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- PDB-5zlu: Ribosome Structure bound to ABC-F protein. -

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Entry
Database: PDB / ID: 5zlu
TitleRibosome Structure bound to ABC-F protein.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Macrolide efflux protein
  • P-site tRNA
  • RNA (25-mer)
KeywordsRIBOSOME / Ribosome / Antibiotics / Macrolides / ABC-F protein / AZM
Function / homologyRibosomal protein L36 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L25, C-terminal / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L19 superfamily ...Ribosomal protein L36 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L25, C-terminal / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L19 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L33 superfamily / ABC transporter / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S14p/S29e / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein L16p/L10e / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S20 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein S2, flavodoxin-like domain superfamily / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein S19, superfamily / Ribosomal protein L31 type A / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S14, type Z / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L10 / Ribosomal protein L5 domain superfamily / Ribosomal protein S10 domain / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L17 superfamily / Ribosomal protein L20, C-terminal / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L24 signature. / L28p-like / Ribosomal protein L21-like / ABC-transporter extension domain / 30S ribosomal protein Thx / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / 30S ribosomal protein / Ribosomal protein L25 / Ribosomal protein L30p/L7e / Ribosomal protein S10p/S20e / Ribosomal protein L2, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S15 signature. / Ribosomal protein S10 signature. / Ribosomal protein S9 signature. / Ribosomal protein L11 signature. / Ribosomal protein L5 signature. / Ribosomal protein S19 signature. / Ribosomal protein S17 signature. / Ribosomal protein L2 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Ribosomal protein S7 signature. / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L22 signature. / Ribosomal protein L3 signature. / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L13 signature. / Ribosomal protein S2 signature 1. / Ribosomal protein L20 signature. / Ribosomal protein L35 signature. / Ribosomal protein L27 signature. / Ribosomal protein L36 signature. / Ribosomal protein L34 signature.
Function and homology information
Specimen sourcePseudomonas aeruginosa (bacteria)
Thermus thermophilus (bacteria)
Thermus thermophilus HB8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsSu, W.X. / Kumar, V. / Ero, R. / Andrew, S.W.W. / Jian, S. / Yong-Gui, G.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Ribosome protection by antibiotic resistance ATP-binding cassette protein.
Authors: Weixin Su / Veerendra Kumar / Yichen Ding / Rya Ero / Aida Serra / Benjamin Sian Teck Lee / Andrew See Weng Wong / Jian Shi / Siu Kwan Sze / Liang Yang / Yong-Gui Gao
Abstract: The ribosome is one of the richest targets for antibiotics. Unfortunately, antibiotic resistance is an urgent issue in clinical practice. Several ATP-binding cassette family proteins confer ...The ribosome is one of the richest targets for antibiotics. Unfortunately, antibiotic resistance is an urgent issue in clinical practice. Several ATP-binding cassette family proteins confer resistance to ribosome-targeting antibiotics through a yet unknown mechanism. Among them, MsrE has been implicated in macrolide resistance. Here, we report the cryo-EM structure of ATP form MsrE bound to the ribosome. Unlike previously characterized ribosomal protection proteins, MsrE is shown to bind to ribosomal exit site. Our structure reveals that the domain linker forms a unique needle-like arrangement with two crossed helices connected by an extended loop projecting into the peptidyl-transferase center and the nascent peptide exit tunnel, where numerous antibiotics bind. In combination with biochemical assays, our structure provides insight into how MsrE binding leads to conformational changes, which results in the release of the drug. This mechanism appears to be universal for the ABC-F type ribosome protection proteins.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 29, 2018 / Release: Aug 1, 2018

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Structure visualization

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Assembly

Deposited unit
W: RNA (25-mer)
A: 30S ribosomal protein S17
B: 30S ribosomal protein S18
C: 30S ribosomal protein S20
D: 30S ribosomal protein S19
E: 30S ribosomal protein S10
F: 30S ribosomal protein Thx
G: 16S ribosomal RNA
H: 30S ribosomal protein S2
I: 30S ribosomal protein S3
J: 30S ribosomal protein S4
K: 30S ribosomal protein S5
L: 30S ribosomal protein S6
M: 30S ribosomal protein S7
N: 30S ribosomal protein S8
O: 30S ribosomal protein S9
P: 30S ribosomal protein S11
Q: 30S ribosomal protein S12
R: 30S ribosomal protein S13
S: 30S ribosomal protein S14 type Z
T: 30S ribosomal protein S15
U: 30S ribosomal protein S16
V: 23S ribosomal RNA
X: 5S ribosomal RNA
Y: 50S ribosomal protein L1
Z: 50S ribosomal protein L2
a: 50S ribosomal protein L3
b: 50S ribosomal protein L4
c: 50S ribosomal protein L5
d: 50S ribosomal protein L6
e: 50S ribosomal protein L10
f: 50S ribosomal protein L11
g: 50S ribosomal protein L13
h: 50S ribosomal protein L14
i: 50S ribosomal protein L15
j: 50S ribosomal protein L16
k: 50S ribosomal protein L17
l: 50S ribosomal protein L18
m: 50S ribosomal protein L19
n: 50S ribosomal protein L20
o: 50S ribosomal protein L21
p: 50S ribosomal protein L22
q: 50S ribosomal protein L23
r: 50S ribosomal protein L24
s: 50S ribosomal protein L25
t: 50S ribosomal protein L27
u: 50S ribosomal protein L29
v: 50S ribosomal protein L30
w: 50S ribosomal protein L31
x: 50S ribosomal protein L32
y: 50S ribosomal protein L33
z: 50S ribosomal protein L34
AA: 50S ribosomal protein L35
BB: 50S ribosomal protein L36
CC: 50S ribosomal protein L31
DD: P-site tRNA
EE: Macrolide efflux protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,280,89261
Polyers2,279,83157
Non-polymers1,0614
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules WGVXDD

#1: RNA chain RNA (25-mer)


Mass: 8156.980 Da / Num. of mol.: 1 / Source: (synth.) Thermus thermophilus HB8 (bacteria)
#8: RNA chain 16S ribosomal RNA /


Mass: 491471.938 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
#23: RNA chain 23S ribosomal RNA /


Mass: 935028.375 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
#24: RNA chain 5S ribosomal RNA /


Mass: 39846.781 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 37223181
#55: RNA chain P-site tRNA


Mass: 24885.000 Da / Num. of mol.: 1 / Source: (synth.) Thermus thermophilus HB8 (bacteria)

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30S ribosomal protein ... , 20 types, 20 molecules ABCDEFHIJKLMNOPQRSTU

#2: Protein/peptide 30S ribosomal protein S17 /


Mass: 12193.475 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P24321
#3: Protein/peptide 30S ribosomal protein S18 /


Mass: 8483.172 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80382
#4: Protein/peptide 30S ribosomal protein S20 /


Mass: 11736.143 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#5: Protein/peptide 30S ribosomal protein S19 /


Mass: 10605.464 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#6: Protein/peptide 30S ribosomal protein S10 /


Mass: 11954.968 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#7: Protein/peptide 30S ribosomal protein Thx / Ribosome / S31


Mass: 3350.030 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3
#9: Protein/peptide 30S ribosomal protein S2 /


Mass: 29317.703 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#10: Protein/peptide 30S ribosomal protein S3 /


Mass: 26751.076 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#11: Protein/peptide 30S ribosomal protein S4 /


Mass: 24373.447 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#12: Protein/peptide 30S ribosomal protein S5 /


Mass: 17583.416 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#13: Protein/peptide 30S ribosomal protein S6 / / TS9


Mass: 11988.753 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#14: Protein/peptide 30S ribosomal protein S7 /


Mass: 18050.973 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#15: Protein/peptide 30S ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY9
#16: Protein/peptide 30S ribosomal protein S9 /


Mass: 14410.614 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#17: Protein/peptide 30S ribosomal protein S11 /


Mass: 13737.868 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#18: Protein/peptide 30S ribosomal protein S12 /


Mass: 14637.384 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#19: Protein/peptide 30S ribosomal protein S13 /


Mass: 14338.861 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#20: Protein/peptide 30S ribosomal protein S14 type Z / Ribosome


Mass: 7158.725 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY6
#21: Protein/peptide 30S ribosomal protein S15 /


Mass: 10578.407 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#22: Protein/peptide 30S ribosomal protein S16 /


Mass: 10409.983 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3

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50S ribosomal protein ... , 30 types, 31 molecules YZabcdefghijklmnopqrstuvwCCxyzAABB

#25: Protein/peptide 50S ribosomal protein L1 /


Mass: 24867.699 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P27150
#26: Protein/peptide 50S ribosomal protein L2 /


Mass: 30532.551 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60405
#27: Protein/peptide 50S ribosomal protein L3 /


Mass: 22450.213 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN8
#28: Protein/peptide 50S ribosomal protein L4 / / L1e


Mass: 23271.914 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN9
#29: Protein/peptide 50S ribosomal protein L5 /


Mass: 21061.596 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ0
#30: Protein/peptide 50S ribosomal protein L6 /


Mass: 19568.926 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY8
#31: Protein/peptide 50S ribosomal protein L10 /


Mass: 18586.639 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8VVE3
#32: Protein/peptide 50S ribosomal protein L11 /


Mass: 15526.111 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP6
#33: Protein/peptide 50S ribosomal protein L13 /


Mass: 15927.903 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60488
#34: Protein/peptide 50S ribosomal protein L14 /


Mass: 13309.586 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60558
#35: Protein/peptide 50S ribosomal protein L15 /


Mass: 16319.142 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ7
#36: Protein/peptide 50S ribosomal protein L16 /


Mass: 15993.909 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60489
#37: Protein/peptide 50S ribosomal protein L17 /


Mass: 13750.148 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q9Z9H5
#38: Protein/peptide 50S ribosomal protein L18 / / TL24


Mass: 12639.845 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ4
#39: Protein/peptide 50S ribosomal protein L19 /


Mass: 17188.830 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60490
#40: Protein/peptide 50S ribosomal protein L20 /


Mass: 13779.275 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60491
#41: Protein/peptide 50S ribosomal protein L21 /


Mass: 11069.153 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60492
#42: Protein/peptide 50S ribosomal protein L22 /


Mass: 12808.055 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP3
#43: Protein/peptide 50S ribosomal protein L23 /


Mass: 10759.808 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP0
#44: Protein/peptide 50S ribosomal protein L24 /


Mass: 12085.611 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP9
#45: Protein/peptide 50S ribosomal protein L25 / / TL5


Mass: 23238.572 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHZ1
#46: Protein/peptide 50S ribosomal protein L27 /


Mass: 9529.074 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60493
#47: Protein/peptide 50S ribosomal protein L29 /


Mass: 8112.597 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q9LCY4
#48: Protein/peptide 50S ribosomal protein L30 /


Mass: 6799.126 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ6
#49: Protein/peptide 50S ribosomal protein L31 /


Mass: 8300.543 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJE1
#50: Protein/peptide 50S ribosomal protein L32 /


Mass: 6722.050 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80339
#51: Protein/peptide 50S ribosomal protein L33 /


Mass: 6632.896 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P35871
#52: Protein/peptide 50S ribosomal protein L34 /


Mass: 6132.449 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80340
#53: Protein/peptide 50S ribosomal protein L35 /


Mass: 7506.178 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SKU1
#54: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B


Mass: 4435.411 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHR2

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Protein/peptide , 1 types, 1 molecules EE

#56: Protein/peptide Macrolide efflux protein / Mel


Mass: 55706.461 Da / Num. of mol.: 1 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mel / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I9WCL8

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Non-polymers , 2 types, 4 molecules

#57: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#58: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Formula: C10H17N6O12P3 / Comment: AMP-PNP (energy-carrying molecule analogue) *YM

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Details

Sequence detailsNatural variant at this position

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Bacterial ribosome in complex with MsrE / Type: RIBOSOME
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55
Source: MULTIPLE SOURCES
Molecular weightValue: 2.8 MDa / Experimental value: NO
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: HB8
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
125 mMTrisTris-HCl1
2100 mMSodium ChlorideNaCl1
3350 uMBeta MercaptoethanolBME1
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/1
EM embeddingMaterial: Ice
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7UCSF Chimeramodel fitting
12RELION2.03D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 127778 / Number of class averages: 15 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL
Least-squares processHighest resolution: 3.6 Å

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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