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- PDB-8rwg: PAO1 wild-type ribosome, R, reference map -

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Basic information

Entry
Database: PDB / ID: 8rwg
TitlePAO1 wild-type ribosome, R, reference map
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 26
  • (Large ribosomal subunit protein ...) x 2
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / PAO1 / wild type / antibiotic resistance
Function / homology
Function and homology information


transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit ...transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytosol / 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 S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / : / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL34 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36A / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein bS21
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsMesa, P. / Montoya, G.
Funding support Denmark, European Union, 6items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Novo Nordisk FoundationNNF10CC1016517 Denmark
Novo Nordisk FoundationNNF0024386 Denmark
Novo Nordisk FoundationNNF17SA0030214 Denmark
Novo Nordisk FoundationNNF18OC0055061 Denmark
European Research Council (ERC)ERC_AdG_101096548European Union
CitationJournal: To Be Published
Title: Detuning of the Ribosome Conformational Landscape Promotes Antibiotic Resistance and Collateral Sensitivity.
Authors: Mesa, P. / Jimenez-Fernandez, A. / La Rosa, R. / Espinosa-Portero, R. / Johansen, H.K. / Molin, S. / Montoya, G.
History
DepositionFeb 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: 50S ribosomal protein L27
2: 50S ribosomal protein L28
3: 50S ribosomal protein L29
4: 50S ribosomal protein L30
5: 50S ribosomal protein L32
6: Large ribosomal subunit protein bL33
7: 50S ribosomal protein L34
8: 50S ribosomal protein L35
9: 50S ribosomal protein L36
A: 23S ribosomal RNA
B: 16S ribosomal RNA
C: 5S ribosomal RNA
D: 50S ribosomal protein L2
E: 50S ribosomal protein L3
F: 50S ribosomal protein L4
G: 50S ribosomal protein L5
H: 50S ribosomal protein L6
I: 50S ribosomal protein L9
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: Large ribosomal subunit protein uL22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
a: 30S ribosomal protein S2
b: 30S ribosomal protein S3
c: 30S ribosomal protein S4
d: 30S ribosomal protein S5
e: 30S ribosomal protein S6
f: 30S ribosomal protein S7
g: 30S ribosomal protein S8
h: 30S ribosomal protein S9
i: 30S ribosomal protein S10
j: 30S ribosomal protein S11
k: 30S ribosomal protein S12
l: 30S ribosomal protein S13
m: 30S ribosomal protein S14
n: 30S ribosomal protein S15
o: 30S ribosomal protein S16
p: 30S ribosomal protein S17
q: 30S ribosomal protein S18
r: 30S ribosomal protein S19
s: 30S ribosomal protein S20
t: 30S ribosomal protein S21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,138,975236
Polymers2,134,43751
Non-polymers4,538185
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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50S ribosomal protein ... , 26 types, 26 molecules 12345789DEFGHIJKLMNOPQRTUV

#1: Protein 50S ribosomal protein L27


Mass: 9010.450 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVL7
#2: Protein 50S ribosomal protein L28


Mass: 9087.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HTN8
#3: Protein 50S ribosomal protein L29


Mass: 7213.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE3
#4: Protein 50S ribosomal protein L30


Mass: 6489.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF3
#5: Protein 50S ribosomal protein L32


Mass: 6807.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HZN4
#7: Protein/peptide 50S ribosomal protein L34


Mass: 5226.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: P29436
#8: Protein 50S ribosomal protein L35


Mass: 7387.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9I0A1
#9: Protein/peptide 50S ribosomal protein L36


Mass: 4447.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF6
#13: Protein 50S ribosomal protein L2


Mass: 29641.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD8
#14: Protein 50S ribosomal protein L3


Mass: 22625.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD5
#15: Protein 50S ribosomal protein L4


Mass: 21673.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD6
#16: Protein 50S ribosomal protein L5


Mass: 20424.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE7
#17: Protein 50S ribosomal protein L6


Mass: 19129.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF0
#18: Protein 50S ribosomal protein L9


Mass: 15551.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HUN2
#19: Protein 50S ribosomal protein L13


Mass: 16058.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVY2
#20: Protein 50S ribosomal protein L14


Mass: 13435.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE5
#21: Protein 50S ribosomal protein L15


Mass: 15204.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF4
#22: Protein 50S ribosomal protein L16


Mass: 15434.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE2
#23: Protein 50S ribosomal protein L17


Mass: 14533.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: O52761
#24: Protein 50S ribosomal protein L18


Mass: 12687.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF1
#25: Protein 50S ribosomal protein L19


Mass: 13055.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HXQ2
#26: Protein 50S ribosomal protein L20


Mass: 13397.972 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9I0A2
#27: Protein 50S ribosomal protein L21


Mass: 11678.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVL6
#29: Protein 50S ribosomal protein L23


Mass: 10969.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD7
#30: Protein 50S ribosomal protein L24


Mass: 11494.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE6
#31: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 21994.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVC4

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Large ribosomal subunit protein ... , 2 types, 2 molecules 6S

#6: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 6060.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HTN9
#28: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 11935.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE0

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RNA chain , 3 types, 3 molecules ABC

#10: RNA chain 23S ribosomal RNA


Mass: 936932.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: GenBank: 110227054
#11: RNA chain 16S ribosomal RNA


Mass: 497802.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: GenBank: 1839535652
#12: RNA chain 5S ribosomal RNA


Mass: 38902.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: GenBank: 1839535652

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

#32: Protein 30S ribosomal protein S2


Mass: 27376.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: O82850
#33: Protein 30S ribosomal protein S3


Mass: 25887.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE1
#34: Protein 30S ribosomal protein S4


Mass: 23318.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: O52759
#35: Protein 30S ribosomal protein S5


Mass: 17650.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF2
#36: Protein 30S ribosomal protein S6


Mass: 16189.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HUM9
#37: Protein 30S ribosomal protein S7


Mass: 17541.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD1
#38: Protein 30S ribosomal protein S8


Mass: 14190.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE9
#39: Protein 30S ribosomal protein S9


Mass: 14643.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVY3
#40: Protein 30S ribosomal protein S10


Mass: 11786.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD4
#41: Protein 30S ribosomal protein S11


Mass: 13654.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF8
#42: Protein 30S ribosomal protein S12


Mass: 13830.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD0
#43: Protein 30S ribosomal protein S13


Mass: 13292.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF7
#44: Protein 30S ribosomal protein S14


Mass: 11591.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE8
#45: Protein 30S ribosomal protein S15


Mass: 10135.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HV58
#46: Protein 30S ribosomal protein S16


Mass: 9219.454 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HXP9
#47: Protein 30S ribosomal protein S17


Mass: 10106.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE4
#48: Protein 30S ribosomal protein S18


Mass: 8892.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HUN0
#49: Protein 30S ribosomal protein S19


Mass: 10382.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD9
#50: Protein 30S ribosomal protein S20


Mass: 9942.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVM1
#51: Protein 30S ribosomal protein S21


Mass: 8508.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9I5V8

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Non-polymers , 3 types, 580 molecules

#52: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#53: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: Mg
#54: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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

ComponentName: PAO1 wild-type ribosome / Type: RIBOSOME / Entity ID: #1-#51 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris bufferTrisHCl1
210 mMmagnesium chlorideMgCl21
3100 mMammonium chlorideNH4Cl1
46 mMbeta-mercaptoethanolBME1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELD / Nominal magnification: 96000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 50 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3773

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Processing

EM software
IDNameVersionCategory
1RELION2.1.0-3.0particle selection
2EPUimage acquisition
4RELION2.1.0-3.0CTF correction
5CTFFIND4.1CTF correction
8UCSF ChimeraXmodel fitting
10PHENIX1.20.1model refinement
11RELION2.1.0-3.0initial Euler assignment
12RELION2.1.0-3.0final Euler assignment
13RELION2.1.0-3.0classification
14RELION2.1.0-3.03D reconstruction
15PHENIX1.20.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 166770 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 4YBB

4ybb


Accession code: 4YBB / Source name: PDB / Type: experimental model

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