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- EMDB-47419: Cryo-EM structure of the ribosome-tunnel occluding hibernation fa... -

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Basic information

Entry
Database: EMDB / ID: EMD-47419
TitleCryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to the Mycobacterium tuberculosis C- 50S ribosomal subunit
Map dataMycobacterium tuberculosis C- 50S ribosomal subunit bound to the ribosome-tunnel occluding hibernation factor-RTOF
Sample
  • Complex: Mycobacterium tuberculosis C- 50S ribosomal subunit bound to the ribosomal tunnel occlusion factor-RTOF
    • Protein or peptide: x 30 types
    • RNA: x 2 types
Keywordshibernating ribosome / Mycobacterium tuberculosis / nascent peptide exit tunnel / 50S / hibernation factor / TRANSLATION / RIBOSOME
Function / homology
Function and homology information


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 ...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 / translation / structural constituent of ribosome / ribonucleoprotein complex / mRNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / : / Ribosomal protein L20 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / : / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L24 / Ribosomal L32p protein family / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L2 signature. / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L13 signature. / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / : / Ribosomal protein L10e/L16 / Ribosomal protein L13, conserved site
Similarity search - Domain/homology
Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL16 ...Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21 / : / Large ribosomal subunit protein uL14
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsMajumdar S / Ojha AK / Agrawal RK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32422 United States
CitationJournal: Biorxiv / Year: 2024
Title: A Novel Actinobacteria-Specific Ribosome Hibernation Factor in Mycobacterium tuberculosis
Authors: Majumdar S / Li Y / Manjari SR / Gamper HB / Hou YM / Banavali NK / Ojha AK / Agrawal RK
History
DepositionOct 21, 2024-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47419.png

Downloads & links

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Map

FileDownload / File: emd_47419.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacterium tuberculosis C- 50S ribosomal subunit bound to the ribosome-tunnel occluding hibernation factor-RTOF
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 428. Å		1.07 Å/pix.
x 400 pix.
= 428. Å		1.07 Å/pix.
x 400 pix.
= 428. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.377
Minimum - Maximum-2.6455827 - 5.3694997
Average (Standard dev.)-0.003449507 (±0.1373951)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 428.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Mycobacterium tuberculosis C- 50S ribosomal subunit bound to...

Fileemd_47419_half_map_1.map
AnnotationMycobacterium tuberculosis C- 50S ribosomal subunit bound to the ribosome-tunnel occluding hibernation factor-RTOF-half map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Mycobacterium tuberculosis C- 50S ribosomal subunit bound to...

Fileemd_47419_half_map_2.map
AnnotationMycobacterium tuberculosis C- 50S ribosomal subunit bound to the ribosome-tunnel occluding hibernation factor-RTOF-half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium tuberculosis C- 50S ribosomal subunit bound to the ...

EntireName: Mycobacterium tuberculosis C- 50S ribosomal subunit bound to the ribosomal tunnel occlusion factor-RTOF
Components
  • Complex: Mycobacterium tuberculosis C- 50S ribosomal subunit bound to the ribosomal tunnel occlusion factor-RTOF
    • Protein or peptide: 50S ribosomal protein bL37
    • RNA: 23S ribosomal RNA
    • Protein or peptide: Ribosomal tunnel occlusion factor-RTOF
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein bL34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein bL36
    • 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 L13
    • Protein or peptide: Large ribosomal subunit protein uL14
    • 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: Large ribosomal subunit protein bL21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein bL33-c minus
    • Protein or peptide: 50S ribosomal protein bL28-c minus
    • Protein or peptide: 50S ribosomal protein uL24

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Supramolecule #1: Mycobacterium tuberculosis C- 50S ribosomal subunit bound to the ...

SupramoleculeName: Mycobacterium tuberculosis C- 50S ribosomal subunit bound to the ribosomal tunnel occlusion factor-RTOF
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: 50S ribosomal protein bL37

MacromoleculeName: 50S ribosomal protein bL37 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 2.882402 KDa
SequenceString:
MAKRGRKKRD RKYSKANHGK RPNS

UniProtKB: UNIPROTKB: A0AB73YSK1

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Macromolecule #3: Ribosomal tunnel occlusion factor-RTOF

MacromoleculeName: Ribosomal tunnel occlusion factor-RTOF / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 6.810468 KDa
SequenceString:
MGESKSPQES SSEGETKRKF REALDRKMAQ SSSGSDHKDG GGKQSRAHGP VASRREFRRK SG

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Macromolecule #4: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 6.525757 KDa
SequenceString:
MAVPKRRKSR SNTRSRRSQW KAAKTELVGV TVAGHAHKVP RRLLKAARLG LIDFDKR

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #5: 50S ribosomal protein bL34

MacromoleculeName: 50S ribosomal protein bL34 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 5.643697 KDa
SequenceString:
MTKGKRTFQP NNRRRARVHG FRLRMRTRAG RSIVSSRRRK GRRTLSA

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Macromolecule #6: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 7.24143 KDa
SequenceString:
MPKAKTHSGA SKRFRRTGTG KIVRQKANRR HLLEHKPSTR TRRLDGRTVV AANDTKRVTS LLNG

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #7: 50S ribosomal protein bL36

MacromoleculeName: 50S ribosomal protein bL36 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 4.323239 KDa
SequenceString:
VKVNPSVKPI CDKCRLIRRH GRVMVICSDP RHKQRQG

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Macromolecule #9: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 30.644002 KDa
SequenceString: MAIRKYKPTT PGRRGASVSD FAEITRSTPE KSLVRPLHGR GGRNAHGRIT TRHKGGGHKR AYRMIDFRRN DKDGVNAKVA HIEYDPNRT ARIALLHYLD GEKRYIIAPN GLSQGDVVES GANADIKPGN NLPLRNIPAG TLIHAVELRP GGGAKLARSA G SSIQLLGK ...String:
MAIRKYKPTT PGRRGASVSD FAEITRSTPE KSLVRPLHGR GGRNAHGRIT TRHKGGGHKR AYRMIDFRRN DKDGVNAKVA HIEYDPNRT ARIALLHYLD GEKRYIIAPN GLSQGDVVES GANADIKPGN NLPLRNIPAG TLIHAVELRP GGGAKLARSA G SSIQLLGK EASYASLRMP SGEIRRVDVR CRATVGEVGN AEQANINWGK AGRMRWKGKR PSVRGVVMNP VDHPHGGGEG KT SGGRHPV SPWGKPEGRT RNANKSSNKF IVRRRRTGKK HSR

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #10: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 23.127533 KDa
SequenceString: MARKGILGTK LGMTQVFDES NRVVPVTVVK AGPNVVTRIR TPERDGYSAV QLAYGEISPR KVNKPLTGQY TAAGVNPRRY LAELRLDDS DAATEYQVGQ ELTAEIFADG SYVDVTGTSK GKGFAGTMKR HGFRGQGASH GAQAVHRRPG SIGGCATPAR V FKGTRMAG ...String:
MARKGILGTK LGMTQVFDES NRVVPVTVVK AGPNVVTRIR TPERDGYSAV QLAYGEISPR KVNKPLTGQY TAAGVNPRRY LAELRLDDS DAATEYQVGQ ELTAEIFADG SYVDVTGTSK GKGFAGTMKR HGFRGQGASH GAQAVHRRPG SIGGCATPAR V FKGTRMAG RMGNDRVTVL NLLVHKVDAE NGVLLIKGAV PGRTGGLVMV RSAIKRGEK

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #11: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 23.779936 KDa
SequenceString: MAAQEQKTLK IDVKTPAGKV DGAIELPAEL FDVPANIALM HQVVTAQRAA ARQGTHSTKT RGEVSGGGRK PYRQKGTGRA RQGSTRAPQ FTGGGVVHGP KPRDYSQRTP KKMIAAALRG ALSDRARNGR IHAITELVEG QNPSTKSARA FLASLTERKQ V LVVIGRSD ...String:
MAAQEQKTLK IDVKTPAGKV DGAIELPAEL FDVPANIALM HQVVTAQRAA ARQGTHSTKT RGEVSGGGRK PYRQKGTGRA RQGSTRAPQ FTGGGVVHGP KPRDYSQRTP KKMIAAALRG ALSDRARNGR IHAITELVEG QNPSTKSARA FLASLTERKQ V LVVIGRSD EAGAKSVRNL PGVHILAPDQ LNTYDVLRAD DVVFSVEALN AYIAANTTTS EEVSA

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #12: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 21.052303 KDa
SequenceString:
MTTAQKVQPR LKERYRSEIR DALRKQFGYG NVMQIPTVTK VVVNMGVGEA ARDAKLINGA VNDLALITGQ KPEVRRARKS IAQFKLREG MPVGVRVTLR GDRMWEFLDR LTSIALPRIR DFRGLSPKQF DGVGNYTFGL AEQAVFHEVD VDKIDRVRGM D INVVTSAA TDDEGRALLR ALGFPFKEN

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #13: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 19.408363 KDa
SequenceString:
MSRIGKQPIP VPAGVDVTIE GQSISVKGPK GTLGLTVAEP IKVARNDDGA IVVTRPDDER RNRSLHGLSR TLVSNLVTGV TQGYTTKME IFGVGYRVQL KGSNLEFALG YSHPVVIEAP EGITFAVQAP TKFTVSGIDK QKVGQIAANI RRLRRPDPYK G KGVRYEGE QIRRKVGKTG K

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #14: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 16.196654 KDa
SequenceString:
MKLILTADVD HLGSIGDTVE VKDGYGRNFL LPRGLAIVAS RGAQKQADEI RRARETKSVR DLEHANEIKA AIEALGPIAL PVKTSADSG KLFGSVTAAD VVAAIKKAGG PNLDKRIVRL PKTHIKAVGT HFVSVHLHPE IDVEVSLDVV AQS

UniProtKB: Large ribosomal subunit protein bL9

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Macromolecule #15: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 21.646121 KDa
SequenceString: MLVGKLLGWR AVRRDLGSMS VAETNPPFTP DRRPGHPGIH PREKKVSAVP TYAPKAGDTT RSWYVIDATD VVLGRLAVAA ANLLRGKHK PTFAPNVDGG DFVIVINADK VAISGDKLQH KMVYRHSGYP GGLHKRTIGE LMQRHPDRVV EKAILGMLPK N RLSRQIQR ...String:
MLVGKLLGWR AVRRDLGSMS VAETNPPFTP DRRPGHPGIH PREKKVSAVP TYAPKAGDTT RSWYVIDATD VVLGRLAVAA ANLLRGKHK PTFAPNVDGG DFVIVINADK VAISGDKLQH KMVYRHSGYP GGLHKRTIGE LMQRHPDRVV EKAILGMLPK N RLSRQIQR KLRVYAGPEH PHSAQQPVPY ELKQVAQ

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #16: Large ribosomal subunit protein uL14

MacromoleculeName: Large ribosomal subunit protein uL14 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 13.451714 KDa
SequenceString:
MIQQESRLKV ADNTGAKEIL CIRVLGGSSR RYAGIGDVIV ATVKDAIPGG NVKRGDVVKA VVVRTVKERR RPDGSYIKFD ENAAVIIKP DNDPRGTRIF GPVGRELREK RFMKIISLAP EVL

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #17: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 15.566126 KDa
SequenceString:
MTLKLHDLRP ARGSKIARTR VGRGDGSKGK TAGRGTKGTR ARKQVPVTFE GGQMPIHMRL PKLKGFRNRF RTEYEIVNVG DINRLFPQG GAVGVDDLVA KGAVRKNALV KVLGDGKLTA KVDVSAHKFS GSARAKITAA GGSATEL

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #18: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 15.724277 KDa
SequenceString:
MLIPRKVKHR KQHHPRQRGI ASGGTTVNFG DYGIQALEHA YVTNRQIESA RIAINRHIKR GGKVWINIFP DRPLTKKPAE TRMGSGKGS PEWWVANVKP GRVLFELSYP NEGVARAALT RAIHKLPIKA RIITREEQF

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #19: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 19.512273 KDa
SequenceString:
MPKPTKGPRL GGSSSHQKAI LANLATSLFE HGRITTTEPK ARALRPYAEK LITHAKKGAL HNRREVLKKL RDKDVVHTLF AEIGPFFAD RDGGYTRIIK IEARKGDNAP MAVIELVREK TVTSEANRAR RVAAAQAKAK KAAAMPTEES EAKPAEEGDV V GASEPDAK APEEPPAEAP EN

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #20: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 13.211122 KDa
SequenceString:
MAQSVSATRR ISRLRRHTRL RKKLSGTAER PRLVVHRSAR HIHVQLVNDL NGTTVAAASS IEADVRGVPG DKKARSVRVG QLIAERAKA AGIDTVVFDR GGYTYGGRIA ALADAARENG LSF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #21: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 13.041126 KDa
SequenceString:
MNRLDFVDKP SLRDDIPAFN PGDTINVHVK VIEGAKERLQ VFKGVVIRRQ GGGIRETFTV RKESYGVGVE RTFPVHSPNI DHIEVVTRG DVRRAKLYYL RELRGKKAKI KEKR

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #22: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 14.557777 KDa
SequenceString:
MARVKRAVNA HKKRRSILKA SRGYRGQRSR LYRKAKEQQL HSLNYAYRDR RARKGEFRKL WIARINAAAR LNDITYNRLI QGLKAAGVE VDRKNLADIA ISDPAAFTAL VDVARAALPE DVNAPSGEAA

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #23: Large ribosomal subunit protein bL21

MacromoleculeName: Large ribosomal subunit protein bL21 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 11.173147 KDa
SequenceString:
MMATYAIVKT GGKQYKVAVG DVVKVEKLES EQGEKVSLPV ALVVDGATVT TDAKALAKVA VTGEVLGHTK GPKIRIHKFK NKTGYHKRQ GHRQQLTVLK VTGIA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #24: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 20.424594 KDa
SequenceString: MTAATKATEY PSAVAKARFV RVSPRKARRV IDLVRGRSVS DALDILRWAP QAASGPVAKV IASAAANAQN NGGLDPATLV VATVYADQG PTAKRIRPRA QGRAFRIRRR TSHITVVVES RPAKDQRSAK SSRARRTEAS KAASKVGATA PAKKAAAKAP A KKAPASSG ...String:
MTAATKATEY PSAVAKARFV RVSPRKARRV IDLVRGRSVS DALDILRWAP QAASGPVAKV IASAAANAQN NGGLDPATLV VATVYADQG PTAKRIRPRA QGRAFRIRRR TSHITVVVES RPAKDQRSAK SSRARRTEAS KAASKVGATA PAKKAAAKAP A KKAPASSG VKKTPAKKAP AKKAPAKASE TSAAKGGSD

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #25: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 10.976785 KDa
SequenceString:
MATLADPRDI ILAPVISEKS YGLLDDNVYT FLVRPDSNKT QIKIAVEKIF AVKVASVNTA NRQGKRKRTR TGYGKRKSTK RAIVTLAPG SRPIDLFGAP A

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #26: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 22.466166 KDa
SequenceString: MAKSASNQLR VTVRTETGKG ASRRARRAGK IPAVLYGHGA EPQHLELPGH DYAAVLRHSG TNAVLTLDIA GKEQLALTKA LHIHPIRRT IQHADLLVVR RGEKVVVEVS VVVEGQAGPD TLVTQETNSI EIEAEALSIP EQLTVSIEGA EPGTQLTAGQ I ALPAGVSL ...String:
MAKSASNQLR VTVRTETGKG ASRRARRAGK IPAVLYGHGA EPQHLELPGH DYAAVLRHSG TNAVLTLDIA GKEQLALTKA LHIHPIRRT IQHADLLVVR RGEKVVVEVS VVVEGQAGPD TLVTQETNSI EIEAEALSIP EQLTVSIEGA EPGTQLTAGQ I ALPAGVSL ISDPDLLVVN VVKAPTAEEL EGEVAGAEEA EEAAVEAGEA EAAGESE

UniProtKB: Large ribosomal subunit protein bL25

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Macromolecule #27: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 8.987272 KDa
SequenceString:
MAHKKGASSS RNGRDSAAQR LGVKRYGGQV VKAGEILVRQ RGTKFHPGVN VGRGGDDTLF AKTAGAVEFG IKRGRKTVSI VGSTTA

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #28: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 8.872015 KDa
SequenceString:
MAVGVSPGEL RELTDEELAE RLRESKEELF NLRFQMATGQ LNNNRRLRTV RQEIARIYTV LRERELGLAT GPDGKES

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #29: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 7.361569 KDa
SequenceString:
MSQLKITQVR STIGARWKQR ESLRTLGLRR IRHSVIREDN AATRGLIAVV RHLVEVEPAQ TGGKT

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #30: 50S ribosomal protein bL33-c minus

MacromoleculeName: 50S ribosomal protein bL33-c minus / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 6.604616 KDa
SequenceString:
MARTDIRPIV KLRSTAGTGY TYTTRKNRRN DPDRLILRKY DPILRRHVDF REER

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Macromolecule #31: 50S ribosomal protein bL28-c minus

MacromoleculeName: 50S ribosomal protein bL28-c minus / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 9.099484 KDa
SequenceString:
LSAHCQVTGR KPGFGNTVSH SHRRSRRRWS PNIQQRTYYL PSEGRRIRLR VSTKGIKVID RDGIEAVVAR LRRQGQRI

+
Macromolecule #32: 50S ribosomal protein uL24

MacromoleculeName: 50S ribosomal protein uL24 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 11.500274 KDa
SequenceString:
MKVHKGDTVL VISGKDKGAK GKVLQAYPDR NRVLVEGVNR IKKHTAISTT QRGARSGGIV TQEAPIHVSN VMVVDSDGKP TRIGYRVDE ETGKRVRISK RNGKDI

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #2: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 1.017792562 MDa
SequenceString: UUGUAAGUGU CUAAGGGCGC AUGGUGGAUG CCUUGGCAUC GAGAGCCGAU GAAGGACGUG GGAGGCUGCG AUAUGCCUCG GGGAGCUGU CAACCGAGCG UGGAUCCGAG GAUUUCCGAA UGGGGAAACC CAGCACGAGU GAUGUCGUGC UACCCGCAUC U GAAUAUAU ...String:
UUGUAAGUGU CUAAGGGCGC AUGGUGGAUG CCUUGGCAUC GAGAGCCGAU GAAGGACGUG GGAGGCUGCG AUAUGCCUCG GGGAGCUGU CAACCGAGCG UGGAUCCGAG GAUUUCCGAA UGGGGAAACC CAGCACGAGU GAUGUCGUGC UACCCGCAUC U GAAUAUAU AGGGUGCGGG AGGGAACGCG GGGAAGUGAA ACAUCUCAGU ACCCGUAGGA GGAGAAAACA AUUGUGAUUC CG CAAGUAG UGGCGAGCGA ACGCGGAACA GGCUAAACCG CACGCAUGGG UAACCGGGUA GGGGUUGUGU GUGCGGGGUU GUG GGAGGA UAUGUCUCAG CGCUACCCGG CUGAGAGGCA GUCAGAAAGU GUCGUGGUUA GCGGAAGUGG CCUGGGAUGG UCUG CCGUA GACGGUGAGA GCCCGGUACG CGAAAACCCG GCACCUGCCU AGUAUCAAUU CCCGAGUAGC AGCGGGCCCG UGGAA UCCG CUGUGAAUCC GCCGGGACCA CCCGGUAAGC CUAAAUACUC CUCGAUGACC GAUAGCGGAU UAGUACCGUG AGGGAA UGG UGAAAAGUAC CCCGGGAGGG GAGUGAAAGA GUACCUGAAA CCGUGUGCCU ACAAUCCGUC AGAGCCUCCU UUUCCUC UC CGGAGGAGGG UGGUGAUGGC GUGCCUUUUG AAGAAUGAGC CUGCGAGUCA GGGACAUGUC GCAAGGUUAA CCCGUGUG G GGUAGCCGCA GCGAAAGCGA GUCUGAAUAG GGCGACCCAC ACGCGCAUAC GCGCGUGUGA AUAGUGGCGU GUUCUGGAC CCGAAGCGGA GUGAUCUACC CAUGGCCAGG GUGAAGCGCG GGUAAGACCG CGUGGAGGCC CGAACCCACU UAGGUUGAAG ACUGAGGGG AUGAGCUGUG GGUAGGGGUG AAAGGCCAAU CAAACUCCGU GAUAGCUGGU UCUCCCCGAA AUGCAUUUAG G UGCAGCGU UGCGUGGUUC ACCGCGGAGG UAGAGCUACU GGAUGGCCGA UGGGCCCUAC UAGGUUACUG ACGUCAGCCA AA CUCCGAA UGCCGUGGUG UAAAGCGUGG CAGUGAGACG GCGGGGGAUA AGCUCCGUAC GUCGAAAGGG AAACAGCCCA GAU CGCCGG CUAAGGCCCC CAAGCGUGUG CUAAGUGGGA AAGGAUGUGC AGUCGCAAAG ACAACCAGGA GGUUGGCUUA GAAG CAGCC ACCCUUGAAA GAGUGCGUAA UAGCUCACUG GUCAAGUGAU UGUGCGCCGA UAAUGUAGCG GGGCUCAAGC ACACC GCCG AAGCCGCGGC ACAUCCACCU UGUGGUGGGU GUGGGUAGGG GAGCGUCCCU CAUUCAGCGA AGCCACCGGG UGACCG GUG GUGGAGGGUG GGGGAGUGAG AAUGCAGGCA UGAGUAGCGA CAAGGCAAGU GAGAACCUUG CCCGCCGAAA GACCAAG GG UUCCUGGGCC AGGCCAGUCC GCCCAGGGUG AGUCGGGACC UAAGGCGAGG CCGACAGGCG UAGUCGAUGG ACAACGGG U UGAUAUUCCC GUACCCGUGU GUGGGCGCCC GUGACGAAUC AGCGGUACUA ACCACCCAAA ACCGGAUCGA UCACUCCCC UUCGGGGGUG UGGAGUUCUG GGGCUGCGUG GGAACUUCGC UGGUAGUAGU CAAGCGAAGG GGUGACGCAG GAAGGUAGCC GUACCAGUC AGUGGUAACA CUGGGGCAAG CCGGUAGGGA GAGCGAUAGG CAAAUCCGUC GCUCACUAAU CCUGAGAGGU G ACGCAUAG CCGGUUGAGG CGAAUUCGGU GAUCCUCUGC UGCCAAGAAA AGCCUCUAGC GAGCACACAC ACGGCCCGUA CC CCAAACC GACACAGGUG GUCAGGUAGA GCAUACCAAG GCGUACGAGA UAACUAUGGU UAAGGAACUC GGCAAAAUGC CCC CGUAAC UUCGGGAGAA GGGGGACCGG AAUAUCGUGA ACACCCUUGC GGUGGGAGCG GGAUCCGGUC GCAGAAACCA GUGA GGAGC GACUGUUUAC UAAAAACACA GGUCCGUGCG AAGUCGCAAG ACGAUGUAUA CGGACUGACG CCUGCCCGGU GCUGG AAGG UUAAGAGGAC CCGUUAACCC GCAAGGGUGA AGCGGAGAAU UUAAGCCCCA GUAAACGGCG GUGGUAACUA UAACCA UCC UAAGGUAGCG AAAUUCCUUG UCGGGUAAGU UCCGACCUGC ACGAAUGGCG UAACGACUUC UCAACUGUCU CAACCAU AG ACUCGGCGAA AUUGCACUAC GAGUAAAGAU GCUCGUUACG CGCGGCAGGA CGAAAAGACC CCGGGACCUU CACUACAA C UUGGUAUUGA UGUUCGGUAC GGUUUGUGUA GGAUAGGUGG GAGACUGUGA AACCUCGACG CCAGUUGGGG CGGAGUCGU UGUUGAAAUA CCACUCUGAU CGUAUUGGGC AUCUAACCUC GAACCCUGAA UCGGGUUUAG GGACAGUGCC UGGCGGGUAG UUUAACUGG GGCGGUUGCC UCCUAAAAUG UAACGGAGGC GCCCAAAGGU UCCCUCAACC UGGACGGCAA UCAGGUGGCG A GUGUAAAU GCACAAGGGA GCUUGACUGC GAGACUUACA AGUCAAGCAG GGACGAAAGU CGGGAUUAGU GAUCCGGCAC CC CCGAGUG GAAGGGGUGU CGCUCAACGG AUAAAAGGUA CCCCGGGGAU AACAGGCUGA UCUUCCCCAA GAGUCCAUAU CGA CGGGAU GGUUUGGCAC CUCGAUGUCG GCUCGUCGCA UCCUGGGGCU GGAGCAGGUC CCAAGGGUUG GGCUGUUCGC CCAU UAAAG CGGCACGCGA GCUGGGUUUA GAACGUCGUG AGACAGUUCG GUCUCUAUCC GCCGCGCGCG UCAGAAACUU GAGGA AACC UGUCCCUAGU ACGAGAGGAC CGGGACGGAC GAACCUCUGG UGCACCAGUU GUCCCGCCAG GGGCACCGCU GGAUAG CCA CGUUCGGUCA GGAUAACCGC UGAAAGCAUC UAAGCGGGAA ACCUUCUCCA AGAUCAGGUU UCUCACCCAC UUGGUGG GA UAAGGCCCCC CGCAGAACAC GGGUUCAAUA GGUCAGACCU GGAAGCUCAG UAAUGGGUGU AGGGAACUGG UGCUAACC G GCCGAAAACU UACAACA

GENBANK: GENBANK: CP010339.1

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Macromolecule #8: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 8 / Number of copies: 1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 37.097238 KDa
SequenceString:
UUACGGCGGC CACAGCGGCA GGGAAACGCC CGGUCCCAUU CCGAACCCGG AAGCUAAGCC UGCCAGCGCC GAUGAUACUG CCCCUCCGG GUGGAAAAGU AGGACACCGC CGAACA

GENBANK: GENBANK: CP023593.1

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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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
95.0 mMKClPotassium chloride
5.0 mMNH4ClAmmonium chloride
5.0 mMMg(OAC)2Magnesium acetate
0.5 mMCaCl2Calcium chloride
8.0 mMPutrescine
1.0 mMSpermidine
5.0 mMKPPotassium phosphate
1.0 mMDithiothreitol

Details: Polymix buffer
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 13499 / Average electron dose: 50.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5471811
CTF correctionSoftware - Name: cryoSPARC (ver. v4.4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.4.0) / Number images used: 257214
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v4.4.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7mt7


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 60.5 / Target criteria: Cross-correlation coefficient
Output model

PDB-9e1s:
Cryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to the Mycobacterium tuberculosis C- 50S ribosomal subunit

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