EMDB-61960: EF-G2 bound 50S ribosome subunit complex of M. smegmatis

Basic information

Entry

Database: EMDB / ID: EMD-61960

• Title: EF-G2 bound 50S ribosome subunit complex of M. smegmatis
• Map data: EF-G2 bound 50S ribosome subunit complex of M. smegmatis

Sample

• Complex: EF-G2 bound 50S ribosomal subunit complex of M. smegmatis
  • Protein or peptide: x 33 types
  • RNA: x 2 types
• Ligand: x 3 types

• Keywords: Mycobacterium 50S ribosomal subunit / elongation factor G2 / stationary phase / RIBOSOME

Function / homology

Function:

ribosome disassembly / translation elongation factor activity / 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 / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / metal ion binding / cytoplasm

Domain/homology:

: / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / : / : / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L11, bacterial-type / Elongation factor Tu domain 2 / Ribosomal protein L31 type A / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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 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 L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / 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 L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 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 L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / 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 L33

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 / Elongation factor G-like protein / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34

• Biological species: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Method: single particle reconstruction / cryo EM / Resolution: 3.6 Å
• Authors: Sengupta J / Baid P

Funding support

India, 3 items

Organization	Grant number	Country
Science and Engineering Research Board (SERB)	SPF/2021/000141	India
Science and Engineering Research Board (SERB)	CRG/2019/001788	India
Council of Scientific & Industrial Research (CSIR)	MLP-139	India

• Citation: Journal: FEBS J / Year: 2025; Title: Cryo-EM structural analyses reveal a unique role for elongation factor G2 (EF-G2) in Mycobacteria.; Authors: Priya Baid / Jayati Sengupta / ; Abstract: The gene-encoding translation elongation factor G (EF-G) has undergone gene duplication across various bacterial species including Mycobacteria, and in mammalian mitochondria, leading to the emergence of the paralogue elongation factor G2 (EF-G2). Our study reveals that mycobacterial EF-G2, unlike EF-G1, neither participates in ribosome-recycling nor significantly contributes to overall translation, suggesting that it plays an alternative role in Mycobacteria. Remarkably, our investigation found a significant overexpression of mycobacterial EF-G2 during the stationary growth phase. Moreover, EF-G2 lacks ribosome-dependent GTPase activity, an observation consistent with previous reports. Cryo-EM analysis of the M. smegmatis 70S ribosome purified from the nutrient-starved (stationary) phase and complexed with EF-G2 unveiled the structural basis for its inability to hydrolyse GTP in a ribosome-dependent manner. Furthermore, we report an unprecedented binding mode of two EF-G2 copies on the 50S ribosomal subunit that impedes subunit association, thereby preventing the formation of active 70S ribosomes. Thus, instead of performing canonical functions, mycobacterial EF-G2 acts as a translation repressor during nutrient starvation. Altogether, our findings shed light on the multifaceted mechanisms by which EF-G2 modulates protein synthesis under nutrient-limited conditions, providing insights into adaptive strategies employed by Mycobacteria to survive in hostile environments.

History

Deposition	Oct 16, 2024	-
Header (metadata) release	Jul 9, 2025	-
Map release	Jul 9, 2025	-
Update	Jul 9, 2025	-
Current status	Jul 9, 2025	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_61960.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: EF-G2 bound 50S ribosome subunit complex of M. smegmatis
• Voxel size: X=Y=Z: 1.38 Å

Density

Contour Level	By AUTHOR: 0.00715
Minimum - Maximum	-0.025269248 - 0.11831812
Average (Standard dev.)	0.00014985882 (±0.0062006204)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z 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

Half map: half map 1 of EF-G2 bound 50S ribosome...

• File: emd_61960_half_map_1.map
• Annotation: half map 1 of EF-G2 bound 50S ribosome subunit complex of M. smegmatis

Half map: half map 2 of EF-G2 bound 50S ribosome...

• File: emd_61960_half_map_2.map
• Annotation: half map 2 of EF-G2 bound 50S ribosome subunit complex of M. smegmatis

Sample components

Entire : EF-G2 bound 50S ribosomal subunit complex of M. smegmatis

• Entire: Name: EF-G2 bound 50S ribosomal subunit complex of M. smegmatis

Components

• Complex: EF-G2 bound 50S ribosomal subunit complex of M. smegmatis
  • Protein or peptide: 50S ribosomal protein bL37
  • Protein or peptide: Translation elongation factor EF-G
  • 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 L9
  • 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: Large ribosomal subunit protein uL24
  • 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: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
• Ligand: MAGNESIUM ION
• Ligand: ZINC ION

Supramolecule #1: EF-G2 bound 50S ribosomal subunit complex of M. smegmatis

• Supramolecule: Name: EF-G2 bound 50S ribosomal subunit complex of M. smegmatis; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #35, #3-#34
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 1.8 MDa

Macromolecule #1: 50S ribosomal protein bL37

• Macromolecule: Name: 50S ribosomal protein 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 #2: Translation elongation factor EF-G

• Macromolecule: Name: Translation elongation factor EF-G / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 75.420797 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

GSVPTAERPA AIRNVALVGP SGGGKTTLVE ALLVAGGVLT RPGSVADGST VCDFDEAEIA QQRSVSLALA SLSHNGIKVN LIDTPGYAD FVGELRAGLR AADCALFVIA ANETIDEPTK TLWQECNEVQ MPRAVVITKL DHPRANYDAA LTAAQEAFGD K VAPLYFPV GDGESCKGVV GLLTRTYYDY SGGTHTARPP DGSHDAAIAE LRGSLIEGVI EESEDETLME RYLGGEEIDE AV LIADLEK AVARASFFPV IPVCSQSGVG TLELLDIISR GFPAPPEHQL PEVFTPQGAP RKPLSCDPDG PLLAEVVKTT SDP YVGRVS LVRVFSGTIR PDATVHVSGH FSAFTDTSGS HGAAAAADGS THSHADHDED ERIGTLSFPL GKQQRPAPTV VAGD ICAIG RLSRAETGDT LSDKTDPLVL RPWTMPDPLL PIAVAPRAKT DEDKLSVGLQ RLAAEDPTLR IEQNPETHQI VLWCM GEAH AAVVLDALSR RYGVSVDTVE LRVPLRETFA GKATGHGRHV KQSGGHGQYA VCDIEVEPLP EGSGFEFVDK VVGGAV PRQ FIPSVEKGVR AQMEKGVTGE SGYPVVDIRV TLFDGKAHSV DSSDFAFQMA GALALRDAAA ATKINLLEPV DDVTIVV PD DLVGTIMGDL SGRRGRVLGT DKHDADRTVI KAEIPEVELV RYAIDLRSMS HGAGQFRRSF ARYEPMP

UniProtKB: Elongation factor G-like 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 L9

• Macromolecule: Name: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 15.949253 KDa

Sequence

String:

MKLILTAEVE HLGAAGDTVE VKDGYGRNYL LPRGLAIVAS RGAERQAEEI RRARESKVIR DIEHANELKT ALEGLGDVTL SVNAAGDTG KLFGSVTAAD VVNAIKKAGG PNLDKRTVQL AKAHIKSVGT HPVTVKLHTG VEAKVSLNVV AQ

UniProtKB: Large ribosomal subunit protein bL9

Macromolecule #10: 50S ribosomal protein L10

• Macromolecule: Name: 50S ribosomal protein L10 / type: protein_or_peptide / ID: 10 / 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 #11: 50S ribosomal protein L11

• Macromolecule: Name: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 11 / 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 #12: 50S ribosomal protein L13

• Macromolecule: Name: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 12 / 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 #13: 50S ribosomal protein L14

• Macromolecule: Name: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 13 / 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 #14: 50S ribosomal protein L15

• Macromolecule: Name: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 14 / 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 #15: 50S ribosomal protein L16

• Macromolecule: Name: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 15 / 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 #16: 50S ribosomal protein L17

• Macromolecule: Name: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 16 / 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 #17: 50S ribosomal protein L18

• Macromolecule: Name: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 17 / 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 #18: 50S ribosomal protein L19

• Macromolecule: Name: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 18 / 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 #19: 50S ribosomal protein L20

• Macromolecule: Name: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 19 / 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 #20: 50S ribosomal protein L21

• Macromolecule: Name: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 20 / 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 #21: 50S ribosomal protein L22

• Macromolecule: Name: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 21 / 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 #22: 50S ribosomal protein L23

• Macromolecule: Name: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 22 / 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 #23: Large ribosomal subunit protein uL24

• Macromolecule: Name: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 23 / 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 #24: 50S ribosomal protein L25

• Macromolecule: Name: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 24 / 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 #25: 50S ribosomal protein L27

• Macromolecule: Name: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 25 / 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 #26: 50S ribosomal protein L28

• Macromolecule: Name: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 26 / 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 #27: 50S ribosomal protein L29

• Macromolecule: Name: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 27 / 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 #28: 50S ribosomal protein L30

• Macromolecule: Name: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 28 / 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 #29: 50S ribosomal protein L32

• Macromolecule: Name: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 29 / 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 #30: 50S ribosomal protein L33 1

• Macromolecule: Name: 50S ribosomal protein L33 1 / type: protein_or_peptide / ID: 30 / 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 #31: 50S ribosomal protein L34

• Macromolecule: Name: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 31 / 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 #32: 50S ribosomal protein L35

• Macromolecule: Name: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 32 / 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 #33: 50S ribosomal protein L36

• Macromolecule: Name: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 33 / 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 #34: 50S ribosomal protein L31

• Macromolecule: Name: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 34 / 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 #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 #35: 23S ribosomal RNA

• Macromolecule: Name: 23S ribosomal RNA / type: rna / ID: 35 / Number of copies: 1
• Source (natural): Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
• Molecular weight: Theoretical: 1.014391625 MDa

Sequence

String:

UUGUAAGUGU UUAAGGGCGC AUGGUGGAUG CCUUGGCACU GGGAGCCGAU GAAGGACGUA GGAGGCUGCG AUAAGCCUCG GGGAGCUGU CAACCGAGCG UUGAUCCGAG GAUGUCCGAA UGGGGAAACC CGGCACGAGU GAUGUCGUGU CACCAGGCGC U GAAUAUAU AGGCGUCUGG GGGGAACGCG GGGAAGUGAA ACAUCUCAGU ACCCGUAGGA AGAGAAAACA AAAUGUGAUU CC GUGAGUA GUGGCGAGCG AAAGCGGAGG AUGGCUAAAC CGUAUGCAUG UGAUACCGGG UAGGGGUUGU GUGUGCGGGG UUG UGGGAC CUAUCUUUCC GGCUCUACCU GGCUGGAGGG CAGUGAGAAA AUGUUGUGGU UAGCGGAAAU GGCUUGGGAU GGCC UGCCG UAGACGGUGA GAGCCCGGUA CGUGAAAACC CGACGUCUGU CUUGAUGGUG UUCCCGAGUA GCAGCGGGCC CGUGG AAUC UGCUGUGAAU CUGCCGGGAC CACCCGGUAA GCCUGAAUAC UUCCCAGUGA CCGAUAGCGG AUUAGUACCG UGAGGG AAU GGUGAAAAGU ACCCCGGGAG GGGAGUGAAA GAGUACCUGA AACCGUGCGC UUACAAUCCG UCAGAGCCCU CGACGUG UC GUGGGGUGAU GGCGUGCCUU UUGAAGAAUG AGCCUGCGAG UCAGGGACAU GUCGCGAGGU UAACCCGGGU GGGGUAGC C GCAGCGAAAG CGAGUCUGAA UAGGGCGUAU CCACACAAGA GUGUGUGGUG UAGUGGUGUG UUCUGGACCC GAAGCGGAG UGAUCUACCC AUGGCCAGGG UGAAGCGCGG GUAAGACCGC GUGGAGGCCC GAACCCACUU AGGUUGAAGA CUGAGGGGAU GAGCUGUGG GUAGGGGUGA AAGGCCAAUC AAACUCCGUG AUAGCUGGUU CUCCCCGAAA UGCAUUUAGG UGCAGCGUCG C AUGUUUCU UGCCGGAGGU AGAGCUACUG GAUGGCCGAU GGGCCCCACA GGGUUACUGA CGUCAGCCAA ACUCCGAAUG CC GGUAAGU CCAAGAGUGC GGCAGUGAGA CGGCGGGGGA UAAGCUCCGU GCGUCGAGAG GGAAACAGCC CAGAUCGCCG GCU AAGGCC CCUAAGCGUG UGCUAAGUGG AAAAGGAUGU GCAGUCGCGA AGACAACCAG GAGGUUGGCU UAGAAGCAGC CACC CUUGA AAGAGUGCGU AAUAGCUCAC UGGUCAAGUG AUUGUGCGCC GAUAAUGUAG CGGGGCUCAA GCACACCGCC GAAGC CGCG GCAGCCAACG UGUUGGCUGG GUAGGGGAGC GUCCUGCAUC CGGUGAAGCC GCCGAGUGAU CGAGUGGUGG AGGGUG UGG GAGUGAGAAU GCAGGCAUGA GUAGCGAUUA GGCAAGUGAG AACCUUGCCC GCCGAAAGAC CAAGGGUUCC UGGGCCA GG CCAGUCCGCC CAGGGUGAGU CGGGACCUAA GGCGAGGCCG ACAGGCGUAG UCGAUGGACA ACGGGUUGAU AUUCCCGU A CCCGUGUAUG UGCGUCCAUG AUGAAUCAGC GGUACUAACC AUCCAAAACC ACCGUGACCG CACCUUUCGG GGUGUGGCG UUGGUGGGGC UGCAUGGGAC CUUCGUUGGU AGUAGUCAAG CGAUGGGGUG ACGCAGGAAG GUAGCCGUAC CGGUCAGUGG UAAUACCGG GGUAAGCCUG UAGGGAGUCA GAUAGGUAAA UCCGUCUGGC AUAUAUCCUG AGAGGUGAUG CAUAGCCGAG U GAGGCGAA UUCGGUGAUC CUAUGCUGCC GAGAAAAGCC UCUAGCGAGG ACAUACACGG CCCGUACCCC AAACCAACAC AG GUGGUCA GGUAGAGAAU ACUAAGGCGU ACGAGUGAAC UAUGGUUAAG GAACUCGGCA AAAUGCCCCC GUAACUUCGG GAG AAGGGG GACCCACAUG GCGUGUAAGC CUUUACGGCC CAAGCGUGAG UGGGUGGCAC AAACCAGUGA GAAGCGACUG UUUA CUAAA AACACAGGUC CGUGCGAAGU CGCAAGACGA UGUAUACGGA CUGACGCCUG CCCGGUGCUG GAAGGUUAAG AGGAC CCGU UAACUCCCUU UGGGGGUGAA GCGGAGAAUU UAAGCCCCAG UAAACGGCGG UGGUAACUAU AACCAUCCUA AGGUAG CGA AAUUCCUUGU CGGGUAAGUU CCGACCUGCA CGAAUGGCGU AACGACUUCU CAACUGUCUC AACCAUAGAC UCGGCGA AA UUGCACUACG AGUAAAGAUG CUCGUUACGC GCGGCAGGAC GAAAAGACCC CGGGACCUUC ACUACAACUU GGUAUUGG U GCUCGAUACG GUUUGUGUAG GAUAGGUGGG AGACUGUGAA GCUCACACGC CAGUGUGGGU GGAGUCGUUG UUGAAAUAC CACUCUGAUC GUAUUGGGCC UCUAACCUCG GACCGUAUAU CCGGUUCAGG GACAGUGCCU GGUGGGUAGU UUAACUGGGG CGGUUGCCU CCUAAAAUGU AACGGAGGCG CCCAAAGGUU CCCUCAACCU GGACGGCAAU CAGGUGUUGA GUGUAAGUGC A CAAGGGAG CUUGACUGCG AGACGGACAU GUCGAGCAGG GACGAAAGUC GGGACUAGUG AUCCGGCACC UCUGAGUGGA AG GGGUGUC GCUCAACGGA UAAAAGGUAC CCCGGGGAUA ACAGGCUGAU CUUCCCCAAG AGUCCAUAUC GACGGGAUGG UUU GGCACC UCGAUGUCGG CUCGUCGCAU CCUGGGGCUG GAGCAGGUCC CAAGGGUUGG GCUGUUCGCC CAUUAAAGCG GCAC GCGAG CUGGGUUUAG AACGUCGUGA GACAGUUCGG UCUCUAUCCG CCGCGCGCGU CAGAAGCUUG AGGAAACCUG UCCCU AGUA CGAGAGGACC GGGACGGACG AACCUCUGGU AUACCAGUUG UCCCACCAGG GGCACGGCUG GAUAGCCACG UUCGGA CAG GAUAACCGCU GAAAGCAUCU AAGCGGGAAA CCUCUUCCAA GACCAGGCUU CUCACCCUCU AGGAGGGAUA AGGCCCC CC GCAGACCACG GGAUUGAUAG ACCAGACCUG GAAGCCUAGU AAUAGGUGCA GGGAACUGGC ACUAACCGGC CGAAAACU U ACAACA

Macromolecule #36: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

• Macromolecule: Name: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 36 / Number of copies: 2 / Formula: GNP
• Molecular weight: Theoretical: 522.196 Da

Chemical component information

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

Macromolecule #37: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 37 / Number of copies: 407 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #38: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 38 / 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: 7.8
• 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

• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

Startup model

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

7xam

• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39621
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: ANGULAR RECONSTITUTION

Atomic model buiding 1

Initial model

PDB ID:

7xam

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

• Refinement: Space: REAL / Protocol: FLEXIBLE FIT

Output model

PDB-9k10:
EF-G2 bound 50S ribosome subunit complex of M. smegmatis