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- EMDB-56461: Empty 50S Subunit of the Coxiella burnetii Ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-56461
TitleEmpty 50S Subunit of the Coxiella burnetii Ribosome
Map data
Sample
  • Complex: Coxiella Ribosome 50S Subunit
    • Protein or peptide: x 29 types
    • RNA: x 2 types
  • Ligand: x 4 types
KeywordsRibosome / C. burnetii / 50S subunit / unbound state / pathogen / ribosomal peptide / CLaSP / cryo-EM
Function / homology
Function and homology information


assembly of large subunit precursor of preribosome / large ribosomal subunit / transferase activity / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding ...assembly of large subunit precursor of preribosome / large ribosomal subunit / transferase activity / ribosome binding / 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 / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA 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 L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain ...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 L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L21, conserved site / : / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / 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 L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / : / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / 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 L34 / Ribosomal protein L34 / 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 L5, conserved site / Ribosomal protein L5 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 L5 domain superfamily / Ribosomal protein L2, conserved site
Similarity search - Domain/homology
Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL13 ...Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 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: Empty 50S Subunit of the Coxiella burnetii Ribosome
Authors: Stuart WS / Isupov MN / McLaren M / Jenkins CH / Monier A / Daum B / Norville IH / Gold VAM / Harmer NJ
History
DepositionJan 22, 2026-
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_56461.png

Downloads & links

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Map

FileDownload / File: emd_56461.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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-0.17786951 - 0.5351538
Average (Standard dev.)0.0011587808 (±0.015868887)
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_56461_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56461_half_map_2.map
Projections & Slices
AxesZYX

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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
    • Protein or peptide: Coxiellacae Large Subunit Peptide (CLaSP)
    • Protein or peptide: Large ribosomal subunit protein bL33
    • Protein or peptide: Large ribosomal subunit protein uL24
    • Protein or peptide: Large ribosomal subunit protein uL18
    • Protein or peptide: Large ribosomal subunit protein bL36
    • RNA: 5S ribosomal RNA
    • Protein or peptide: Large ribosomal subunit protein bL19
    • Protein or peptide: Large ribosomal subunit protein uL3
    • Protein or peptide: Large ribosomal subunit protein bL20
    • Protein or peptide: Large ribosomal subunit protein uL5
    • Protein or peptide: Large ribosomal subunit protein uL6
    • Protein or peptide: Large ribosomal subunit protein bL21
    • Protein or peptide: Large ribosomal subunit protein uL13
    • Protein or peptide: Large ribosomal subunit protein uL22
    • Protein or peptide: Large ribosomal subunit protein uL15
    • Protein or peptide: Large ribosomal subunit protein bL17
    • Protein or peptide: Large ribosomal subunit protein uL2
    • Protein or peptide: Large ribosomal subunit protein bL9
    • Protein or peptide: Large ribosomal subunit protein uL29
    • Protein or peptide: Large ribosomal subunit protein uL16
    • Protein or peptide: Large ribosomal subunit protein uL30
    • Protein or peptide: Large ribosomal subunit protein bL25
    • Protein or peptide: Large ribosomal subunit protein bL32
    • Protein or peptide: Large ribosomal subunit protein uL4
    • Protein or peptide: Large ribosomal subunit protein uL14
    • Protein or peptide: Large ribosomal subunit protein bL34
    • Protein or peptide: Large ribosomal subunit protein bL35
    • RNA: 23S ribosomal RNA
    • Protein or peptide: Large ribosomal subunit protein bL27
    • Protein or peptide: Large ribosomal subunit protein uL23
    • Protein or peptide: Large ribosomal subunit protein bL28
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM 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-#31
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII

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Macromolecule #1: Coxiellacae Large Subunit Peptide (CLaSP)

MacromoleculeName: Coxiellacae Large Subunit Peptide (CLaSP) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 2.53008 KDa
SequenceString:
MPRGRGPHGP KKFRKRNKKS R

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Macromolecule #2: Large ribosomal subunit protein bL33

MacromoleculeName: Large ribosomal subunit protein bL33 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 8.054479 KDa
SequenceString:
MAVSPREKIM LQSTGKTKAG KPTGTFYTTY KNKRNTTDKL NIKKFDPRAW NSETSKCGMH VLFKEKKIPK

UniProtKB: Large ribosomal subunit protein bL33

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Macromolecule #3: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 11.814896 KDa
SequenceString:
MAIKKIKKDD TVIVITGRDK GRQGKVLKVL PNSRLLVEGI NLVKKHVKPN PNKNEQGGIL ERELSIHVSN VAIYNPAAKK ADRVGIKTL EDGSKVRIFK SNGEVIDV

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #4: Large ribosomal subunit protein uL18

MacromoleculeName: Large ribosomal subunit protein uL18 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 13.137419 KDa
SequenceString:
MDKQEKRIRR ARRTRAKIKE LGAVRLCVHR SLNHIYAQLI SPRDSKVLVC ASTLEKEVRS QIKHGGNIQA ATAIGKLIAQ RAKKAGVTK VAFDRSGYKY HGRVRALAEA VREGGIEF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #5: Large ribosomal subunit protein bL36

MacromoleculeName: Large ribosomal subunit protein bL36 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 4.668729 KDa
SequenceString:
MKVRASVKRM CRNCKVIRRN GVVRVICSDA RHKQRQKGGK

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #7: Large ribosomal subunit protein bL19

MacromoleculeName: Large ribosomal subunit protein bL19 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 13.302429 KDa
SequenceString:
MNNIIQLLET EQTQGKEIPD FRAGDTVTVQ VKVKEGNRER LQAFEGVVIA RRHRGLNSSF TVRKVSHGEG VERVFQLYSP LIASIKVNR RGDVRRAKLY YLRNLRGRKA KIKEKI

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #8: Large ribosomal subunit protein uL3

MacromoleculeName: Large ribosomal subunit protein uL3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 23.547062 KDa
SequenceString: MSIGLIGRKC GMTRIFTETG SSIPVTVVEV ILNRITQVKT VETDGYRAFQ VAYGKKSSAR VNKPLAGHYS KAAVEAGNAL REFRLGNEE LTEAKAGDEL KVDIFKEGQV VDVRGLTRGK GFAGTVKRHN FRTQDATHGN SLSHRAPGSI GQCQTPGRVW K GKKMAGQL ...String:
MSIGLIGRKC GMTRIFTETG SSIPVTVVEV ILNRITQVKT VETDGYRAFQ VAYGKKSSAR VNKPLAGHYS KAAVEAGNAL REFRLGNEE LTEAKAGDEL KVDIFKEGQV VDVRGLTRGK GFAGTVKRHN FRTQDATHGN SLSHRAPGSI GQCQTPGRVW K GKKMAGQL GNVYCTVQSQ EIIKVDVERN LLLIKGALPG APGGEVIITQ SSKKRKEDK

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #9: Large ribosomal subunit protein bL20

MacromoleculeName: Large ribosomal subunit protein bL20 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 13.475973 KDa
SequenceString:
MPRVKRGVTA RARHKKVLTK AKGYYGARSR VFRVAKQAVI KAAQYAYRDR KQRKRQFRAL WIVRINAAAR EHGLSYSRLI NGLMKASVA IDRKNLAELA VYDKAAFGKL AEKAKQALGG

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #10: Large ribosomal subunit protein uL5

MacromoleculeName: Large ribosomal subunit protein uL5 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 20.782402 KDa
SequenceString:
MVELQELYKK TITPALQKEF GFKSVMAVPR LEKITLNMGL GEAVADKKVI ERAMDDMIKI SGQKPLITYA RKSEAGFKIR AGWPIGCKV TLRRDRMYEF LKRLISIAIP RIRDFRGLSP KSFDGRGNYS LGIREQIVFP EIQYDKVDAI RGMDITITTT A RTDEEGRA LLKAFGFPLK DESR

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #11: Large ribosomal subunit protein uL6

MacromoleculeName: Large ribosomal subunit protein uL6 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 19.228453 KDa
SequenceString:
MVSRVAKNPI KIPTGVEVNV AGQQITVKGK LGTLTRVIHR AVKVTKTDAE LQTICANDSP GSNALAGTAR AVLANMVQGV HTGFQRKLV MVGVGYRAKA EGKKLNLTVG LSHPVNIEMP EGITVETPSQ TEIIVKGADK QRVSQVAANI REIRPPEPYK G KGIRYDNE RVILKEAKKK

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #12: Large ribosomal subunit protein bL21

MacromoleculeName: Large ribosomal subunit protein bL21 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 12.785894 KDa
SequenceString:
MYAIIKTGGK QYRVTEGQML KVEKLAQDVG QSVKFDDVLM VAAGDELHIG TPSVKDAAVT AEVVDQGRQA KIEIIKFKRR KHHMKRQGH RQDFTAVKIT EIALGKAKKE VKTDGA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #13: Large ribosomal subunit protein uL13

MacromoleculeName: Large ribosomal subunit protein uL13 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 15.840458 KDa
SequenceString:
MATYMANAKT VSPRWLLVNA EGKTLGRLAS RIAAILRGKH KAEFTPHVDA GDFVVVINVD KLKVTGNKTQ DKQYHHHSGY PGGLKTINF ADLQAKKPQR ILELAIKGML PKGPLGRQLY RKLKIYAGDQ HPHQAQQPEL IDL

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #14: Large ribosomal subunit protein uL22

MacromoleculeName: Large ribosomal subunit protein uL22 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 12.60547 KDa
SequenceString:
MEVAAKLKYA RISAQKARLV ADQVRGLGAE QAVNLLRFSN KKAAALMKKV LDSAIANAEH NEGADIDELK VSTVMVDEGP SARRFHARA RGRANQILKR TCHITVKVSD SQVEND

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #15: Large ribosomal subunit protein uL15

MacromoleculeName: Large ribosomal subunit protein uL15 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 15.320006 KDa
SequenceString:
MQLNDLKPAK GARHQKLRVG RGIGSGKGKT AGRGHKGQHS RAGGYHKVGF EGGQMPLQRR VPKFGFTSRK ELISAEVRLG ELNKISGDV VDLASLKAAN IISRQIKRVK IFAAGKLEKP VTIRGLRVTK GVKAAVEAAG GKIE

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #16: Large ribosomal subunit protein bL17

MacromoleculeName: Large ribosomal subunit protein bL17 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 14.574902 KDa
SequenceString:
MHHRKSGRHL NRTSAHRKAM LRNMAVSLFQ HELIKTTLPK AKELRRVVEP LITLAKEDTV ANRRLAFNRL RDDAIVAKLF KEIAPRHKE RPGGYCRVLK YGFRNGDSAP MAIVELVDRE ESESSED

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #17: Large ribosomal subunit protein uL2

MacromoleculeName: Large ribosomal subunit protein uL2 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 30.481426 KDa
SequenceString: MALVKTKPTS PGRRFVVKVV HPELHKGDPY APLVESKNRI NSRNNQGRIT VRRRGGGHKR NYRIIDFKRD KEGIEGKVER LEYDPNRSA HIALVLYPDG ERRYIIAPKG VHKGSKVVSG REAPIRPGNC LPLQNIPLGA TIHNIELKPG KGAQLVRSAG A SAQLAAKE ...String:
MALVKTKPTS PGRRFVVKVV HPELHKGDPY APLVESKNRI NSRNNQGRIT VRRRGGGHKR NYRIIDFKRD KEGIEGKVER LEYDPNRSA HIALVLYPDG ERRYIIAPKG VHKGSKVVSG REAPIRPGNC LPLQNIPLGA TIHNIELKPG KGAQLVRSAG A SAQLAAKE GIYAIIRMRS GETRKILAVC RACIGEVSNS EHNLRSLGKA GAKRWRGRRP TVRGVAMNPV DHPHGGGEGK TS GGRHPVS PTGKPTKGYK TRRNKRTSNM IIRDRRKK

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #18: Large ribosomal subunit protein bL9

MacromoleculeName: Large ribosomal subunit protein bL9 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 16.603986 KDa
SequenceString:
MKLILQEKVA NLGNIGDQVV VKPGYARNFL LPLGKAVPAT PEHIAEFEKQ RAELEKAAAE LLAKAKARAK KLEDKSFKIT ANASDEGRL FGSIGPREIA QAITEAGIEI EKREVDLSQG PIRQVGEYEV PLRLHTDVSV NVKIEVAPEN SNS

UniProtKB: Large ribosomal subunit protein bL9

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Macromolecule #19: Large ribosomal subunit protein uL29

MacromoleculeName: Large ribosomal subunit protein uL29 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 7.717034 KDa
SequenceString:
MNVNDLRNKT KAELKKELLE LLKEQFNLRM QKGGGEAPRP HLFKRVRRDI ARVKTLLGEK ERNNE

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #20: Large ribosomal subunit protein uL16

MacromoleculeName: Large ribosomal subunit protein uL16 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 15.532356 KDa
SequenceString:
MLQPSNRKYR KDFKGRNRGV ASRGNRVSFG EFGLKATECA RITARQLEAA RRTIARHIKR GGKITIRIFP DKPITKKPLE VRQGKGKGS VEYWVALVQP GRMIFEIEGV DEALAREAFS RAAAKLPLKC LFVKRTVM

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #21: Large ribosomal subunit protein uL30

MacromoleculeName: Large ribosomal subunit protein uL30 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 7.312629 KDa
SequenceString:
MVQEKKLRVT LVKSKYGRKP GHRECIEGLG LRRMHQTVEV TDTPANRGMI EKVSYLLMID EEV

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #22: Large ribosomal subunit protein bL25

MacromoleculeName: Large ribosomal subunit protein bL25 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 26.577008 KDa
SequenceString: MAAESFELIA ELREFTGKSA ARRMRRFEDK VPGTVYGAGK APQSITLLQK DLLKALESES TFSSILTLKV GDKKQKVILK ALQRHHTKP KIVHIDFQRI KASEKLIMNV PLHFLGEDDC PGVEAGGVVS HLQSEVEIRC LPADLPEYIE VDLSHLQLDE S VHLSNLKL ...String:
MAAESFELIA ELREFTGKSA ARRMRRFEDK VPGTVYGAGK APQSITLLQK DLLKALESES TFSSILTLKV GDKKQKVILK ALQRHHTKP KIVHIDFQRI KASEKLIMNV PLHFLGEDDC PGVEAGGVVS HLQSEVEIRC LPADLPEYIE VDLSHLQLDE S VHLSNLKL PAGVGLTSAV DEEHDSPIAS VHMPRVSKAD VEAEAAEAAL AKEAATEAAE EEETEKPASE AEASGEAEQA DT DKKE

UniProtKB: Large ribosomal subunit protein bL25

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Macromolecule #23: Large ribosomal subunit protein bL32

MacromoleculeName: Large ribosomal subunit protein bL32 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 7.486457 KDa
SequenceString:
MAVQKSRKTR SRRGMRRSHD ALRGAMLSKD PTTGETHLRH HISPEGYYKG RQILTPKESY EDEE

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #24: Large ribosomal subunit protein uL4

MacromoleculeName: Large ribosomal subunit protein uL4 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 22.409729 KDa
SequenceString: MELPVNSFDK KEASTLTVAD SAFGSEYKEG LVHQVVNAYL AGGRAGTKAQ KTRREVSGGG AKPWRQKGTG RARAGSSRSP LWRSGGVAF AAKPRDFTQK VNRKMYRSAM ASILSELIRR EQLVVVDSLK LNEPKTRELK ESLKKLNLGN VLIIIDGDDR N INLASRNM ...String:
MELPVNSFDK KEASTLTVAD SAFGSEYKEG LVHQVVNAYL AGGRAGTKAQ KTRREVSGGG AKPWRQKGTG RARAGSSRSP LWRSGGVAF AAKPRDFTQK VNRKMYRSAM ASILSELIRR EQLVVVDSLK LNEPKTRELK ESLKKLNLGN VLIIIDGDDR N INLASRNM VGVSVCDALH VDPVSLVAAE NIVVTVDAVK RLEERLS

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #25: Large ribosomal subunit protein uL14

MacromoleculeName: Large ribosomal subunit protein uL14 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 13.564108 KDa
SequenceString:
MIQTQSIVDV ADNSGARRVM CIKVLGGSKR RYANIGDVIK VSIKEAIPRG KVKKGDVMHA VVVRTRKGVR RNDGSLIRFD NNAVVLLNN QLQLVGTRVF GPVVRELRTD KFMKIISLAL EVL

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #26: Large ribosomal subunit protein bL34

MacromoleculeName: Large ribosomal subunit protein bL34 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 5.357379 KDa
SequenceString:
MKRTYQPSKQ KRNRTHGFRA RMATKNGRQV LNRRRAKGRK RLTV

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #27: Large ribosomal subunit protein bL35

MacromoleculeName: Large ribosomal subunit protein bL35 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 7.415878 KDa
SequenceString:
MPKLKTNRGA VKRFKVTGSG KIKRAASNHN HILTKKSQKR KRRLRKIHEV APSDMRAVSE MLRD

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #29: Large ribosomal subunit protein bL27

MacromoleculeName: Large ribosomal subunit protein bL27 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 10.069655 KDa
SequenceString:
MAHKKAGGST RNGRDSNPKM LGVKRFGGER VLAGNIIVRQ RGTHYRPGEN MGMGRDHTLY ALIEGKVKFT RKGPKKRNFV SIEPLEESQ P

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #30: Large ribosomal subunit protein uL23

MacromoleculeName: Large ribosomal subunit protein uL23 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 10.828598 KDa
SequenceString:
MNEERLFEIL LAPHISEKGA LTTGQYVFEV MPDATKPEIK RAVEKQFNVT VKSVRTCNVK GKTTRFRQVR GRRKNWKKAY VMLAPGSEI DIAAGE

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #31: Large ribosomal subunit protein bL28

MacromoleculeName: Large ribosomal subunit protein bL28 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 9.266986 KDa
SequenceString:
MAKVCQVTGK RPQSGNNVSH ANKKTNRRFL PNLKKRRFWL PDEKRFITLT VSTHGMRIID KLGINAVLKK IREREKESK

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #6: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 37.630352 KDa
SequenceString:
UUCCUGGCGG CCAUAGCGAG CGGGCCCCAC CUGAUUCCAU UCCGAACUCA GAAGUGAAAA CGCUUAGCGC CGAUGAUAGU GUGGGUCUC CCAUGCGAAA GUAGGUCACC GCCAGGUU

GENBANK: GENBANK: CP103432.1

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Macromolecule #28: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 28 / Number of copies: 1
Source (natural)Organism: Coxiella burnetii (bacteria)
Molecular weightTheoretical: 947.544938 KDa
SequenceString: GGUUGCAUGG UCAAGUGAAU AAGCGCAUAU GGUGGAUGCC UUGGCAGUAA GAGGCGAUGA AGGACGUAGU AGCCUGCGAU AAGCUUCGG GGAGCUGGCA AACAAGCGAU GAUCCGGAGA UUUCCGAAUG GGGAAACCCA ACCUUUCGAG GUUAUCGUAU A CUGAAUUC ...String:
GGUUGCAUGG UCAAGUGAAU AAGCGCAUAU GGUGGAUGCC UUGGCAGUAA GAGGCGAUGA AGGACGUAGU AGCCUGCGAU AAGCUUCGG GGAGCUGGCA AACAAGCGAU GAUCCGGAGA UUUCCGAAUG GGGAAACCCA ACCUUUCGAG GUUAUCGUAU A CUGAAUUC AUAGGUAUAC GAGGCGAACC UGGGGAACUG AAACAUCUAA GUACCCAGAG GAAAAGAAAU CAACCGAGAU UC CGUCAGU AGCGGCGAGC GAAAGCGGAA CAGCCCAGUU ACUAAAUCAU UAUUUGUUCU AGCAGAAUGU UCUGGAAAGU UCA GCCAUA GCGGGUGAUA GCCCCGUACG CGAAAGAGUA AAUAAUGUGG GUAACGAUGA GUAGGUCGGG ACACGUGGUA UCUU GACUG AACAUGGGGG GACCAUCCUC CAAGGCUAAA UACUCCUUAC UGACCGAUAG CGAACCAGUA CCGUGAGGGA AAGGU GAAA AGAACCCCGG CGAGGGGAGU GAAAUAGAAC CUGAAACCGU AUGCGUACAA GCAGUAGGAG CAUUUCUUCG GAAAUG UGA CUGCGUACCU UUUGUAUAAU GGGUCAGCGA CUUACUUGUU GUAGCGAGCU UAACCGUCUA GGGGAGGCGU AGGGAAA CC GAGUCCGAAA UGGGCGUUUA GUUGCAACGA GUAGACCCGA AACCGAGCGA UCUAUCUAUG GCCAGGGUGA AGGUCAGG U AACACUGACU GGAGGCCCGA ACCCACUAAU GUUGAAAAAU UAGGGGAUGA GCUGUGGAUA GGAGUGAAAG GCUAAUCAA GCUCGGAGAU AGCUGGUUCU CCUCGAAAGC UAUUUAGGUA GCGCCUCGUG UAUGACUCUU GGGGGUAGAG CACUGUUUCG GCUAGGGGG CCAUCCCGGC CUACCAAACC GAGGCAAACU CCGAAUACCA AGAAGUUUUA GCACGGGAGA CACACUGCGG G (PSU)GAUAAGG UCCGUGGUGG AAAGGGAAAC AGCCCAGAUC GCCAGCUAAG GUCCCAAAAU CACAGUUAAG UGGAAAAC G AUGUGGGAAG GCUCAGACAG CCAGGAGGUU GGCUUAGAAG CAGCCAUCCU UUAAAGAAAG CGUAAUAGCU CACUGGUCG AGUCGUCCUG CGCGGAAGAU UUAACGGGGC UCAAACUGUG UACCGAAGCU GCGGCAUCAG AAGACACUGU CUUCUGAUGG GUAGAGGAG CGUUCUGUAA GCCUGUGAAG GUGAAUCGAG AGGUUUGCUG GAGGUAUCAG AAGUGCGAAU GCUGACAUAA G UAACGAUA AUGUGGGUGA AAAACCCACA CGCCGAAAGU CUAAGGUUUC CUGCGCAACG UUAAUCGACG CAGGGUGAGU CG GCCCCUA AGGCGAGGCA GAAAUGCGUA GUCGAUGGGA AACGGGUUAA UAUUCCCGUA CUUUAUAAUA CUGCGAUGGG AGG ACGGAG AAGGCUAGGU CAGCCACCCG AUGGUUGUGG UGGUUUAAGU GUGUAGGAAG GGUUCUUUGG CAAAUCCGGG AACU CAAUU CCGAGACAUG AUGACGAAGU ACGAACUUGU UCGUGCAAAG UGAUUGAUGC CACGCUUCCA GGAAAAGUCC CUAAG CUUC AGGUAUUGUA AAACCGUACU AUAAACCGAC ACAGGUGGAC AGGUAGAGAA UACCAAGGCG CUUGAGAGAA CUUGGG UGA AGGAACUAGG CAAAAUGGCA CCGUAACUUC GGGAGAAGGU GCGCCCUUGG UAAGUGAAGG UCCUUGCGAC UGGAGCU GA AAAGGGUUGC AGAUACCAGG UGGCUGCGAC UGUUUACUAA AAACACAGCA CUCUGCAAAC UCGUAAGAGG ACGUAUAG G GUGUGACGCC UGCCCGGUGC CGGAAGGUUA AGUGAUGGGG UUAGCCCUCG GGCGAAGCUC UUGAUCGAAG CCCCGGUAA ACGGCGGCCG (PSU)AACUA(PSU)AAC GGUCCUAAGG UAGCGAAAUU CCUUGUCGGG UAAGUUCCGA CCUGCACGAA UG GCGUAAC GAUAGCCACG CUGUCUCCAC CCAAGACUCA GUGAAAUUGA AAUCGCUGUG AAGAUGCAGC GUACCCGCGG CUA GACGGA AAGACCCCGU GAACCUUUAC UACAGCUUUA CACUGAACUU UGAAUAUGCC UGUGUAGGAU AGGUGGGAGG CUUU GAAGC UGGAGCGCUA GCUCCAGUGG AGCCAACCUU GAAAUACCAC CCUGGCGUGU UUGAGGUUCU AACCCUGUCC CGUAA UCCG GGUCGGGAAC AGUGUAUGGU GGGUAGUUUG ACUG(OMG)GGCGG UCUCCUCCAA AAGAGUAACG GAGGAGUACA AA GGUACCC UCAGCACGGU CGGAAAUCGU GCAUUGUGUG CAAAGGCAUA AGGGUGCUUG ACUGCGAGAC UGACAAGUCG AGC AGGUAC GAAAGUAGGU CUUAGUGAUC CGGUGGUCCU UUAUGGAAGG GCCAUCGCUC AACGGAUAAA AGGUACUCCG GGGA UAACA GGCUGAUACC ACCCAAGAGU UCAUAUCGAC GGUGGUGUUU GGCACCUCG(2MA) (PSU)GUCGGCUCA UCACAUC CU GGGGCUGUAG CCGGUCCCAA GGGUAUGGC(OMU) GUUCGCCAUU UAAAGUGGUA CGUGAGC(PSU)GG GUUUAGAACG UCGUGAGAC AGU(PSU)CGGUCC CUAUCUGCCG UGGGCGUUGG AGAUUUGAGA GGAGCUGCUC CUAGUACGAG AGGACCG GA GUGGACGUAC CUCUGGUGUU CCGGUUGUCA CGCCAGUGGC AUUGCCGGGU AGCUAAGUAC GGACGGGAUA ACCGCUGA A AGCAUCUAAG CGGGAAGCCC CCCUCAAGAU GAGAUCUCCC GGACCUUUAA GGUCCCUAAA GAUUCGUUGA AGACGACAA CGUUGAUAGG CAGGGUGUGG AAGCUCAGUA AUGAGUGAAG CUAACCUGUA CUAAUUAAUC GUGCGACUUG ACUAUGUAAC C

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Macromolecule #32: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 32 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #33: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 33 / Number of copies: 162 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #34: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 34 / Number of copies: 136 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #35: water

MacromoleculeName: water / type: ligand / ID: 35 / Number of copies: 7 / 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 - Film thickness: 2
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
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 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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio reconstruction in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 129328
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5 / 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
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-9tz9:
Empty 50S Subunit of the Coxiella burnetii Ribosome

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