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- EMDB-55416: HPFcold Bound Hibernating C. burnetii 30S Ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-55416
TitleHPFcold Bound Hibernating C. burnetii 30S Ribosome
Map dataLocal refinement of the HPFcold bound Coxiella burnetii 30S subunit following classification
Sample
  • Complex: Coxiella Ribosome 50S Subunit
    • Complex: 16S
      • Protein or peptide: x 6 types
    • Complex: Ribosomal Protein
    • Protein or peptide: x 15 types
    • RNA: x 1 types
  • Ligand: x 4 types
KeywordsRibosome / C. burnetii / 30S subunit / cold shock domain / pathogen / ribosomal peptide / hibernation / cryo-EM
Function / homology
Function and homology information


negative regulation of translational elongation / ribosomal small subunit binding / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / nucleic acid binding / tRNA binding / rRNA binding ...negative regulation of translational elongation / ribosomal small subunit binding / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / nucleic acid binding / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 ...Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, 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 S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S9, bacterial/plastid / 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 / K Homology domain / K homology RNA-binding domain / Ribosomal protein S18 superfamily / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / : / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / 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 S7, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / : / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S13-like, H2TH / Ribosomal protein S10p/S20e / S4 RNA-binding domain
Similarity search - Domain/homology
Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 ...Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Ribosome hibernation promoting factor
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsStuart WS / Isupov MN / Harmer NJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009122/1 United Kingdom
CitationJournal: To Be Published
Title: HPFcold Bound Hibernating C. burnetii 30S Ribosome
Authors: Stuart WS / Isupov MN / McLaren M / Jenkins CH / Monier A / Daum B / Norville IH / Gold VAM / Harmer NJ
History
DepositionOct 20, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55416.png

Downloads & links

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Map

FileDownload / File: emd_55416.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement of the HPFcold bound Coxiella burnetii 30S subunit following classification
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.07388234 - 0.32178324
Average (Standard dev.)0.002173091 (±0.015754847)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55416_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55416_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Coxiella Ribosome 50S Subunit

EntireName: Coxiella Ribosome 50S Subunit
Components
  • Complex: Coxiella Ribosome 50S Subunit
    • Complex: 16S
      • Protein or peptide: Small ribosomal subunit protein uS17
      • Protein or peptide: Large ribosomal subunit protein bL31
      • Protein or peptide: Small ribosomal subunit protein uS7
      • Protein or peptide: Small ribosomal subunit protein uS10
      • Protein or peptide: Small ribosomal subunit protein uS11
      • Protein or peptide: Small ribosomal subunit protein bS18
    • Complex: Ribosomal Protein
    • Protein or peptide: Small ribosomal subunit protein uS13
    • Protein or peptide: Small ribosomal subunit protein uS14
    • Protein or peptide: Ribosome hibernation promoting factor
    • Protein or peptide: Small ribosomal subunit protein uS19
    • RNA: 16S ribosomal RNA
    • Protein or peptide: Small ribosomal subunit protein uS15
    • Protein or peptide: Small ribosomal subunit protein uS3
    • Protein or peptide: Small ribosomal subunit protein uS9
    • Protein or peptide: Small ribosomal subunit protein bS21
    • Protein or peptide: Small ribosomal subunit protein bS6
    • Protein or peptide: Small ribosomal subunit protein bS20
    • Protein or peptide: Small ribosomal subunit protein uS4
    • Protein or peptide: Small ribosomal subunit protein uS5
    • Protein or peptide: Small ribosomal subunit protein uS8
    • Protein or peptide: Small ribosomal subunit protein bS16
    • Protein or peptide: Small ribosomal subunit protein uS12
  • Ligand: ZINC ION
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Coxiella Ribosome 50S Subunit

SupramoleculeName: Coxiella Ribosome 50S Subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII

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Supramolecule #2: 16S

SupramoleculeName: 16S / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #17-#22
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII

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Supramolecule #3: Ribosomal Protein

SupramoleculeName: Ribosomal Protein / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII

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Macromolecule #1: Small ribosomal subunit protein uS13

MacromoleculeName: Small ribosomal subunit protein uS13 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 13.420679 KDa
SequenceString:
MAARIAGVNI PVQKHARIAL QAIYGIGNSR ALEICKEAKI DPATKVKDLS EAELDALRTE VGKFSVEGDL RRERSMDIKR KMDLGAYEG IRHRRGLPLR GQRTRSNART RKGKRKPIRS

UniProtKB: Small ribosomal subunit protein uS13

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Macromolecule #2: Small ribosomal subunit protein uS14

MacromoleculeName: Small ribosomal subunit protein uS14 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 11.599955 KDa
SequenceString:
MAKLSVIERN KKRVRKSQSA RKKRLELKKI IKKGTPEEQE QALLKLQKRP RDESPVRTRD RCRLCGRPCG TFKKFGLCRI HLREAAMRA DVPGLKKASW

UniProtKB: Small ribosomal subunit protein uS14

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Macromolecule #3: Ribosome hibernation promoting factor

MacromoleculeName: Ribosome hibernation promoting factor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 21.176209 KDa
SequenceString:
MRRSFMQVPL QITLRNIDPT PAIEDRIHKK ADKLSQYSDQ IISCHIVVEL PKRHQHQGKL YNVRINLTLP GKEFAVNRNE VEDLYVAIR NAFDDMARKV EEEMRMRMGH VKTHPELLQG EIVRLFKEKD FGFIATPDGE EFYFNAGNVV HPTFEKLEVG T TVQFIEAI GDDGAQAHRV SAKER

UniProtKB: Ribosome hibernation promoting factor

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Macromolecule #4: Small ribosomal subunit protein uS19

MacromoleculeName: Small ribosomal subunit protein uS19 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 10.842623 KDa
SequenceString:
MPRSTNKGPF VDHHLMKKVD QAQKEGSKRP IKTWSRRSMV VPEMVGLTIA IHNGRQHVPV YISENMVGHK LGEFAITRTF RAHSGDRKA KKEGEK

UniProtKB: Small ribosomal subunit protein uS19

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Macromolecule #6: Small ribosomal subunit protein uS15

MacromoleculeName: Small ribosomal subunit protein uS15 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 10.340205 KDa
SequenceString:
MSLASAETAK IVKEYQLGKD DTGSPEVQVA ILTAKIIKLT DHMKAHKHDH HSRRGLLRMV SQRRKLLNFL KRNDLQRYLK LIERLGLRS

UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #7: Small ribosomal subunit protein uS3

MacromoleculeName: Small ribosomal subunit protein uS3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 25.671746 KDa
SequenceString: MGQKVNPVGM RIGITRDWTS NWYADKKDFA DRLNEDLNVR QLLQKRLKGA AVSRIQIERP ARNAKIIIHS ARPGVIIGKK GGEIEALRD EIFKVMKVPV HITIEEVRKP ELDAKLVAEN IAQQLERRVM FRRAMKRAVQ NTLRQGALGV KISVSGRLGG A EIARTEWY ...String:
MGQKVNPVGM RIGITRDWTS NWYADKKDFA DRLNEDLNVR QLLQKRLKGA AVSRIQIERP ARNAKIIIHS ARPGVIIGKK GGEIEALRD EIFKVMKVPV HITIEEVRKP ELDAKLVAEN IAQQLERRVM FRRAMKRAVQ NTLRQGALGV KISVSGRLGG A EIARTEWY REGRVPLHTF RADIDYATAS AKTTYGIIGV KVWIFKGEVH APKPQAEEAA PQETEEEVK

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #8: Small ribosomal subunit protein uS9

MacromoleculeName: Small ribosomal subunit protein uS9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 15.332496 KDa
SequenceString:
MAQAAKKQNL GTGRRKTSSA RVFLRSGTGQ IIINGLPLDE YFGRETARMV VRQPLVKLDV QSRFDVYATV QGGGDSGQAG AIRHGITRA LIQYDEEGGE GGTWRSTLRK AGFVTRDPRM VERKKVGLHG ARRGTQFSKR

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #9: Small ribosomal subunit protein bS21

MacromoleculeName: Small ribosomal subunit protein bS21 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 8.927503 KDa
SequenceString:
MPMIDVPDNN AFDVAMRRFK RACEKAGILS KLRQIEYYEK PTSKRKRKRA AAVKRYAKKL QKEQEALERE RTRY

UniProtKB: Small ribosomal subunit protein bS21

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Macromolecule #10: Small ribosomal subunit protein bS6

MacromoleculeName: Small ribosomal subunit protein bS6 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 14.603657 KDa
SequenceString:
MRHYEIVILV HPDQSSQVPA MVERYQSMIK EKDGKVHRLE DWGRRQLAYS IDKVHKAHYL LMNIESDQGV ISELENAFRY NDAVIRSLI LKRDHAITKS SLIMQGAEKG KSSRKEKVAA EAEASEEA

UniProtKB: Small ribosomal subunit protein bS6

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Macromolecule #11: Small ribosomal subunit protein bS20

MacromoleculeName: Small ribosomal subunit protein bS20 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 9.981456 KDa
SequenceString:
MANSAQAKKR ARQNEKRELH NASQRSAVRT AVKKILKSLQ ANDSSAAQSA YQHAVQILDK AAGRRIIHPN KAARLKSRLS QKIKNLSSS Q

UniProtKB: Small ribosomal subunit protein bS20

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Macromolecule #12: Small ribosomal subunit protein uS4

MacromoleculeName: Small ribosomal subunit protein uS4 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 23.770688 KDa
SequenceString: MARYLGPKCR LSRREKTDLQ LKSGIRAIDS KCNIERIPGM HWQRRGRTTD YGVQLRMKQM IKRYYDVLEK QFANYYKQAD RLKGSTGDN LLKLLESRLD NVVYRMGFAA TRAEARQLIS HKAILVNGEV VNIPSYQVKP GDIIEVRSRA KGQLRIKGAL E LAQQRAPI ...String:
MARYLGPKCR LSRREKTDLQ LKSGIRAIDS KCNIERIPGM HWQRRGRTTD YGVQLRMKQM IKRYYDVLEK QFANYYKQAD RLKGSTGDN LLKLLESRLD NVVYRMGFAA TRAEARQLIS HKAILVNGEV VNIPSYQVKP GDIIEVRSRA KGQLRIKGAL E LAQQRAPI SWIEVDTKKM TGTFKEQPDV AELPAEFKVN LVVELYSK

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #13: Small ribosomal subunit protein uS5

MacromoleculeName: Small ribosomal subunit protein uS5 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 17.510307 KDa
SequenceString:
MQEAGIGTTT DGIQEKLVAV RRTAKVVKGG RVFGFSALVV AGDGDGKVGF GLGKAREVPS AIQKATENAR RNMISVPLYG ATLHHAIKA THASSTVLML PASEGTGVIA GNAMRAIFEV MGVQNVLAKC IGSSNPINVV RATFKGLKQM ETPESVAAKR G KAIEEIVE

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #14: Small ribosomal subunit protein uS8

MacromoleculeName: Small ribosomal subunit protein uS8 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 14.59201 KDa
SequenceString:
MMQDPISDML TRIRNAQAVR KKEVVMPRSK LKMSIANVLK EEGYIVDYRE EGDLTKAQLV ITLKYHEGES VISEIRRVSS PALQVYKSK DELPKVKNGL GIAIISTSKG VMSDRQARRL GEGGEVLCYV S

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #15: Small ribosomal subunit protein bS16

MacromoleculeName: Small ribosomal subunit protein bS16 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 15.592907 KDa
SequenceString:
MVVIRLARGG SKKNPFYHIV VADRRKPRDG RFIERVGYYN PMARGQDIRL QLEKERISHW LNQGAQTSLR VKHLIKKLEK SPEEAQKGG MRKGEFKRLQ AEQAAKAQKK AVATEEPKAE EAKEAPPAES QAAEGKEE

UniProtKB: Small ribosomal subunit protein bS16

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Macromolecule #16: Small ribosomal subunit protein uS12

MacromoleculeName: Small ribosomal subunit protein uS12 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 13.786059 KDa
SequenceString:
MARINQLVRK PRRARAKKSD VPALEGCPQR RGVCTRVYTT TPKKPNSALR KVARVRITNG AEVTAYIGGE GHNLQEHSVV LIRGGRVKD LPGVRYHIVR GSLDTAGVSG RRRGRSKYGE KKPKE

UniProtKB: Small ribosomal subunit protein uS12

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Macromolecule #17: Small ribosomal subunit protein uS17

MacromoleculeName: Small ribosomal subunit protein uS17 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 10.328146 KDa
SequenceString:
MNKNEKMVRS LMGTVVSNKM NDTVVVRVER RVKHPKYGKF IKRSTKIHAH DKGNEGQIGD IVTIRECRPI SKTKSWTLVK INERAEKVE

UniProtKB: Small ribosomal subunit protein uS17

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Macromolecule #18: Large ribosomal subunit protein bL31

MacromoleculeName: Large ribosomal subunit protein bL31 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 9.096483 KDa
SequenceString:
MKENIHPPYK QIKVTCSCGN TFMTGSTLDR ELHLEICSAC HPFYTGQQKM VDTAGRVERF RKKYAKRRAA NASPEDEKK

UniProtKB: Large ribosomal subunit protein bL31

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Macromolecule #19: Small ribosomal subunit protein uS7

MacromoleculeName: Small ribosomal subunit protein uS7 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 21.334717 KDa
SequenceString:
MARRKAAPKR ETLPDPLFHS ELLAKFINAV MRNGKKSVAE KIVYGALDVV AKRVQNKSGE QGDGDGESGG KAGGIKKRSL GDIRTDENA RALALETFKG ALDKVMPNVE VKSRRVGGST YQVPVEIRMA RRQALARRWL VEYANKRNEK TMVLRLAHEI L DAVEGRGG AIKKREDVHR MAKANQAFAH YKW

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #20: Small ribosomal subunit protein uS10

MacromoleculeName: Small ribosomal subunit protein uS10 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 12.614599 KDa
SequenceString:
MSDNQRIRIR LKAFDHRLID RSTREIVETA RRTGAIIRGP ILLPTKIERY TVLISPNIDK DARDQYEIRT HKRLVDISEP TDKTVDALM KLDLAAGVDV QIELLNKKSG A

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #21: Small ribosomal subunit protein uS11

MacromoleculeName: Small ribosomal subunit protein uS11 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 13.534661 KDa
SequenceString:
MAKKRYRKVT EGIAHIKATF NNTMISVSDP QGNVLCFRSA GGSGFKGSRK GTPYGAQMAS EEVGRLARDN FDMRRIAVRV KGPGAGRDS AIRGLRSAGL EVIHLEDRTP LPHNGCRPRK KRRV

UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #22: Small ribosomal subunit protein bS18

MacromoleculeName: Small ribosomal subunit protein bS18 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 8.569 KDa
SequenceString:
MSFRRKKFCA FDAKNLQEID YKDVNTLKDY IMESGRVVPS RITGTCAKHQ RQISRAIKLA RYLALLPYCD THQ

UniProtKB: Small ribosomal subunit protein bS18

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Macromolecule #5: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Molecular weightTheoretical: 497.437656 KDa
SequenceString: AAUUGAAGAG UUUGAUUCUG GCUCAGAUUG AACGCUAGCG GCAUGCUUAA CACAUGCAAG UCGAACGGCA GCGCGGGGAG CUUGCUCCC UGGCGGCGAG UGGCGGACGG GUGAGUAAUG CGUAGGAAUC UACCUUGUAG UGGGGGAUAA CCUGGGGAAA C UCGGGCUA ...String:
AAUUGAAGAG UUUGAUUCUG GCUCAGAUUG AACGCUAGCG GCAUGCUUAA CACAUGCAAG UCGAACGGCA GCGCGGGGAG CUUGCUCCC UGGCGGCGAG UGGCGGACGG GUGAGUAAUG CGUAGGAAUC UACCUUGUAG UGGGGGAUAA CCUGGGGAAA C UCGGGCUA AUACCGCAUA AUCUCUUUGG AGCAAAGCGG GGGAUCUUCG GACCUCGUGC UAUAAGAUGA GCCUACGUCG GA UUAGCUU GUUGGUGGGG UAAUGGCCUA CCAAGGCGAC GAUCCGUAGC UGGUCUGAGA GGACGAUCAG CCACACUGGG ACU GAGACA CGGCCCAGAC UCCUACGGGA GGCAGCAGUG GGGAAUAUUG GACAAUGGGG GAAACCCUGA UCCAGCAAUG CCGC GUGUG UGAAGAAGGC CUUCGGGUUG UAAAGCACUU UCGGUGGGGA AGAAAUUCUC AAGGGUAAUA UCCUUGGGCG UUGAC GUUA CCCACAGAAG AAGCACUGGC UAACUCUGUG CCAGCAGCC(G7M) CGGUAAUACA GAGAGUGCAA GCGUUAAUCG GA AUCACUG GGCGUAAAGC GCGCGUAGGU GGAUAUUUAA GUCGGAUGUG AAAGCCCUGG GCUUAACCUG GGAAUUGCAC CCG AUACUG GGUAUCUUGA GUAUGGUAGA GGGAAGUGGA AUUUCCGGUG UAGCGGUGAA AUGCGUAGAU AUCGGAAAGA ACAC CAGUG GCGAAGGCGA CUUCCUGGAC CAAUACUGAC ACUGAGGCGC GAAAGCGUGG GGAGCAAACA GGAUUAGAGA CCCUG GUAG UCCACGCCGU CAACGAUGAG AACUAGCUGU UGGGAAGUUC ACUUCUUAGU AGCGAAGCUA ACGCGUUAAG UUCUCC GCC UGGGGAGUAC GGCCGCAAGG UUAAAACUCA AAGAAAUUGA CGGGGGCCCG CACAAGCGGU GGAGCAUGUG GUUUAAU UC GAU(2MG)(5MC)AACGC GAAAAACCUU ACCUACCCUU GACAUCCUCG GAACUUGUCA GAGAUGAUUU GGUGCCUUCG GGAACCGAG UGACAGGUGC UGCAUGGCUG UCGUCAGCUC GUGUCGUGAG AUGUUGGGUU AAGUCCCGUA ACGAGCGCAA C CCUCGUCC UUAGUUGCCA GCGAGUCAAG UCGGGAACUC UAAGGAGACU GCCGGUGAUA AACCGGAGGA AGGUGGGGAU GA UGUCAAG UCAUCAUGGC CCUUACGGGU AGGGCUACAC ACGUGCUACA AUGGGCAGUA CAAAGGGUUG CCAAGCCGCG AGG UGGAGC UAAUCCCAGA AAACUGCUCG UAGUCCGGAU UGGAGUCUGC AACUCGACUC CAUGAAGUUG GAAUCGCUAG UAAU CGCGA AUCAGCAUGU CGCGGUGAAU ACGUUCUCGG GCCUUGUACA CACCG(4OC)CCGU CACACCAUGG GAGUGAAUUG U ACCAGAAG CGGGUAGGCU AACCUUCGGG AGGCCGCUCA CCACGGUAUG AUCCAUGACU GGGGUGAAGU CG(UR3)AACAA G GUAGCCGUAG G(2MG)G(MA6)(MA6)CCUGC GGCUGGAUCA CCUC

+
Macromolecule #23: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 23 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #24: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 24 / Number of copies: 34 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #25: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 25 / Number of copies: 53 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #26: water

MacromoleculeName: water / type: ligand / ID: 26 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.05 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
100.0 mMKOAcPotassium Acetate
15.0 mMMg(OAc)Magnesium Acetate
1.0 mMC4H10O2S2DTT

Details: BS100 ribosomal resuspension buffer
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 4 s, blot force 1, blot total 1.

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
DetailsSuper-resolution binned 2 in EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 22295 / Average exposure time: 3.0 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio reconstruction in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 24143
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
source_name: AlphaFold, initial_model_type: in silico model
source_name: Other, initial_model_type: in silico modelModel Angelo
SoftwareName: UCSF ChimeraX (ver. 1.9)
Output model

PDB-9t0z:
HPFcold Bound Hibernating C. burnetii 30S Ribosome

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