13, 2022	-
Header (metadata) release	May 3, 2023	-
Map release	May 3, 2023	-
Update	May 15, 2024	-
Current status	May 15, 2024	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_33599.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth
• Voxel size: X=Y=Z: 1.38 Å

Density

Contour Level	By AUTHOR: 0.03
Minimum - Maximum	-0.09313059 - 0.21231179
Average (Standard dev.)	0.00014898977 (±0.008581964)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order Z Y X Origin 0 0 0 Dimensions 350 350 350 Spacing 350 350 350
Cell	A=B=C: 483.0 Å α=β=γ: 90.0 °

Supplemental data

Additional map: Mycobacterium smegmatis 50S ribosomal subunit alternative conformation found...

• File: emd_33599_additional_1.map
• Annotation: Mycobacterium smegmatis 50S ribosomal subunit alternative conformation found in Log Phase of growth

Half map: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase...

• File: emd_33599_half_map_1.map
• Annotation: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth Half Map 1

Half map: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase...

• File: emd_33599_half_map_2.map
• Annotation: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth Half Map 2

Sample components

Entire : Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth

• Entire: Name: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth

Components

• Complex: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth
  • Protein or peptide: 50S ribosomal subunit bL37
  • RNA: 23S ribosomal RNA
  • RNA: 5S 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 L10
  • Protein or peptide: 50S ribosomal protein L11
  • 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 L25
  • Protein or peptide: 50S ribosomal protein L27
  • Protein or peptide: 50S ribosomal protein L28
  • Protein or peptide: 50S ribosomal protein L29
  • Protein or peptide: 50S ribosomal protein L30
  • 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 L31
• Ligand: MAGNESIUM ION
• Ligand: ZINC ION

Supramolecule #1: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth

• Supramolecule: Name: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#33
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 1.8 MDa

Macromolecule #1: 50S ribosomal subunit bL37

• Macromolecule: Name: 50S ribosomal subunit bL37 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 2.841375 KDa

Sequence

String:

MAKRGRKKRD RKHSKANHGK RPNA

UniProtKB: Uncharacterized protein

Macromolecule #4: 50S ribosomal protein L2

• Macromolecule: Name: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 30.425945 KDa

Sequence

String:

MGIRKYKPTT PGRRGASVSD FAEITRSTPE KSLVRPLHGK GGRNAHGRIT TRHKGGGHKR AYRVIDFRRH DKDGVNAKVA HIEYDPNRT ANIALLHYLD GEKRYIIAPQ GLKQGDVIES GANADIKPGN NLPLRNIPAG TVIHAVELRP GGGAKLARSA G VSIQLLGK EGTYAALRMP SGEIRRVDVR CRATVGEVGN AEQSNINWGK AGRMRWKGKR PTVRGVVMNP VDHPHGGGEG KT SGGRHPV SPWGKPEGRT RKPNKPSDKL IVRRRRTGKK R

UniProtKB: Large ribosomal subunit protein uL2

Macromolecule #5: 50S ribosomal protein L3

• Macromolecule: Name: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 23.011393 KDa

Sequence

String:

MARKGILGTK LGMTQVFDEN NKVVPVTVVK AGPNVVTRIR TTERDGYSAV QLAYGEISPR KVIKPVAGQF AAAGVNPRRH VAELRLDDE AAVAEYEVGQ ELTAEIFSDG AYVDVTGTSK GKGFAGTMKR HGFRGQGAAH GAQAVHRRPG SIGGCATPGR V FKGTRMSG RMGNDRVTTQ NLKVHKVDAE NGVLLIKGAI PGRNGGLVVV RSAIKRGEK

UniProtKB: Large ribosomal subunit protein uL3

Macromolecule #6: 50S ribosomal protein L4

• Macromolecule: Name: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 22.920949 KDa

Sequence

String:

MTLKVDVKTP AGKTDGSVEL PAELFDVEPN IALMHQVVTA QLAAKRQGTH STKTRGEVSG GGKKPYRQKG TGRARQGSTR APQFTGGGT VHGPKPRDYS QRTPKKMIAA ALRGALSDRA RNDRIHAVTE LVEGQTPSTK SAKTFLGTLT ENKKVLVVIG R TDEVGAKS VRNLPGVHVI SPDQLNTYDV LNADDVVFSV EALNAYISAN SKEGASV

UniProtKB: Large ribosomal subunit protein uL4

Macromolecule #7: 50S ribosomal protein L5

• Macromolecule: Name: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 21.152328 KDa

Sequence

String:

MTTTEKALPR LKQRYREEIR EALQQEFNYA NVMQIPGVVK VVVNMGVGDA ARDAKLINGA INDLALITGQ KPEVRRARKS IAQFKLREG MPIGARVTLR GDRMWEFLDR LISIALPRIR DFRGLSPKQF DGTGNYTFGL NEQSMFHEID VDSIDRPRGM D ITVVTTAT NDAEGRALLR ALGFPFKEN

UniProtKB: Large ribosomal subunit protein uL5

Macromolecule #8: 50S ribosomal protein L6

• Macromolecule: Name: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 19.483361 KDa

Sequence

String:

MSRIGKQPVP VPSGVDVTIN GQNLSVKGPK GTLTLDVAEP ISVSRAEDGA IVVTRPDDER RSRSLHGLSR TLIANLVTGV TEGYTQKME IFGVGYRVQL KGQNLEFALG YSHPVLIEAP EGITFAVESP TKFSVSGIDK QKVGQISAVI RRLRRPDPYK G KGVRYEGE QIRRKVGKTG K

UniProtKB: Large ribosomal subunit protein uL6

Macromolecule #9: 50S ribosomal protein L10

• Macromolecule: Name: 50S ribosomal protein L10 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 18.035736 KDa

Sequence

String:

MAKADKATAV ADIAEQFKAS TATVVTEYRG LTVANLAELR RALGDSATYT VAKNTLVKRA ASEAGIEGLD ELFAGPTAIA FVKGEAVDA AKAIKKFAKD NKALVIKGGY MDGKALSVAD VEKIADLESR EVLLAKLAGA MKGNLSKAAG LFNAPASQVA R LAAALQEK KAGEEAA

UniProtKB: Large ribosomal subunit protein uL10

Macromolecule #10: 50S ribosomal protein L11

• Macromolecule: Name: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 15.023374 KDa

Sequence

String:

MAPKKKVAGL IKLQIQAGQA NPAPPVGPAL GQHGVNIMEF CKAYNAATES QRGNVIPVEI TVYEDRSFTF ALKTPPAAKL LLKAAGVQK GSGEPHKTKV AKVTWDQVRE IAETKKADLN ANDIDAAAKI IAGTARSMGI TVE

UniProtKB: Large ribosomal subunit protein uL11

Macromolecule #11: 50S ribosomal protein L13

• Macromolecule: Name: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 16.146689 KDa

Sequence

String:

MPTYTPKAGD TTRSWYVIDA SDVVLGRLAS AAATLLRGKH KPTFTPNVDG GDFVIVINAD KIAVSGDKLT KKFAYRHSGY PGGLRKRTI GELLEKHPTR VVENAIIGML PHNKLGRQIQ KKLKVYAGPD HPHAAQQPIP FEIKQVAQ

UniProtKB: Large ribosomal subunit protein uL13

Macromolecule #12: 50S ribosomal protein L14

• Macromolecule: Name: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 13.400625 KDa

Sequence

String:

MIQQESRLKV ADNTGAKEIL CIRVLGGSSR RYAGIGDVIV ATVKDAIPGG NVKRGDVVKA VVVRTVKERR RADGSYIKFD ENAAVIIKN DNDPRGTRIF GPVGRELREK KFMKIVSLAP EVL

UniProtKB: Large ribosomal subunit protein uL14

Macromolecule #13: 50S ribosomal protein L15

• Macromolecule: Name: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 15.602244 KDa

Sequence

String:

MSVIKLHDLK PAPGEKKAKT RVGRGEGSKG KTAGRGTKGT KARKNVPVMF EGGQMPIHMR LPKLKGFKNR FRTEYQVVNV GDINKAFPQ GGTVGVDELV AKGLVRKNSL VKVLGDGKLT VKVDVTANKF SGSAREAITA AGGSATEL

UniProtKB: Large ribosomal subunit protein uL15

Macromolecule #14: 50S ribosomal protein L16

• Macromolecule: Name: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 15.77424 KDa

Sequence

String:

MLIPRKVKHR KQHHPEQRGI ASGGTSVSFG DYGIQALEHA YITNRQIESA RIAINRHIKR GGKVWINIFP DRPLTKKPAE TRMGSGKGS PEWWVANVKP GRVLFELSYP DEKTARDALT RAIHKLPIKA RIVTREEQF

UniProtKB: Large ribosomal subunit protein uL16

Macromolecule #15: 50S ribosomal protein L17

• Macromolecule: Name: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 21.892246 KDa

Sequence

String:

MPKPTKGPRL GGSSSHQSAL LANLATSLFE HGRIKTTEPK ARALRPYAEK LITHAKKGAL HNRREVMKKI RDKDVVHTLF AEIGPFYAD RNGGYTRIIK VENRKGDNAP MAVIELVREK TVTDEANRAR RAAASQAKAD ERADEKADEK AEETVEETTE A PAEESTEA AAEETVEETT EAPAEESTEA AEESEAKDDT K

UniProtKB: Large ribosomal subunit protein bL17

Macromolecule #16: 50S ribosomal protein L18

• Macromolecule: Name: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 13.711728 KDa

Sequence

String:

MAHKPVGQNI SEVRRNARLR RHARLRKKVA GTAEVPRLVV NRSARHIHVQ LVNDLNGTTL AAASSIEADV RAIDGDKKAH SVRVGQLIA ERAKAAGVET VVFDRGGYTY GGRIAALADA AREAGLKF

UniProtKB: Large ribosomal subunit protein uL18

Macromolecule #17: 50S ribosomal protein L19

• Macromolecule: Name: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 12.892806 KDa

Sequence

String:

MNTLDFVDQA SLRDDIPTFS PGDTVNVHVK VIEGSKERIQ VFKGVVIRRQ GGGISETFTV RKESYGVGVE RTFPVHSPNI DHIDVLTRG DVRRAKLYYL RELRGKKAKI KEKR

UniProtKB: Large ribosomal subunit protein bL19

Macromolecule #18: 50S ribosomal protein L20

• Macromolecule: Name: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 14.494693 KDa

Sequence

String:

MARVKRALNA QKKRRTVLKA SKGYRGQRSR LYRKAKEQQL HSLTYAYRDR RARKGEFRKL WISRINAAAR ANDITYNRLI QGLKAAGVE VDRKNLAELA VSDPAAFTAL VDVARAALPE DVNAPSGEAA

UniProtKB: Large ribosomal subunit protein bL20

Macromolecule #19: 50S ribosomal protein L21

• Macromolecule: Name: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 11.055894 KDa

Sequence

String:

MATYAIVKTG GKQYKVAAGD VVKVEKLDSE PGASVSLPVA LVVDGANVTS KADDLAKVAV TAEVLEHTKG PKIRIHKFKN KTGYHKRQG HRQQLTVLKV TGIK

UniProtKB: Large ribosomal subunit protein bL21

Macromolecule #20: 50S ribosomal protein L22

• Macromolecule: Name: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 16.3536 KDa

Sequence

String:

MSTVTEFPSA TAKARYVRVS ATKARRVIDL VRGKSVEEAL DILRWAPQAA SEPVAKVIAS AAANAQNNEG LDPSTLVVAT VYADEGPTA KRIRPRAQGR AFRIRKRTSH ITVIVESRPP KQKGASAASA RSRRAQGSKA AATKKSAETK EGSE

UniProtKB: Large ribosomal subunit protein uL22

Macromolecule #21: 50S ribosomal protein L23

• Macromolecule: Name: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 11.047836 KDa

Sequence

String:

MATITDPRDI ILAPVISEKS YGLIEDNVYT FVVHPDSNKT QIKIAIEKIF DVKVDSVNTA NRQGKRKRTR TGFGKRKSTK RAIVKLAAG SKPIDLFGAP A

UniProtKB: Large ribosomal subunit protein uL23

Macromolecule #22: 50S ribosomal protein L24

• Macromolecule: Name: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 11.228946 KDa

Sequence

String:

MKVHKGDTVL VISGKDKGAK GKVLVAYPDR NKVLVEGVNR IKKHTAVSAN ERGASSGGIV TQEAPIHVSN VMVVDSDGKP TRVGYRIDD ETGKKVRIAK TNGKDI

UniProtKB: Large ribosomal subunit protein uL24

Macromolecule #23: 50S ribosomal protein L25

• Macromolecule: Name: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 22.571078 KDa

Sequence

String:

MAKTANIPNK LTANVRTRTG KGASRQARRD GKVPAVLYGH GTDPQHLELN ARDFAAVLRS HGTNAILTLD IEGTEQLALT KALDVHPIR RNIQHADLLV VQRGEKVTVE VTVLVEGDAT PGTLVTQDAN TIEIEAEALS IPEQLTVSVE GVEAGTQITA G QISLPEGV NLISDPELLV VNVVEAPSAE ALEEEGAGET GAAEAPAEEA PAEEPAE

UniProtKB: Large ribosomal subunit protein bL25

Macromolecule #24: 50S ribosomal protein L27

• Macromolecule: Name: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 9.249582 KDa

Sequence

String:

MAHKKGASSS RNGRDSAAQR LGVKRFGGQV VKAGEILVRQ RGTHFHPGVN VGRGGDDTLF ALAPGAVEFG AKRGRKTVNI VPVARPEA

UniProtKB: Large ribosomal subunit protein bL27

Macromolecule #25: 50S ribosomal protein L28

• Macromolecule: Name: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 6.891016 KDa

Sequence

String:

MAAVCDICGK GPGFGKSVSH SHRRTSRRWN PNIQPVRAVT RPGGNKQRIN ACTSCIKAGK VSRA

UniProtKB: Large ribosomal subunit protein bL28

Macromolecule #26: 50S ribosomal protein L29

• Macromolecule: Name: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 8.790895 KDa

Sequence

String:

MAVGTTPGEL RELTDDELKD KLRESKEELF NLRFQMATGQ LSNNRRLRTV RQEIARVYTV LRERELGLAS GPAGEES

UniProtKB: Large ribosomal subunit protein uL29

Macromolecule #27: 50S ribosomal protein L30

• Macromolecule: Name: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 7.022147 KDa

Sequence

String:

MAELKITQVR STIGARWKQR ESLRTLGLKK IRQSVVREDN AQTRGLINTV HHLVEVEEVG K

UniProtKB: Large ribosomal subunit protein uL30

Macromolecule #28: 50S ribosomal protein L32

• Macromolecule: Name: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 6.467719 KDa

Sequence

String:

MAVPKRRMSR ANTRSRRAQW KAEAPGLVTV SVAGQQRKVP RRLLKAARLG LVDLDKR

UniProtKB: Large ribosomal subunit protein bL32

Macromolecule #29: 50S ribosomal protein L33 1

• Macromolecule: Name: 50S ribosomal protein L33 1 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 6.468501 KDa

Sequence

String:

MASSTDVRPK ITLACEVCKH RNYITKKNRR NDPDRLEIKK FCPNCGTHQP HKESR

UniProtKB: Large ribosomal subunit protein bL33A

Macromolecule #30: 50S ribosomal protein L34

• Macromolecule: Name: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 5.52258 KDa

Sequence

String:

MAKGKRTFQP NNRRRARVHG FRLRMRTRAG RAIVANRRSK GRRALTA

UniProtKB: Large ribosomal subunit protein bL34

Macromolecule #31: 50S ribosomal protein L35

• Macromolecule: Name: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 7.298505 KDa

Sequence

String:

MPKAKTHSGA SKRFRRTGTG KIVRQKANRR HLLEHKPTKR TRRLDGRTTV SAADNSRINK LLNG

UniProtKB: Large ribosomal subunit protein bL35

Macromolecule #32: 50S ribosomal protein L36

• Macromolecule: Name: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 4.341277 KDa

Sequence

String:

MKVNPSVKPI CDKCRVIRRH GRVMVICSDP RHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

Macromolecule #33: 50S ribosomal protein L31

• Macromolecule: Name: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 8.312485 KDa

Sequence

String:

MKTGIHPEYV DTTVQCGCGH SFTTRSTKQS GTIVVEVCSQ CHPFYTGKQK ILDSGGRVAR FEKRYGKRNK AAADK

UniProtKB: Large ribosomal subunit protein bL31

Macromolecule #2: 23S ribosomal RNA

• Macromolecule: Name: 23S ribosomal RNA / type: rna / ID: 2 / Number of copies: 1
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 1.012140938 MDa

Sequence

String:

UAAGUGUUUA AGGGCGCAUG GUGGAUGCCU UGGCACUGGG AGCCGAUGAA GGACGUAGGA GGCUGCGAUA AGCCUCGGGG AGCUGUCAA CCGAGCGUUG AUCCGAGGAU GUCCGAAUGG GGAAACCCGG CACGAGUGAU GUCGUGUCAC CAGGCGCUGA A UAUAUAGG CGUCUGGGGG GAACGCGGGG AAGUGAAACA UCUCAGUACC CGUAGGAAGA GAAAACAAAA UGUGAUUCCG UG AGUAGUG GCGAGCGAAA GCGGAGGAUG GCUAAACCGU AUGCAUGUGA UACCGGGUAG GGGUUGUGUG UGCGGGGUUG UGG GACCUA UCUUUCCGGC UCUACCUGGC UGGAGGGCAG UGAGAAAAUG UUGUGGUUAG CGGAAAUGGC UUGGGAUGGC CUGC CGUAG ACGGUGAGAG CCCGGUACGU GAAAACCCGA CGUCUGUCUU GAUGGUGUUC CCGAGUAGCA GCGGGCCCGU GGAAU CUGC UGUGAAUCUG CCGGGACCAC CCGGUAAGCC UGAAUACUUC CCAGUGACCG AUAGCGGAUU AGUACCGUGA GGGAAU GGU GAAAAGUACC CCGGGAGGGG AGUGAAAGAG UACCUGAAAC CGUGCGCUUA CAAUCCGUCA GAGCCCUCGA CGUGUCG UG GGGUGAUGGC GUGCCUUUUG AAGAAUGAGC CUGCGAGUCA GGGACAUGUC GCGAGGUUAA CCCGGGUGGG GUAGCCGC A GCGAAAGCGA GUCUGAAUAG GGCGUAUCCA CACAAGAGUG UGUGGUGUAG UGGUGUGUUC UGGACCCGAA GCGGAGUGA UCUACCCAUG GCCAGGGUGA AGCGCGGGUA AGACCGCGUG GAGGCCCGAA CCCACUUAGG UUGAAGACUG AGGGGAUGAG CUGUGGGUA GGGGUGAAAG GCCAAUCAAA CUCCGUGAUA GCUGGUUCUC CCCGAAAUGC AUUUAGGUGC AGCGUCGCAU G UUUCUUGC CGGAGGUAGA GCUACUGGAU GGCCGAUGGG CCCCACAGGG UUACUGACGU CAGCCAAACU CCGAAUGCCG GU AAGUCCA AGAGUGCGGC AGUGAGACGG CGGGGGAUAA GCUCCGUGCG UCGAGAGGGA AACAGCCCAG AUCGCCGGCU AAG GCCCCU AAGCGUGUGC UAAGUGGAAA AGGAUGUGCA GUCGCGAAGA CAACCAGGAG GUUGGCUUAG AAGCAGCCAC CCUU GAAAG AGUGCGUAAU AGCUCACUGG UCAAGUGAUU GUGCGCCGAU AAUGUAGCGG GGCUCAAGCA CACCGCCGAA GCCGC GGCA GCCAACGUGU UGGCUGGGUA GGGGAGCGUC CUGCAUCCGG UGAAGCCGCC GAGUGAUCGA GUGGUGGAGG GUGUGG GAG UGAGAAUGCA GGCAUGAGUA GCGAUUAGGC AAGUGAGAAC CUUGCCCGCC GAAAGACCAA GGGUUCCUGG GCCAGGC CA GUCCGCCCAG GGUGAGUCGG GACCUAAGGC GAGGCCGACA GGCGUAGUCG AUGGACAACG GGUUGAUAUU CCCGUACC C GUGUAUGUGC GUCCAUGAUG AAUCAGCGGU ACUAACCAUC CAAAACCACC GUGACCGCAC CUUUCGGGGU GUGGCGUUG GUGGGGCUGC AUGGGACCUU CGUUGGUAGU AGUCAAGCGA UGGGGUGACG CAGGAAGGUA GCCGUACCGG UCAGUGGUAA UACCGGGGU AAGCCUGUAG GGAGUCAGAU AGGUAAAUCC GUCUGGCAUA UAUCCUGAGA GGUGAUGCAU AGCCGAGUGA G GCGAAUUC GGUGAUCCUA UGCUGCCGAG AAAAGCCUCU AGCGAGGACA UACACGGCCC GUACCCCAAA CCAACACAGG UG GUCAGGU AGAGAAUACU AAGGCGUACG AGUGAACUAU GGUUAAGGAA CUCGGCAAAA UGCCCCCGUA ACUUCGGGAG AAG GGGGAC CCACAUGGCG UGUAAGCCUU UACGGCCCAA GCGUGAGUGG GUGGCACAAA CCAGUGAGAA GCGACUGUUU ACUA AAAAC ACAGGUCCGU GCGAAGUCGC AAGACGAUGU AUACGGACUG ACGCCUGCCC GGUGCUGGAA GGUUAAGAGG ACCCG UUAA CUCCCUUUGG GGGUGAAGCG GAGAAUUUAA GCCCCAGUAA ACGGCGGUGG UAACUAUAAC CAUCCUAAGG UAGCGA AAU UCCUUGUCGG GUAAGUUCCG ACCUGCACGA AUGGCGUAAC GACUUCUCAA CUGUCUCAAC CAUAGACUCG GCGAAAU UG CACUACGAGU AAAGAUGCUC GUUACGCGCG GCAGGACGAA AAGACCCCGG GACCUUCACU ACAACUUGGU AUUGGUGC U CGAUACGGUU UGUGUAGGAU AGGUGGGAGA CUGUGAAGCU CACACGCCAG UGUGGGUGGA GUCGUUGUUG AAAUACCAC UCUGAUCGUA UUGGGCCUCU AACCUCGGAC CGUAUAUCCG GUUCAGGGAC AGUGCCUGGU GGGUAGUUUA ACUGGGGCGG UUGCCUCCU AAAAUGUAAC GGAGGCGCCC AAAGGUUCCC UCAACCUGGA CGGCAAUCAG GUGUUGAGUG UAAGUGCACA A GGGAGCUU GACUGCGAGA CGGACAUGUC GAGCAGGGAC GAAAGUCGGG ACUAGUGAUC CGGCACCUCU GAGUGGAAGG GG UGUCGCU CAACGGAUAA AAGGUACCCC GGGGAUAACA GGCUGAUCUU CCCCAAGAGU CCAUAUCGAC GGGAUGGUUU GGC ACCUCG AUGUCGGCUC GUCGCAUCCU GGGGCUGGAG CAGGUCCCAA GGGUUGGGCU GUUCGCCCAU UAAAGCGGCA CGCG AGCUG GGUUUAGAAC GUCGUGAGAC AGUUCGGUCU CUAUCCGCCG CGCGCGUCAG AAGCUUGAGG AAACCUGUCC CUAGU ACGA GAGGACCGGG ACGGACGAAC CUCUGGUAUA CCAGUUGUCC CACCAGGGGC ACGGCUGGAU AGCCACGUUC GGACAG GAU AACCGCUGAA AGCAUCUAAG CGGGAAACCU CUUCCAAGAC CAGGCUUCUC ACCCUCUAGG AGGGAUAAGG CCCCCCG CA GACCACGGGA UUGAUAGACC AGACCUGGAA GCCUAGUAAU AGGUGCAGGG AACUGGCACU AACCGGCCGA AAACUUAC

GENBANK: GENBANK: CP000480.1

Macromolecule #3: 5S ribosomal RNA

• Macromolecule: Name: 5S ribosomal RNA / type: rna / ID: 3 / Number of copies: 1
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 38.061816 KDa

Sequence

String:

GUUACGGCGG UCCAUAGCGG CAGGGAAACG CCCGGUCCCA UCCCGAACCC GGAAGCUAAG CCUGCCAGCG CCGAUGAUAC UACCCAUCC GGGUGGAAAA GUAGGACACC GCCGAACAC

GENBANK: GENBANK: CP000480.1

Macromolecule #34: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 34 / Number of copies: 407 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #35: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 35 / Number of copies: 4 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.6
• Grid: Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 54.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.8 µm
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

Startup model

Type of model: PDB ENTRY
PDB model - PDB ID:

5o60

• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 29350
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
• Final angle assignment: Type: ANGULAR RECONSTITUTION

Atomic model buiding 1

Initial model

PDB ID:

5o60

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

• Refinement: Space: REAL / Protocol: FLEXIBLE FIT

Output model

PDB-7y41:
Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth