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- EMDB-37561: Cryo- EM structure of Mycobacterium smegmatis 30S ribosomal subun... -

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Basic information

Entry
Database: EMDB / ID: EMD-37561
TitleCryo- EM structure of Mycobacterium smegmatis 30S ribosomal subunit (body 2) of 70S ribosome, bS1 and RafH.
Map dataMycobacterium smegmatis 30S ribosome (body2) of 70S ribosome, bs1 and RafH complex.
Sample
  • Complex: 70S ribosome + RafH protein
    • Complex: 70S ribosome
      • RNA: x 1 types
      • Protein or peptide: x 22 types
    • Complex: RafH
      • Protein or peptide: x 1 types
KeywordsRibosome / protein synthesis / Mycobacterium smegmatis / hibernation promotion factor / HPF / RafH / hypoxia stress / Cryo- EM / Single particle reconstruction
Function / homology
Function and homology information


nucleotidyltransferase activity / small ribosomal subunit rRNA binding / regulation of translation / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...nucleotidyltransferase activity / small ribosomal subunit rRNA binding / regulation of translation / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S1-like / Mitochondrial mRNA-processing protein COX24, C-terminal ...: / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S1-like / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / S1 domain profile. / Ribosomal protein S14, type Z / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / S1 domain / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18
Similarity search - Domain/homology
Small ribosomal subunit protein bS6 / Conserved domain protein / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 ...Small ribosomal subunit protein bS6 / Conserved domain protein / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS1 / Sigma 54 modulation/S30EA ribosomal protein C-terminal domain-containing protein / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS18B
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKumar N / Sharma S / Kaushal PS
Funding support India, 1 items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
CitationJournal: Nat Commun / Year: 2024
Title: Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH.
Authors: Niraj Kumar / Shivani Sharma / Prem S Kaushal /
Abstract: Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium ...Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium tuberculosis encounters hypoxia (low oxygen) as a major stress in the host macrophages, and upregulates the expression of RafH protein, which is crucial for its survival. The RafH, a dual domain HPF, an orthologue of bacterial long HPF (HPF), hibernates ribosome in 70S monosome form, whereas in other bacteria, the HPF induces 70S ribosome dimerization and hibernates its ribosome in 100S disome form. Here, we report the cryo- EM structure of M. smegmatis, a close homolog of M. tuberculosis, 70S ribosome in complex with the RafH factor at an overall 2.8 Å resolution. The N- terminus domain (NTD) of RafH binds to the decoding center, similarly to HPF NTD. In contrast, the C- terminus domain (CTD) of RafH, which is larger than the HPF CTD, binds to a distinct site at the platform binding center of the ribosomal small subunit. The two domain-connecting linker regions, which remain mostly disordered in earlier reported HPF structures, interact mainly with the anti-Shine Dalgarno sequence of the 16S rRNA.
History
DepositionSep 24, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37561.png

Downloads & links

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Map

FileDownload / File: emd_37561.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacterium smegmatis 30S ribosome (body2) of 70S ribosome, bs1 and RafH complex.
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 380 pix.
= 406.6 Å		1.07 Å/pix.
x 380 pix.
= 406.6 Å		1.07 Å/pix.
x 380 pix.
= 406.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.03355433 - 0.19593088
Average (Standard dev.)0.00117021 (±0.0081765205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 406.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Mycobacterium smegmatis 30S ribosome (body2) of 70S ribosome,...

Fileemd_37561_half_map_1.map
AnnotationMycobacterium smegmatis 30S ribosome (body2) of 70S ribosome, bs1 and RafH complex, half 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Mycobacterium smegmatis 30S ribosome (body2) of 70S ribosome,...

Fileemd_37561_half_map_2.map
AnnotationMycobacterium smegmatis 30S ribosome (body2) of 70S ribosome, bs1 and RafH complex, half2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 70S ribosome + RafH protein

EntireName: 70S ribosome + RafH protein
Components
  • Complex: 70S ribosome + RafH protein
    • Complex: 70S ribosome
      • RNA: 16S rRNA
      • Protein or peptide: 30S ribosomal protein bS1
      • Protein or peptide: 30S ribosomal protein S22
      • Protein or peptide: 30S ribosomal protein S3
      • Protein or peptide: 30S ribosomal protein S4
      • Protein or peptide: 30S ribosomal protein S5
      • Protein or peptide: 30S ribosomal protein S6
      • Protein or peptide: 30S ribosomal protein S7
      • Protein or peptide: 30S ribosomal protein S8
      • Protein or peptide: 30S ribosomal protein S9
      • Protein or peptide: 30S ribosomal protein S10
      • Protein or peptide: 30S ribosomal protein S11
      • Protein or peptide: 30S ribosomal protein S12
      • Protein or peptide: 30S ribosomal protein S13
      • Protein or peptide: 30S ribosomal protein S14A
      • Protein or peptide: 30S ribosomal protein S15
      • Protein or peptide: 30S ribosomal protein S16
      • Protein or peptide: 30S ribosomal protein S17
      • Protein or peptide: 30S ribosomal protein S18B
      • Protein or peptide: 30S ribosomal protein S19
      • Protein or peptide: 30S ribosomal protein S20
      • Protein or peptide: 30S ribosomal protein S2
      • Protein or peptide: 50S ribosomal protein L31
    • Complex: RafH
      • Protein or peptide: Ribosome hibernation promotion factor RafH

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Supramolecule #1: 70S ribosome + RafH protein

SupramoleculeName: 70S ribosome + RafH protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155

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Supramolecule #2: 70S ribosome

SupramoleculeName: 70S ribosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#23

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Supramolecule #3: RafH

SupramoleculeName: RafH / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #24

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Macromolecule #1: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 495.373656 KDa
SequenceString: UUUUUGUUUG GAGAGUUUGA UCCUGGCUCA GGACGAACGC UGGCGGCGUG CUUAACACAU GCAAGUCGAA CGGAAAGGCC CUUUCGGGG GUACUCGAGU GGCGAACGGG UGAGUAACAC GUGGGUGAUC UGCCCUGCAC UUUGGGAUAA GCCUGGGAAA C UGGGUCUA ...String:
UUUUUGUUUG GAGAGUUUGA UCCUGGCUCA GGACGAACGC UGGCGGCGUG CUUAACACAU GCAAGUCGAA CGGAAAGGCC CUUUCGGGG GUACUCGAGU GGCGAACGGG UGAGUAACAC GUGGGUGAUC UGCCCUGCAC UUUGGGAUAA GCCUGGGAAA C UGGGUCUA AUACCGAAUA CACCCUGCUG GUCGCAUGGC CUGGUAGGGG AAAGCUUUUG CGGUGUGGGA UGGGCCCGCG GC CUAUCAG CUUGUUGGUG GGGUGAUGGC CUACCAAGGC GACGACGGGU AGCCGGCCUG AGAGGGUGAC CGGCCACACU GGG ACUGAG AUACGGCCCA GACUCCUACG GGAGGCAGCA GUGGGGAAUA UUGCACAAUG GGCGCAAGCC UGAUGCAGCG ACGC CGCGU GAGGGAUGAC GGCCUUCGGG UUGUAAACCU CUUUCAGCAC AGACGAAGCG CAAGUGACGG UAUGUGCAGA AGAAG GACC GGCCAACUAC GUGCCAGCAG CCGCGGUAAU ACGUAGGGUC CGAGCGUUGU CCGGAAUUAC UGGGCGUAAA GAGCUC GUA GGUGGUUUGU CGCGUUGUUC GUGAAAACUC ACAGCUUAAC UGUGGGCGUG CGGGCGAUAC GGGCAGACUA GAGUACU GC AGGGGAGACU GGAAUUCCUG GUGUAGCGGU GGAAUGCGCA GAUAUCAGGA GGAACACCGG UGGCGAAGGC GGGUCUCU G GGCAGUAACU GACGCUGAGG AGCGAAAGCG UGGGGAGCGA ACAGGAUUAG AUACCCUGGU AGUCCACGCC GUAAACGGU GGGUACUAGG UGUGGGUUUC CUUCCUUGGG AUCCGUGCCG UAGCUAACGC AUUAAGUACC CCGCCUGGGG AGUACGGCCG CAAGGCUAA AACUCAAAGG AAUUGACGGG GGCCCGCACA AGCGGCGGAG CAUGUGGAUU AAUUCGAUGC AACGCGAAGA A CCUUACCU GGGUUUGACA UGCACAGGAC GCCGGCAGAG AUGUCGGUUC CCUUGUGGCC UGUGUGCAGG UGGUGCAUGG CU GUCGUCA GCUCGUGUCG UGAGAUGUUG GGUUAAGUCC CGCAACGAGC GCAACCCUUG UCUCAUGUUG CCAGCACGUU AUG GUGGGG ACUCGUGAGA GACUGCCGGG GUCAACUCGG AGGAAGGUGG GGAUGACGUC AAGUCAUCAU GCCCCUUAUG UCCA GGGCU UCACACAUGC UACAAUGGCC GGUACAAAGG GCUGCGAUGC CGUGAGGUGG AGCGAAUCCU UUCAAAGCCG GUCUC AGUU CGGAUCGGGG UCUGCAACUC GACCCCGUGA AGUCGGAGUC GCUAGUAAUC GCAGAUCAGC AACGCUGCGG UGAAUA CGU UCCCGGGCCU UGUACACACC GCCCGUCACG UCAUGAAAGU CGGUAACACC CGAAGCCGGU GGCCUAACCC UUGUGGA GG GAGCCGUCGA AGGUGGGAUC GGCGAUUGGG ACGAAGUCGU AACAAGGUAG CCGUACCGGA AGGUGCGGCU GGAUCACC U CCUUUCU

GENBANK: GENBANK: CP000480.1

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Macromolecule #2: 30S ribosomal protein bS1

MacromoleculeName: 30S ribosomal protein bS1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 53.383695 KDa
SequenceString: MPSPSVTSPQ VAVNDIGSAE DFLAAIDKTI KYFNDGDIVE GTIVKVDRDE VLLDIGYKTE GVIPSRELSI KHDVDPNEVV SVGDEVEAL VLTKEDKEGR LILSKKRAQY ERAWGTIEEL KEKDEAVKGT VIEVVKGGLI LDIGLRGFLP ASLVEMRRVR D LQPYIGKE ...String:
MPSPSVTSPQ VAVNDIGSAE DFLAAIDKTI KYFNDGDIVE GTIVKVDRDE VLLDIGYKTE GVIPSRELSI KHDVDPNEVV SVGDEVEAL VLTKEDKEGR LILSKKRAQY ERAWGTIEEL KEKDEAVKGT VIEVVKGGLI LDIGLRGFLP ASLVEMRRVR D LQPYIGKE IEAKIIELDK NRNNVVLSRR AWLEQTQSEV RSEFLNQLQK GAIRKGVVSS IVNFGAFVDL GGVDGLVHVS EL SWKHIDH PSEVVQVGDE VTVEVLDVDM DRERVSLSLK ATQEDPWRHF ARTHAIGQIV PGKVTKLVPF GAFVRVEEGI EGL VHISEL SERHVEVPDQ VVQVGDDAMV KVIDIDLERR RISLSLKQAN EDYTEEFDPS KYGMADSYDE QGNYIFPEGF DPET NEWLE GFDKQREEWE ARYAEAERRH KMHTAQMEKF AAAEAEAANA PVSNGSSRSE ESSGGTLASD AQLAALREKL AGNA

UniProtKB: Small ribosomal subunit protein bS1

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Macromolecule #3: 30S ribosomal protein S22

MacromoleculeName: 30S ribosomal protein S22 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 4.1643 KDa
SequenceString:
MGSVIKKRRK RMSKKKHRKL LRRTRVQRRK LGK

UniProtKB: Conserved domain protein

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Macromolecule #4: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 30.191227 KDa
SequenceString: MGQKINPHGF RLGITTEWKS RWYADKQYKD YVKEDVAIRK LLATGLERAG IADVEIERTR DRVRVDIHTA RPGIVIGRRG TEADRIRAD LEKLTGKQVQ LNILEVKNPE SQAQLVAQGV AEQLSNRVAF RRAMRKAIQS AMRQPNVKGI RVQCSGRLGG A EMSRSEFY ...String:
MGQKINPHGF RLGITTEWKS RWYADKQYKD YVKEDVAIRK LLATGLERAG IADVEIERTR DRVRVDIHTA RPGIVIGRRG TEADRIRAD LEKLTGKQVQ LNILEVKNPE SQAQLVAQGV AEQLSNRVAF RRAMRKAIQS AMRQPNVKGI RVQCSGRLGG A EMSRSEFY REGRVPLHTL RADIDYGLYE AKTTFGRIGV KVWIYKGDIV GGKRELAAAA PASDRPRRER PSGTRPRRSG SA GTTATST EAGRAATSDA PAAGTAAAAE APAESTES

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #5: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 23.415787 KDa
SequenceString: MARYTGPATR KSRRLGVDLV GGDQSFEKRP YPPGQHGRAR IKESEYRQQL QEKQKARFSY GVMEKQFRRY YEEANRQPGK TGDNLLRIL ESRLDNVVYR AGLARTRRMA RQLVSHGHFL VNGVKVDIPS YRVSQYDIID VKEKSLNTLP FQIARETAGE R PIPSWLQV ...String:
MARYTGPATR KSRRLGVDLV GGDQSFEKRP YPPGQHGRAR IKESEYRQQL QEKQKARFSY GVMEKQFRRY YEEANRQPGK TGDNLLRIL ESRLDNVVYR AGLARTRRMA RQLVSHGHFL VNGVKVDIPS YRVSQYDIID VKEKSLNTLP FQIARETAGE R PIPSWLQV VGERQRILVH QLPERAQIDV PLTEQLIVEL YSK

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #6: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 21.94609 KDa
SequenceString: MAEQAGAGSA QDNRGGRGRR DDRGGRGRDG GDKSNYIERV VSINRVSKVV KGGRRFSFTA LVIVGDGKGM VGVGYGKAKE VPAAIAKGV EEARKNFFRV PLIGSTITHP VQGEAAAGVV MLRPASPGTG VIAGGAARAV LECAGVHDIL AKSLGSDNAI N VVHATVAA ...String:
MAEQAGAGSA QDNRGGRGRR DDRGGRGRDG GDKSNYIERV VSINRVSKVV KGGRRFSFTA LVIVGDGKGM VGVGYGKAKE VPAAIAKGV EEARKNFFRV PLIGSTITHP VQGEAAAGVV MLRPASPGTG VIAGGAARAV LECAGVHDIL AKSLGSDNAI N VVHATVAA LKLLQRPEEV AARRGLPIED VAPAGMLKAR RESEALAAAA AREGSA

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #7: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 10.991637 KDa
SequenceString:
MRPYEIMVIL DPTLDERTVA PSLETFLNVI RKDGGTVDKV DIWGRRRLAY EIAKHAEGIY AVIDVKAEPA TVSELDRQLN LNESVLRTK VLRTDKH

UniProtKB: Small ribosomal subunit protein bS6

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Macromolecule #8: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 17.660375 KDa
SequenceString:
MPRKGPAPKR PLVNDPVYGS QLVTQLVNKV LLEGKKSLAE RIVYGALEQA REKTGTDPVV TLKRALDNVK PALEVRSRRV GGATYQVPV EVRPDRSTTL ALRWLVNFSR QRREKTMVER LANEILDASN GLGASVKRRE DTHKMAEANR AFAHYRW

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #9: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 14.492638 KDa
SequenceString:
MTMTDPIADF LTRLRNANSA YHDEVTLPHS KLKANIAEIL KREGYISDYR TEDARVGKSL VVQLKYGPSR ERSIAGLRRV SKPGLRVYA KSTNLPRVLG GLGVAIISTS SGLLTDRQAA RQGVGGEVLA YVW

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #10: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 16.794365 KDa
SequenceString:
MTDVTETEVV TESAEPREPV IIDRPIQTVG RRKEAVVRVR LVPGTGQFNL DGRTLENYFP NKVHQQLIKA PLVTVDRVDQ FDIYAHLDG GGPSGQAGAL RLAIARALIL VQPEDRPALK KAGFLTRDPR AIERKKYGLK KARKAPQYSK R

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #11: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 11.454313 KDa
SequenceString:
MAGQKIRIRL KAYDHEAIDA SARKIVETVT RTGASVVGPV PLPTEKNVYC VIRSPHKYKD SREHFEMRTH KRLIDILDPT PKTVDALMR IDLPASVDVN IQ

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #12: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 14.671762 KDa
SequenceString:
MAQAKKGGTA AKKGQKTRRR EKKNVPHGAA HIKSTFNNTI VSITDPQGNV IAWASSGHVG FKGSRKSTPF AAQLAAENAA RKAQEHGVK KVDVFVKGPG SGRETAIRSL QAAGLEVGTI SDVTPQPHNG CRPPKRRRV

UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #13: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 13.896366 KDa
SequenceString:
MPTIQQLVRK GRRDKIAKVK TAALKGSPQR RGVCTRVYTT TPKKPNSALR KVARVKLTSQ VEVTAYIPGE GHNLQEHSMV LVRGGRVKD LPGVRYKIIR GSLDTQGVKN RKQARSRYGA KKEKS

UniProtKB: Small ribosomal subunit protein uS12

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Macromolecule #14: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 14.249619 KDa
SequenceString:
MARLVGVDLP RDKRMEIALT YIYGIGRTRS NEILAATGID KNMRTKDLTD DQVTVLRDYI EGNLKVEGDL RREVQADIRR KIEIGCYQG LRHRRGLPVR GQRTKTNART RKGPKRTIAG KKKAR

UniProtKB: Small ribosomal subunit protein uS13

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Macromolecule #15: 30S ribosomal protein S14A

MacromoleculeName: 30S ribosomal protein S14A / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 6.976409 KDa
SequenceString:
MAKKALVHKA NKKPKFAVRA YTRCNKCGRP HSVYRKFGLC RICLREMAHA GELPGVQKSS W

UniProtKB: Small ribosomal subunit protein uS14B

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Macromolecule #16: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 10.368097 KDa
SequenceString:
MALTAEQKKE ILGQYGLHDT DTGSPEAQVA LLTKRIQDLT EHLKVHKHDH HSRRGLLLLV GRRRRLLKYV AQVDVARYRS LIERLGLRR

UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #17: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 16.795207 KDa
SequenceString:
MAVKIKLTRL GKIRNPQYRI IVADARTRRD GRAIEVIGRY HPKEEPSLIQ IDSERAQYWL GVGAQPTEPV LALLKITGDW QKFKGLPGA EGTLKVKEPK PSKLDLFNAA LAEAESGTTA AATTPKKKKA PKKDEAAEAP AEAAEAPAEA ADAASES

UniProtKB: Small ribosomal subunit protein bS16

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Macromolecule #18: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 11.127002 KDa
SequenceString:
MADQKGPKYT PAAEKPRGRR KTAIGYVVSD KMQKTIVVEL EDRKSHPLYG KIIRTTKKVK AHDENGEAGI GDRVSLMETR PLSATKRWR LVEILEKAK

UniProtKB: Small ribosomal subunit protein uS17

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Macromolecule #19: 30S ribosomal protein S18B

MacromoleculeName: 30S ribosomal protein S18B / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 9.524188 KDa
SequenceString:
MAKSNKRRPA PEKPVKTRKC VFCSKKGQTI DYKDTALLRT YISERGKIRA RRVTGNCVQH QRDIAVAVKN AREVALLPFG SSTR

UniProtKB: Small ribosomal subunit protein bS18B

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Macromolecule #20: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 10.800602 KDa
SequenceString:
MPRSLKKGPF VDDHLLKKVD VQNEKNTKQV IKTWSRRSTI IPDFIGHTFA VHDGRKHVPV FVTEAMVGHK LGEFAPTRTF KGHIKDDRK SKRR

UniProtKB: Small ribosomal subunit protein uS19

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Macromolecule #21: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 9.556104 KDa
SequenceString:
MANIKSQIKR IRTNERRRLR NQSVKSSLRT AIRGFREAVD AGDKDKASEL LHATSRKLDK AASKGVIHPN QAANKKSALA LALNKL

UniProtKB: Small ribosomal subunit protein bS20

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Macromolecule #22: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 30.14523 KDa
SequenceString: MAVVTMKQLL DSGAHFGHQT RRWNPKMKRF IFTDRNGIYI IDLQQTLTYI DKAYEFVKET VAHGGTVLFV GTKKQAQESI AEEATRVGM PYVNQRWLGG MLTNFSTVHK RLQRLKELEA MEQTGGFEGR TKKEILMLTR EKNKLERSLG GIRDMQKVPS A VWVVDTNK ...String:
MAVVTMKQLL DSGAHFGHQT RRWNPKMKRF IFTDRNGIYI IDLQQTLTYI DKAYEFVKET VAHGGTVLFV GTKKQAQESI AEEATRVGM PYVNQRWLGG MLTNFSTVHK RLQRLKELEA MEQTGGFEGR TKKEILMLTR EKNKLERSLG GIRDMQKVPS A VWVVDTNK EHIAVGEARK LGIPVIAILD TNCDPDVVDY PIPGNDDAIR SAALLTKVIA SAVAEGLQAR AGQGSGEKPA EG AEPLAEW EQELLAGATA GAADASAEGA AAPESSTDAS

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #23: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155
Molecular weightTheoretical: 1.34255 KDa
SequenceString:
GRVARFEKRY G

UniProtKB: Large ribosomal subunit protein bL31

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Macromolecule #24: Ribosome hibernation promotion factor RafH

MacromoleculeName: Ribosome hibernation promotion factor RafH / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 29.898936 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDVDVSTDGE LPGAAEYARE KIGRLSRRAH RPVLHARVRL TRHGDPAVER PVIAQANLDV NGRQVRAQVE GVNAREAVDR LEARLRSRL ERIAEHWEAR RGGVPAEAGR EWRHESEPAR RPGYFPRPPE ERRIIRRKSF SMVPCTVDEA ALEMEMLDYD F HLFTEKGT ...String:
MDVDVSTDGE LPGAAEYARE KIGRLSRRAH RPVLHARVRL TRHGDPAVER PVIAQANLDV NGRQVRAQVE GVNAREAVDR LEARLRSRL ERIAEHWEAR RGGVPAEAGR EWRHESEPAR RPGYFPRPPE ERRIIRRKSF SMVPCTVDEA ALEMEMLDYD F HLFTEKGT GFAAVLYKGG PTGYRLVLVI PVPADELSPF EKPITISTHP APCLTQRDAV ERLGLLGLPF LFYIDAAEGR AS VIYRRYD GHYGLITPAD GHHHHHH

UniProtKB: Sigma 54 modulation/S30EA ribosomal protein C-terminal domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 3 / Number real images: 12343 / Average exposure time: 2.0 sec. / Average electron dose: 1.34 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DARK FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1202461
Startup modelType of model: EMDB MAP
EMDB ID:

8932

Final reconstructionNumber classes used: 3 / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Details: Ad-hoc low pass filter 3.5 Angstrom / Number images used: 110934
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.4)
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8whx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8wi9:
Cryo- EM structure of Mycobacterium smegmatis 30S ribosomal subunit (body 2) of 70S ribosome, bS1 and RafH.

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