[English] 日本語
Yorodumi
- PDB-9nl6: E. coli initiation complex with EQ2-YbiT in Non-hydrolytic 1/PtIM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nl6
TitleE. coli initiation complex with EQ2-YbiT in Non-hydrolytic 1/PtIM(a) conformation
Components
  • (30S ribosomal protein ...) x 9
  • (50S ribosomal protein ...) x 12
  • (Large ribosomal subunit protein ...) x 17
  • (Small ribosomal subunit protein ...) x 11
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Probable ATP-binding protein YbiT
  • mRNA
  • tRNA
KeywordsRIBOSOME / ABCF / initiation-complex / ATPase
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / ribosome assembly ...negative regulation of cytoplasmic translational initiation / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / translational initiation / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / 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 / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / ABC-transporter extension domain / ABC transporter / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. ...: / ABC-transporter extension domain / ABC transporter / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 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 L28 family / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / N-FORMYLMETHIONINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...ADENOSINE-5'-TRIPHOSPHATE / N-FORMYLMETHIONINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS5 / Probable ATP-binding protein YbiT / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL19
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSingh, S. / Hunt, J.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: E. coli initiation complex with EQ2-YbiT in Non-hydrolytic 1/PtIM(a) conformation
Authors: Singh, S. / Hunt, J.F.
History
DepositionMar 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Large ribosomal subunit protein uL1
13: Large ribosomal subunit protein uL13
14: 50S ribosomal protein L14
15: Large ribosomal subunit protein uL15
16: 50S ribosomal protein L16
17: Large ribosomal subunit protein bL17
18: Large ribosomal subunit protein uL18
19: 50S ribosomal protein L19
2: 50S ribosomal protein L2
20: Large ribosomal subunit protein bL20
21: Large ribosomal subunit protein bL21
22: Large ribosomal subunit protein uL22
23: Large ribosomal subunit protein uL23
24: Large ribosomal subunit protein uL24
25: Large ribosomal subunit protein bL25
27: 50S ribosomal protein L27
28: 50S ribosomal protein L28
29: Large ribosomal subunit protein uL29
3: 50S ribosomal protein L3
30: 50S ribosomal protein L30
31: Large ribosomal subunit protein bL31
32: 50S ribosomal protein L32
34: 50S ribosomal protein L34
35: Large ribosomal subunit protein bL35
36: 50S ribosomal protein L36
4: Large ribosomal subunit protein uL4
5: 50S ribosomal protein L5
6: Large ribosomal subunit protein uL6
9: Large ribosomal subunit protein bL9
R1: 23S ribosomal RNA
R2: 5S ribosomal RNA
R3: 16S ribosomal RNA
T: tRNA
Y: Probable ATP-binding protein YbiT
M: mRNA
sb: Small ribosomal subunit protein uS2
sc: Small ribosomal subunit protein uS3
sd: 30S ribosomal protein S4
se: Small ribosomal subunit protein uS5
sf: 30S ribosomal protein S6, non-modified isoform
sg: 30S ribosomal protein S7
sh: 30S ribosomal protein S8
si: Small ribosomal subunit protein uS9
sj: 30S ribosomal protein S10
sk: Small ribosomal subunit protein uS11
sl: Small ribosomal subunit protein uS12
sm: 30S ribosomal protein S13
sn: Small ribosomal subunit protein uS14
so: Small ribosomal subunit protein uS15
sp: Small ribosomal subunit protein bS16
sq: Small ribosomal subunit protein uS17
sr: 30S ribosomal protein S18
ss: 30S ribosomal protein S19
st: 30S ribosomal protein S20
su: Small ribosomal subunit protein bS21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,224,897312
Polymers2,217,53555
Non-polymers7,362257
Water00
1


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

-
Components

-
Large ribosomal subunit protein ... , 17 types, 17 molecules 113151718202122232425293135469

#1: Protein Large ribosomal subunit protein uL1 / 50S ribosomal protein L1


Mass: 23392.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplA, b3984, JW3947 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L0
#2: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplM, b3231, JW3200 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA10
#4: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplO, b3301, JW3263 / Production host: Escherichia coli (E. coli) / References: UniProt: P02413
#6: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 13721.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplQ, b3294, JW3256 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG44
#7: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 12663.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplR, b3304, JW3266 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C018
#10: Protein Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3T7Q7
#11: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplU, UTI89_C3620 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1R6F0
#12: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplV, UTI89_C3767 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1R610
#13: Protein Large ribosomal subunit protein uL23


Mass: 10546.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SQV2
#14: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11078.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplX / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9LWC1
#15: Protein Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplY / Production host: Escherichia coli (E. coli) / References: UniProt: P68919
#18: Protein Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SQY2
#21: Protein Large ribosomal subunit protein bL31 / 50S ribosomal protein L31


Mass: 7516.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmE, b3936, JW3907 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7M9
#24: Protein Large ribosomal subunit protein bL35


Mass: 7181.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmI / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Q2
#26: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplD, eryA, b3319, JW3281 / Production host: Escherichia coli (E. coli) / References: UniProt: P60723
#28: Protein Large ribosomal subunit protein uL6


Mass: 18801.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SR17
#29: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplI, b4203, JW4161 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R1

-
50S ribosomal protein ... , 12 types, 12 molecules 141619227283303234365

#3: Protein 50S ribosomal protein L14


Mass: 13451.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplN, A13A_03633 / Production host: Escherichia coli (E. coli) / References: UniProt: S1NW45
#5: Protein 50S ribosomal protein L16 / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplP, b3313, JW3275 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY7
#8: Protein 50S ribosomal protein L19


Mass: 13028.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplS, A13A_02795 / Production host: Escherichia coli (E. coli) / References: UniProt: S1PSA3
#9: Protein 50S ribosomal protein L2 / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplB, b3317, JW3279 / Production host: Escherichia coli (E. coli) / References: UniProt: P60422
#16: Protein 50S ribosomal protein L27


Mass: 8174.394 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmA, ECVG_02038 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3JCC7
#17: Protein 50S ribosomal protein L28


Mass: 8896.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmB, G925_03874 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2KZD0
#19: Protein 50S ribosomal protein L3 / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplC, b3320, JW3282 / Production host: Escherichia coli (E. coli) / References: UniProt: P60438
#20: Protein 50S ribosomal protein L30 / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmD, b3302, JW3264 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG51
#22: Protein 50S ribosomal protein L32


Mass: 6332.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmF, ECDEC2D_1303 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A828UBL8
#23: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmH / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGC4
#25: Protein/peptide 50S ribosomal protein L36


Mass: 4377.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmJ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2L017
#27: Protein 50S ribosomal protein L5


Mass: 20073.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplE, CCU01_002520 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P8BX24

-
RNA chain , 5 types, 5 molecules R1R2R3TM

#30: RNA chain 23S ribosomal RNA


Mass: 941322.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 2019144442
#31: RNA chain 5S ribosomal RNA


Mass: 38483.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1815787944
#32: RNA chain 16S ribosomal RNA


Mass: 498725.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1338015391
#33: RNA chain tRNA


Mass: 24807.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 932857508
#35: RNA chain mRNA


Mass: 2886.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

-
Protein , 1 types, 1 molecules Y

#34: Protein Probable ATP-binding protein YbiT


Mass: 59924.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ybiT, b0820, JW0804 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9U3

-
Small ribosomal subunit protein ... , 11 types, 11 molecules sbscsesiskslsnsospsqsu

#36: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 24253.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsB, b0169, JW0164 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V0
#37: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 23078.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsC, Z4685, ECs4179 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V5
#39: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 16532.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsE, spc, b3303, JW3265 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W1
#43: Protein Small ribosomal subunit protein uS9


Mass: 14554.882 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SRY2
#45: Protein Small ribosomal subunit protein uS11


Mass: 12388.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SR57
#46: Protein Small ribosomal subunit protein uS12


Mass: 13636.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SQR7
#48: Protein Small ribosomal subunit protein uS14


Mass: 11475.364 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsN, EIMP300_17810 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8S0FJJ0
#49: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10159.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsO, secC, b3165, JW3134 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#50: Protein Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsP / Production host: Escherichia coli (E. coli) / References: UniProt: C3SYP2
#51: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9263.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsQ, neaA, b3311, JW3273 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG63
#55: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 8392.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsU, b3065, JW3037 / Production host: Escherichia coli (E. coli) / References: UniProt: P68679

-
30S ribosomal protein ... , 9 types, 9 molecules sdsfsgshsjsmsrssst

#38: Protein 30S ribosomal protein S4


Mass: 23383.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SR62
#40: Protein 30S ribosomal protein S6, non-modified isoform


Mass: 11669.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsF, b4200, JW4158 / Production host: Escherichia coli (E. coli) / References: UniProt: P02358
#41: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 16861.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsG, b3341, JW3303 / Production host: Escherichia coli (E. coli) / References: UniProt: P02359
#42: Protein 30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsH, ECDEC2D_3910 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A828U358
#44: Protein 30S ribosomal protein S10


Mass: 11196.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsJ, NRG857_16455 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3EQD3
#47: Protein 30S ribosomal protein S13


Mass: 12625.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsM, A13A_03621 / Production host: Escherichia coli (E. coli) / References: UniProt: S1P5F8
#52: Protein 30S ribosomal protein S18


Mass: 7606.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsR, ECW_m4565 / Production host: Escherichia coli (E. coli) / References: UniProt: E0J6I2
#53: Protein 30S ribosomal protein S19


Mass: 9057.626 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsS, ECKIH15140_04691 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9LGZ0
#54: Protein 30S ribosomal protein S20


Mass: 9506.190 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsT / Production host: Escherichia coli (E. coli) / References: UniProt: C3TRH7

-
Non-polymers , 4 types, 257 molecules

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


Mass: 24.305 Da / Num. of mol.: 252 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S
#58: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#59: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: complex of E. coli 70S ribosome, mRNA, tRNA and YbiT / Type: RIBOSOME / Entity ID: #1-#55 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 56.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78136 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 45.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0057162052
ELECTRON MICROSCOPYf_angle_d0.623241771
ELECTRON MICROSCOPYf_chiral_restr0.039930739
ELECTRON MICROSCOPYf_plane_restr0.005113411
ELECTRON MICROSCOPYf_dihedral_angle_d14.161762779

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more