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- PDB-6ha8: Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 6ha8
TitleCryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosome
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 28
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Nucleotide-binding protein ExpZ
  • P-tRNA(Leu)
  • mRNAMessenger RNA
KeywordsRIBOSOME / single particle cryo-EM / ABCF / ATPase / antibiotic resistiance
Function / homology
Function and homology information


positive regulation of rRNA processing / nucleoid / rescue of stalled ribosome / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit ...positive regulation of rRNA processing / nucleoid / rescue of stalled ribosome / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosome protection protein VmlR / ABC-transporter extension domain / ABC transporter / Ribosomal protein L1, bacterial-type / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like ...Ribosome protection protein VmlR / ABC-transporter extension domain / ABC transporter / Ribosomal protein L1, bacterial-type / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein S14/S29 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / 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 S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / ABC transporter / ABC transporter-like, ATP-binding domain / Ribosomal protein S13, bacterial-type / ATP-binding cassette, ABC transporter-type domain profile. / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / TELITHROMYCIN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 ...ADENOSINE-5'-TRIPHOSPHATE / TELITHROMYCIN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL28 / Ribosome protection protein VmlR / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Escherichia coli (E. coli)
Bacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCrowe-McAuliffe, C. / Graf, M. / Huter, P. / Abdelshahid, M. / Novacek, J. / Wilson, D.N.
Funding support Germany, Czech Republic, 4items
OrganizationGrant numberCountry
German Research FoundationFOR-1805 Germany
German Research FoundationWI3285/6-1 Germany
Ministry of Education (Czech Republic)CIISB project number LM2015043 Czech Republic
European UnioniNext project number 2992 Czech Republic
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structural basis for antibiotic resistance mediated by the ABCF ATPase VmlR.
Authors: Caillan Crowe-McAuliffe / Michael Graf / Paul Huter / Hiraku Takada / Maha Abdelshahid / Jiří Nováček / Victoriia Murina / Gemma C Atkinson / Vasili Hauryliuk / Daniel N Wilson /
Abstract: Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In , the RPP VmlR confers resistance to lincomycin (Lnc) ...Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In , the RPP VmlR confers resistance to lincomycin (Lnc) and the streptogramin A (S) antibiotic virginiamycin M (VgM). VmlR is an ATP-binding cassette (ABC) protein of the F type, which, like other antibiotic resistance (ARE) ABCF proteins, is thought to bind to antibiotic-stalled ribosomes and promote dissociation of the drug from its binding site. To investigate the molecular mechanism by which VmlR confers antibiotic resistance, we have determined a cryo-electron microscopy (cryo-EM) structure of an ATPase-deficient VmlR-EQ mutant in complex with a ErmDL-stalled ribosomal complex (SRC). The structure reveals that VmlR binds within the E site of the ribosome, with the antibiotic resistance domain (ARD) reaching into the peptidyltransferase center (PTC) of the ribosome and a C-terminal extension (CTE) making contact with the small subunit (SSU). To access the PTC, VmlR induces a conformational change in the P-site tRNA, shifting the acceptor arm out of the PTC and relocating the CCA end of the P-site tRNA toward the A site. Together with microbiological analyses, our study indicates that VmlR allosterically dissociates the drug from its ribosomal binding site and exhibits specificity to dislodge VgM, Lnc, and the pleuromutilin tiamulin (Tia), but not chloramphenicol (Cam), linezolid (Lnz), nor the macrolide erythromycin (Ery).
History
DepositionAug 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.3Jan 27, 2021Group: Data collection / Structure summary / Category: chem_comp / pdbx_validate_chiral / Item: _chem_comp.pdbx_synonyms

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Structure visualization

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Assembly

Deposited unit
A: 23S rRNA
B: 5S rRNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: Nucleotide-binding protein ExpZ
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33 1
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
6: 50S ribosomal protein L31
7: mRNA
8: 50S ribosomal protein L1
a: 16S rRNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
x: P-tRNA(Leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,219,81056
Polymers2,217,98453
Non-polymers1,8263
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules AB7ax

#1: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 949646.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: GenBank: 467326
#2: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 36157.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: GenBank: 1150402534
#31: RNA chain mRNA / Messenger RNA


Mass: 872.556 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#33: RNA chain 16S rRNA /


Mass: 503369.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: GenBank: 225184640
#53: RNA chain P-tRNA(Leu)


Mass: 24199.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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50S ribosomal protein ... , 28 types, 28 molecules CDEFGJKLMNOPQRSTUWXYZ0123468

#3: Protein 50S ribosomal protein L2 / / BL2


Mass: 30335.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P42919
#4: Protein 50S ribosomal protein L3 / / BL3


Mass: 22723.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P42920
#5: Protein 50S ribosomal protein L4 /


Mass: 22424.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P42921
#6: Protein 50S ribosomal protein L5 / / BL6


Mass: 20177.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P12877
#7: Protein 50S ribosomal protein L6 / / BL10


Mass: 19543.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P46898
#8: Protein 50S ribosomal protein L13 /


Mass: 16407.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P70974
#9: Protein 50S ribosomal protein L14 /


Mass: 13175.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P12875
#10: Protein 50S ribosomal protein L15 /


Mass: 15410.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P19946
#11: Protein 50S ribosomal protein L16 /


Mass: 16223.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P14577
#12: Protein 50S ribosomal protein L17 / / BL15 / BL21


Mass: 13774.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P20277
#13: Protein 50S ribosomal protein L18 / / BL16


Mass: 12993.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P46899
#14: Protein 50S ribosomal protein L19 /


Mass: 13416.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: O31742
#15: Protein 50S ribosomal protein L20 /


Mass: 13669.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P55873
#16: Protein 50S ribosomal protein L21 / / BL20


Mass: 11296.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P26908
#17: Protein 50S ribosomal protein L22 /


Mass: 12481.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P42060
#18: Protein 50S ribosomal protein L23 /


Mass: 10978.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P42924
#19: Protein 50S ribosomal protein L24 / / 12 kDa DNA-binding protein / BL23 / HPB12


Mass: 11166.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P0CI78
#21: Protein 50S ribosomal protein L27 / / BL24 / BL30


Mass: 10391.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P05657
#22: Protein 50S ribosomal protein L28 /


Mass: 6826.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P37807
#23: Protein 50S ribosomal protein L29 /


Mass: 7728.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P12873
#24: Protein 50S ribosomal protein L30 / / BL27


Mass: 6650.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P19947
#25: Protein 50S ribosomal protein L32 /


Mass: 6745.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: O34687
#26: Protein/peptide 50S ribosomal protein L33 1 / Ribosome


Mass: 5915.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P56849
#27: Protein/peptide 50S ribosomal protein L34 /


Mass: 5271.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P05647
#28: Protein 50S ribosomal protein L35 /


Mass: 7581.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P55874
#29: Protein/peptide 50S ribosomal protein L36 / / BL38 / Ribosomal protein B / Ribosomal protein II


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P20278
#30: Protein 50S ribosomal protein L31 /


Mass: 7458.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: Q03223
#32: Protein 50S ribosomal protein L1 / / BL1


Mass: 25026.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: Q06797

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Protein , 1 types, 1 molecules V

#20: Protein Nucleotide-binding protein ExpZ


Mass: 60272.344 Da / Num. of mol.: 1 / Mutation: Q129E, Q432E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: expZ, BSU05610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39115

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30S ribosomal protein ... , 19 types, 19 molecules bcdefghijklmnopqrst

#34: Protein 30S ribosomal protein S2 / / BS1 / Vegetative protein 209 / VEG209


Mass: 28009.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21464
#35: Protein 30S ribosomal protein S3 / / BS3 / BS2


Mass: 24364.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21465
#36: Protein 30S ribosomal protein S4 / / BS4


Mass: 22874.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21466
#37: Protein 30S ribosomal protein S5 / / BS5


Mass: 17650.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21467
#38: Protein 30S ribosomal protein S6 / / BS9


Mass: 11140.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21468
#39: Protein 30S ribosomal protein S7 / / BS7


Mass: 17915.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21469
#40: Protein 30S ribosomal protein S8 / / BS8


Mass: 14901.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P12879
#41: Protein 30S ribosomal protein S9 / / BS10


Mass: 14335.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21470
#42: Protein 30S ribosomal protein S10 / / BS13


Mass: 11687.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21471
#43: Protein 30S ribosomal protein S11 / / BS11


Mass: 13952.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P04969
#44: Protein 30S ribosomal protein S12 / / BS12


Mass: 15248.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21472
#45: Protein 30S ribosomal protein S13 / / BS14


Mass: 13818.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P20282
#46: Protein 30S ribosomal protein S14 / / 30S ribosomal protein S14 type Z / 30S ribosomal protein S14-1 / BS-A


Mass: 7263.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P12878
#47: Protein 30S ribosomal protein S15 / / BS18


Mass: 10597.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21473
#48: Protein 30S ribosomal protein S16 / / BS17


Mass: 10153.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21474
#49: Protein 30S ribosomal protein S17 / / BS16


Mass: 10220.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P12874
#50: Protein 30S ribosomal protein S18 / / BS21


Mass: 8990.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21475
#51: Protein 30S ribosomal protein S19 / / BS19


Mass: 10607.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21476
#52: Protein 30S ribosomal protein S20 / / BS20


Mass: 9622.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / References: UniProt: P21477

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Non-polymers , 2 types, 3 molecules

#54: Chemical ChemComp-TEL / TELITHROMYCIN / (3aS,4R,7R,9R,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxo-1-{4-[4-(pyridin-3-yl)-1H-imidazol-1-yl]butyl}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside / Telithromycin


Mass: 812.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H65N5O10 / Comment: antibiotic*YM
#55: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of translating 70S ribosome with ABCF antibiotic resistance protein vmlRRIBOSOME#1-#530MULTIPLE SOURCES
2RibosomeRIBOSOME#1-#19, #21-#531NATURAL
3Nucleotide-binding protein ExpZCOMPLEX#201RECOMBINANT
4tRNATransfer RNACOMPLEX#531NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bacillus subtilis subsp. subtilis str. 168 (bacteria)224308
23Bacillus subtilis subsp. subtilis str. 168 (bacteria)224308
34Escherichia coli (E. coli)562
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.425 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.56particle selection
4Gctf1.06CTF correction
7Coot0.8.8model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIXdev-2947-000model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28972 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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