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- PDB-9zn2: Escherichia coli 70S ribosome initiation complex bound to IF1 and... -

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Basic information

Entry
Database: PDB / ID: 9zn2
TitleEscherichia coli 70S ribosome initiation complex bound to IF1 and extended IF2-GDPCP (70S IC*)
Components
  • (30S ribosomal protein ...) x 4
  • (50S ribosomal protein ...) x 16
  • (Large ribosomal subunit protein ...) x 12
  • (Small ribosomal subunit protein ...) x 16
  • (Translation initiation factor IF- ...) x 2
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 24MF mRNA
  • 5S Ribosomal RNA
  • Ribosomal protein L21
  • initiator tRNA fMet, DNA (5'-R(P*A)-3')
KeywordsRIBOSOME / E.coli / 70S / IF1 / IF2 / cryo-EM / tRNA
Function / homology
Function and homology information


guanosine tetraphosphate binding / negative regulation of cytoplasmic translational initiation / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / translation initiation factor activity ...guanosine tetraphosphate binding / negative regulation of cytoplasmic translational initiation / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / translation initiation factor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / cytosolic ribosome assembly / ribosome assembly / assembly of large subunit precursor of preribosome / transcription antitermination / response to radiation / regulation of cell growth / translational initiation / regulation of translation / maintenance of translational fidelity / mRNA 5'-UTR binding / transferase activity / large ribosomal subunit / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / tRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / structural constituent of ribosome / ribosome / translation / negative regulation of DNA-templated transcription / mRNA binding / GTPase activity / GTP binding / metal ion binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-1 / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / : / Elongation factor G domain 2 ...Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-1 / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / : / Elongation factor G domain 2 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Putative DNA-binding domain superfamily / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S21, conserved site / Elongation factor Tu domain 2 / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S1-like RNA-binding domain / 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 S21 superfamily / Ribosomal protein S21 / S1 domain / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / Ribosomal protein L9 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L6, conserved site / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L6 signature 1. / Ribosomal protein L9, C-terminal domain superfamily / : / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S3, bacterial-type / : / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / : / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type
Similarity search - Domain/homology
N-FORMYLMETHIONINE / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS18 ...N-FORMYLMETHIONINE / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS13 / Translation initiation factor IF-1 / Translation initiation factor IF-2 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL21 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL15
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsBasu, R.S. / Valdez, N.A. / Guerra, G.S. / Demo, G. / Gagnon, M.G.
Funding support United States, Czech Republic, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM136936 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM158272 United States
Welch FoundationH-2032-20230405 United States
Czech Science FoundationG26-20643S Czech Republic
CitationJournal: To Be Published
Title: Time-resolved visualization of IF1- and IF2-driven translation initiation in bacteria
Authors: Guerra, G.S. / Zafar, H. / Ge, X. / Basu, R.S. / Huang, C. / Hassan, A. / Valdez, N.A. / Brabencova, S. / Slamova, L. / Mandava, C.S. / Gamper, H. / Hou, Y. / Gagnon, M.G. / Sanyal, S. / Demo, G.
History
DepositionDec 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: 16S Ribosomal RNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: Small ribosomal subunit protein uS4
e: Small ribosomal subunit protein uS5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
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 uS14
o: Small ribosomal subunit protein uS15
p: Small ribosomal subunit protein bS16
q: Small ribosomal subunit protein uS17
r: Small ribosomal subunit protein bS18
s: Small ribosomal subunit protein uS19
t: Small ribosomal subunit protein bS20
u: Small ribosomal subunit protein bS21
w: 24MF mRNA
v: initiator tRNA fMet, DNA (5'-R(P*A)-3')
x: Translation initiation factor IF-2
y: Translation initiation factor IF-1
A: 23S Ribosomal RNA
B: 5S Ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL5
G: Large ribosomal subunit protein uL6
H: Large ribosomal subunit protein bL9
L: Large ribosomal subunit protein uL13
M: Large ribosomal subunit protein uL14
N: 50S ribosomal protein L15
O: Large ribosomal subunit protein uL16
P: Large ribosomal subunit protein bL17
Q: Large ribosomal subunit protein uL18
R: Large ribosomal subunit protein bL19
S: 50S ribosomal protein L20
T: Ribosomal protein L21
U: 50S ribosomal protein L22
V: 50S ribosomal protein L23
W: 50S ribosomal protein L24
X: Large ribosomal subunit protein bL25
Y: 50S ribosomal protein L27
Z: 50S ribosomal protein L28
1: Large ribosomal subunit protein uL29
2: 50S ribosomal protein L30
3: 50S ribosomal protein L31
4: 50S ribosomal protein L32
5: 50S ribosomal protein L33
6: 50S ribosomal protein L34
7: 50S ribosomal protein L35
8: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,284,180361
Polymers2,276,03556
Non-polymers8,145305
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules awvAB

#1: RNA chain 16S Ribosomal RNA


Mass: 499873.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 1700704455
#22: RNA chain 24MF mRNA


Mass: 7804.735 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic 24MF mRNA / Source: (synth.) Escherichia phage T4 (virus)
#23: RNA chain initiator tRNA fMet, DNA (5'-R(P*A)-3')


Mass: 24846.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 732678099
#26: RNA chain 23S Ribosomal RNA


Mass: 941811.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#27: RNA chain 5S Ribosomal RNA


Mass: 38814.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 1817378070

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30S ribosomal protein ... , 4 types, 4 molecules bcfg

#2: Protein 30S ribosomal protein S2


Mass: 26795.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: J7QM75
#3: Protein 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V3
#6: Protein 30S ribosomal protein S6


Mass: 15211.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SFQ7
#7: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 17637.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02359

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Small ribosomal subunit protein ... , 16 types, 16 molecules dehijklmnopqrstu

#4: Protein Small ribosomal subunit protein uS4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V8
#5: Protein Small ribosomal subunit protein uS5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7W1
#8: Protein Small ribosomal subunit protein uS8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SR12
#9: Protein Small ribosomal subunit protein uS9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SRY2
#10: Protein Small ribosomal subunit protein uS10


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SQT7
#11: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13871.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A7ZSI6
#12: Protein Small ribosomal subunit protein uS12


Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A0F1AUC4
#13: Protein Small ribosomal subunit protein uS13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A7U9IV78
#14: Protein Small ribosomal subunit protein uS14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A2X1PQW4
#15: Protein Small ribosomal subunit protein uS15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SSQ7
#16: Protein Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SYP2
#17: Protein Small ribosomal subunit protein uS17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SQY7
#18: Protein Small ribosomal subunit protein bS18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A0E2KXL3
#19: Protein Small ribosomal subunit protein uS19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SQW2
#20: Protein Small ribosomal subunit protein bS20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3TRH7
#21: Protein Small ribosomal subunit protein bS21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A0E2L2J1

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Translation initiation factor IF- ... , 2 types, 2 molecules xy

#24: Protein Translation initiation factor IF-2


Mass: 97498.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A7ZS65
#25: Protein Translation initiation factor IF-1


Mass: 8262.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A7ZJV1

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50S ribosomal protein ... , 16 types, 16 molecules CDNSUVWYZ2345678

#28: Protein 50S ribosomal protein L2 / Large ribosomal subunit protein uL2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60422
#29: Protein 50S ribosomal protein L3


Mass: 22291.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SQU2
#36: Protein 50S ribosomal protein L15


Mass: 14994.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: S5NDE9
#41: Protein 50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MAS6
#43: Protein 50S ribosomal protein L22 / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P61175
#44: Protein 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SQV2
#45: Protein 50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SQZ7
#47: Protein 50S ribosomal protein L27 / Large ribosomal subunit protein bL27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7L8
#48: Protein 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A1X3JA73
#50: Protein 50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SR32
#51: Protein 50S ribosomal protein L31 / Large ribosomal subunit protein bL31-A


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7M9
#52: Protein 50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3TE02
#53: Protein 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SME7
#54: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MGC4
#55: Protein 50S ribosomal protein L35 / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7Q1
#56: Protein/peptide 50S ribosomal protein L36


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A0E2L017

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Large ribosomal subunit protein ... , 12 types, 12 molecules EFGHLMOPQRX1

#30: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60723
#31: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P62399
#32: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG55
#33: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7R1
#34: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AA10
#35: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0ADY3
#37: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15343.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A7ZSK2
#38: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG44
#39: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0C018
#40: Protein Large ribosomal subunit protein bL19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7K8
#46: Protein Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P68919
#49: Protein Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SQY2

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Protein , 1 types, 1 molecules T

#42: Protein Ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3SSG2

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Non-polymers , 5 types, 579 molecules

#57: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: Mg
#58: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S
#59: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#60: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#61: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: E.coli 70S ribosome bound to IF1 and extended IF2 / Type: RIBOSOME / Entity ID: #1-#22, #24-#56 / Source: NATURAL
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 295 K

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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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 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: 1.68 sec. / Electron dose: 40.299 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12290
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
2SerialEMimage acquisition
3cryoSPARC4.7.0masking
4cryoSPARC4.7.1CTF correction
7UCSF Chimera1.17.3model fitting
8PHENIX1.19.2.4158model refinement
10cryoSPARC4.7.1initial Euler assignment
11cryoSPARC4.7.1final Euler assignment
12cryoSPARC4.7.1classification
13cryoSPARC4.7.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64469 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 8G7P

8g7p


Accession code: 8G7P / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007157445
ELECTRON MICROSCOPYf_angle_d0.688235557
ELECTRON MICROSCOPYf_dihedral_angle_d14.26361673
ELECTRON MICROSCOPYf_chiral_restr0.04430164
ELECTRON MICROSCOPYf_plane_restr0.00612903

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