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- PDB-9k0z: EF-G2 bound 70S ribosome complex of M. smegmatis -

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Entry
Database: PDB / ID: 9k0z
TitleEF-G2 bound 70S ribosome complex of M. smegmatis
Components
  • (50S ribosomal protein ...) x 5
  • (Large ribosomal subunit protein ...) x 28
  • (Small ribosomal subunit protein ...) x 19
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • P/P-site Phe-tRNA(Phe)
  • Translation elongation factor EF-G
  • mRNA fragment
KeywordsRIBOSOME / Mycobacterium 70S ribosome / stationary phase / elongation factor G2 / non-canonical factor
Function / homology
Function and homology information


ribosome disassembly / translation elongation factor activity / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding ...ribosome disassembly / translation elongation factor activity / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / Elongation factor G, domain III / EFG, domain V / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / : ...: / Elongation factor G, domain III / EFG, domain V / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / : / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Translation elongation factor EFG/EF2, domain IV / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Elongation factor G, domain IV / Ribosomal protein TL5, C-terminal domain / Elongation factor G, domain IV / Elongation factor G C-terminus / Ribosomal protein L10 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / : / : / Ribosomal protein S14, type Z / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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 L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / 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 L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / 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 / Ribosomal protein L9, N-terminal domain superfamily / 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 L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / PHENYLALANINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / PHENYLALANINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein bL12 / 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 uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Uncharacterized protein / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Elongation factor G-like protein / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein bS18B / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsSengupta, J. / Baid, P.
Funding support India, 3items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)SPF/2021/000141 India
Science and Engineering Research Board (SERB)CRG/2019/001788 India
Council of Scientific & Industrial Research (CSIR)MLP-139 India
CitationJournal: FEBS J / Year: 2025
Title: Cryo-EM structural analyses reveal a unique role for elongation factor G2 (EF-G2) in Mycobacteria.
Authors: Priya Baid / Jayati Sengupta /
Abstract: The gene-encoding translation elongation factor G (EF-G) has undergone gene duplication across various bacterial species including Mycobacteria, and in mammalian mitochondria, leading to the ...The gene-encoding translation elongation factor G (EF-G) has undergone gene duplication across various bacterial species including Mycobacteria, and in mammalian mitochondria, leading to the emergence of the paralogue elongation factor G2 (EF-G2). Our study reveals that mycobacterial EF-G2, unlike EF-G1, neither participates in ribosome-recycling nor significantly contributes to overall translation, suggesting that it plays an alternative role in Mycobacteria. Remarkably, our investigation found a significant overexpression of mycobacterial EF-G2 during the stationary growth phase. Moreover, EF-G2 lacks ribosome-dependent GTPase activity, an observation consistent with previous reports. Cryo-EM analysis of the M. smegmatis 70S ribosome purified from the nutrient-starved (stationary) phase and complexed with EF-G2 unveiled the structural basis for its inability to hydrolyse GTP in a ribosome-dependent manner. Furthermore, we report an unprecedented binding mode of two EF-G2 copies on the 50S ribosomal subunit that impedes subunit association, thereby preventing the formation of active 70S ribosomes. Thus, instead of performing canonical functions, mycobacterial EF-G2 acts as a translation repressor during nutrient starvation. Altogether, our findings shed light on the multifaceted mechanisms by which EF-G2 modulates protein synthesis under nutrient-limited conditions, providing insights into adaptive strategies employed by Mycobacteria to survive in hostile environments.
History
DepositionOct 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: P/P-site Phe-tRNA(Phe)
3: 50S ribosomal protein bL37
4: mRNA fragment
5: Large ribosomal subunit protein bL12
7: Translation elongation factor EF-G
A: 16S ribosomal RNA
B: 5S ribosomal RNA
C: Small ribosomal subunit protein uS3
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6
G: Small ribosomal subunit protein uS7
H: Small ribosomal subunit protein uS8
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14B
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18B
S: Small ribosomal subunit protein uS19
T: Small ribosomal subunit protein bS20
U: Large ribosomal subunit protein uL23
V: Small ribosomal subunit protein uS2
W: Large ribosomal subunit protein bL25
X: Large ribosomal subunit protein bL27
Y: Large ribosomal subunit protein bL28
Z: Large ribosomal subunit protein uL29
a: Large ribosomal subunit protein uL30
b: Large ribosomal subunit protein bL32
c: Large ribosomal subunit protein bL33A
d: Large ribosomal subunit protein bL34
e: Large ribosomal subunit protein bL35
f: 50S ribosomal protein L36
g: Large ribosomal subunit protein bL31
i: Large ribosomal subunit protein uL2
j: Large ribosomal subunit protein uL3
k: Large ribosomal subunit protein uL4
l: Large ribosomal subunit protein uL5
m: Large ribosomal subunit protein uL6
n: 50S ribosomal protein L9
o: Large ribosomal subunit protein uL10
p: Large ribosomal subunit protein uL11
q: Large ribosomal subunit protein uL13
r: 50S ribosomal protein L14
s: Large ribosomal subunit protein uL15
t: Large ribosomal subunit protein uL16
u: Large ribosomal subunit protein bL17
v: Large ribosomal subunit protein uL18
w: 50S ribosomal protein L19
x: Large ribosomal subunit protein bL20
y: Large ribosomal subunit protein bL21
z: Large ribosomal subunit protein uL22
1: Large ribosomal subunit protein uL24
h: 23S ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,325,32378
Polymers2,323,95258
Non-polymers1,37120
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 5 molecules 24ABh

#1: RNA chain P/P-site Phe-tRNA(Phe)


Mass: 24420.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#3: RNA chain mRNA fragment


Mass: 5866.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#6: RNA chain 16S ribosomal RNA


Mass: 490111.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: GenBank: 118168627
#7: RNA chain 5S ribosomal RNA


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: GenBank: 118168627
#58: RNA chain 23S ribosomal RNA


Mass: 1014391.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)

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50S ribosomal protein ... , 5 types, 5 molecules 3fnrw

#2: Protein/peptide 50S ribosomal protein bL37


Mass: 2710.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTP4
#37: Protein/peptide 50S ribosomal protein L36


Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL4
#44: Protein 50S ribosomal protein L9


Mass: 15949.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R7F6
#48: Protein 50S ribosomal protein L14


Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSF9
#53: Protein 50S ribosomal protein L19


Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QV42

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Large ribosomal subunit protein ... , 28 types, 28 molecules 5UWXYZabcdegijklmopqstuvxyz1

#4: Protein Large ribosomal subunit protein bL12


Mass: 7199.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS63
#26: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 10748.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD3
#28: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 20331.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7GFB2
#29: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 8322.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R150
#30: Protein Large ribosomal subunit protein bL28


Mass: 6759.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7FJ52
#31: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7590.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD9
#32: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6761.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG7
#33: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6050.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R3I9
#34: Protein/peptide Large ribosomal subunit protein bL33A / 50S ribosomal protein L33 1


Mass: 5833.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS39
#35: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5391.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R7K0
#36: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7167.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QYU7
#38: Protein/peptide Large ribosomal subunit protein bL31 / 50S ribosomal protein L31


Mass: 5257.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R215
#39: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 30008.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD4
#40: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 22621.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD1
#41: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22346.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD2
#42: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20588.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG1
#43: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19165.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG4
#45: Protein Large ribosomal subunit protein uL10 / 50S ribosomal protein L10


Mass: 13095.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS62
#46: Protein Large ribosomal subunit protein uL11 / 50S ribosomal protein L11


Mass: 14109.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS45
#47: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16015.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSP8
#49: Protein Large ribosomal subunit protein uL15


Mass: 15383.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7G436
#50: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15498.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD8
#51: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 13210.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL9
#52: Protein Large ribosomal subunit protein uL18


Mass: 13580.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7FGD9
#54: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 14035.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QYU6
#55: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 10724.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R151
#56: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12408.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD6
#57: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG0

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Protein , 1 types, 1 molecules 7

#5: Protein Translation elongation factor EF-G


Mass: 75420.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_6535 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R6G0

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Small ribosomal subunit protein ... , 19 types, 19 molecules CDEFGHIJKLMNOPQRSTV

#8: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 23617.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD7
#9: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23284.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL7
#10: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 18481.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG6
#11: Protein Small ribosomal subunit protein bS6


Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0A2U9Q0X2
#12: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17529.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS97
#13: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14361.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG3
#14: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14093.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSP9
#15: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11252.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD0
#16: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 12151.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL6
#17: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13678.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS96
#18: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13374.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL5
#19: Protein Small ribosomal subunit protein uS14B / 30S ribosomal protein S14 type Z


Mass: 6845.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG2
#20: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10236.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QVQ3
#21: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 12635.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QV37
#22: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 10680.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSE0
#23: Protein Small ribosomal subunit protein bS18B / 30S ribosomal protein S18 2


Mass: 7353.585 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R7F7
#24: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 9379.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD5
#25: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9424.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R102
#27: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 25576.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QVB8

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Non-polymers , 4 types, 20 molecules

#59: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#60: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#61: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#62: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationN

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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: EF-G2 bound 70S ribosome complex of M. smegmatis / Type: COMPLEX / Entity ID: #1-#58 / Source: NATURAL
Molecular weightValue: 2.7 MDa / Experimental value: YES
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3300 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 54 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19431 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 5O61

5o61


Accession code: 5O61 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005168631
ELECTRON MICROSCOPYf_angle_d0.648251725
ELECTRON MICROSCOPYf_dihedral_angle_d16.17978023
ELECTRON MICROSCOPYf_chiral_restr0.03932116
ELECTRON MICROSCOPYf_plane_restr0.00614173

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