[English] 日本語
Yorodumi
- PDB-9gup: 30S mRNA delivery complex (open head) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gup
Title30S mRNA delivery complex (open head)
Components
  • (30S ribosomal protein ...) x 17
  • (Small ribosomal subunit protein ...) x 4
  • 16S ribosomal RNA
  • mRNA
KeywordsRIBOSOME / Transcription / translation / coupling / Ribosome.
Function / homology
Function and homology information


: / positive regulation of cytoplasmic translation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / negative regulation of cytoplasmic translation / four-way junction DNA binding / regulation of mRNA stability ...: / positive regulation of cytoplasmic translation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / negative regulation of cytoplasmic translation / four-way junction DNA binding / regulation of mRNA stability / positive regulation of RNA splicing / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / ribosome biogenesis / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / single-stranded RNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / Ribosomal protein S1 / Ribosomal protein S1-like / S1 domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein S21 superfamily ...: / Ribosomal protein S1 / Ribosomal protein S1-like / S1 domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S2 signature 2. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / : / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S15 signature.
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS1 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRahil, H. / Weixlbaumer, A. / Webster, M.W.
Funding supportEuropean Union, France, United States, United Kingdom, 6items
OrganizationGrant numberCountry
European Research Council (ERC)679734European Union
Agence Nationale de la Recherche (ANR)ANR-10-LABX-0030-INRT France
Agence Nationale de la Recherche (ANR)ANR-10-IDEX-0002-02 France
European Molecular Biology Organization (EMBO)European Union
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131922 United States
Wellcome Trust203149 United Kingdom
CitationJournal: Science / Year: 2024
Title: Molecular basis of mRNA delivery to the bacterial ribosome.
Authors: Michael W Webster / Adrien Chauvier / Huma Rahil / Andrea Graziadei / Kristine Charles / Nataliya Miropolskaya / Maria Takacs / Charlotte Saint-André / Juri Rappsilber / Nils G Walter / Albert Weixlbaumer /
Abstract: Protein synthesis begins with the formation of a ribosome-messenger RNA (mRNA) complex. In bacteria, the small ribosomal subunit (30) is recruited to many mRNAs through base pairing with the Shine- ...Protein synthesis begins with the formation of a ribosome-messenger RNA (mRNA) complex. In bacteria, the small ribosomal subunit (30) is recruited to many mRNAs through base pairing with the Shine-Dalgarno (SD) sequence and RNA binding by ribosomal protein bS1. Translation can initiate on nascent mRNAs, and RNA polymerase (RNAP) can promote the recruitment of the pioneering 30. Here, we examined 30 recruitment to nascent mRNAs using cryo-electron microscopy, single-molecule fluorescence colocalization, and in-cell cross-linking mass spectrometry. We show that bS1 delivers the mRNA to the ribosome for SD duplex formation and 30 activation. Additionally, bS1 and RNAP stimulate translation initiation. Our work provides a mechanistic framework for how the SD duplex, ribosomal proteins, and RNAP cooperate in 30 recruitment to mRNAs and establish transcription-translation coupling.
History
DepositionSep 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S ribosomal RNA
B: 30S ribosomal protein S1
C: 30S ribosomal protein S2
D: Small ribosomal subunit protein uS3
E: Small ribosomal subunit protein uS4
F: 30S ribosomal protein S5
G: Small ribosomal subunit protein bS6
H: 30S ribosomal protein S7
I: 30S ribosomal protein S8
J: 30S ribosomal protein S9
K: 30S ribosomal protein S10
L: 30S ribosomal protein S11
M: 30S ribosomal protein S12
N: 30S ribosomal protein S13
O: 30S ribosomal protein S14
P: Small ribosomal subunit protein uS15
Q: 30S ribosomal protein S16
R: 30S ribosomal protein S17
S: 30S ribosomal protein S18
T: 30S ribosomal protein S19
U: 30S ribosomal protein S20
V: 30S ribosomal protein S21
X: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)865,656109
Polymers863,56623
Non-polymers2,09086
Water00
1


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

-
Components

-
RNA chain , 2 types, 2 molecules AX

#1: RNA chain 16S ribosomal RNA


Mass: 499505.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli K-12 (bacteria) / References: GenBank: 1929590828
#23: RNA chain mRNA


Mass: 17060.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
30S ribosomal protein ... , 17 types, 17 molecules BCFHIJKLMNOQRSTUV

#2: Protein 30S ribosomal protein S1 / Bacteriophage Q beta RNA-directed RNA polymerase subunit I / Small ribosomal subunit protein bS1


Mass: 61238.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsA, ssyF, b0911, JW0894 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG67
#3: Protein 30S ribosomal protein S2 / Small ribosomal subunit protein uS2


Mass: 26781.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsB, b0169, JW0164 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7V0
#6: Protein 30S ribosomal protein S5 / Small ribosomal subunit protein uS5


Mass: 16475.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsE, spc, b3303, JW3265 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7W1
#8: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 17637.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsG, b3341, JW3303 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P02359
#9: Protein 30S ribosomal protein S8 / Small ribosomal subunit protein uS8


Mass: 14146.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsH, b3306, JW3268 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7W7
#10: Protein 30S ribosomal protein S9 / Small ribosomal subunit protein uS9


Mass: 14886.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsI, b3230, JW3199 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7X3
#11: Protein 30S ribosomal protein S10 / Small ribosomal subunit protein uS10 / Transcription termination/antitermination protein NusE


Mass: 11755.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsJ, nusE, b3321, JW3283 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R5
#12: Protein 30S ribosomal protein S11 / Small ribosomal subunit protein uS11


Mass: 13870.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsK, b3297, JW3259 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R9
#13: Protein 30S ribosomal protein S12 / Small ribosomal subunit protein uS12


Mass: 13814.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsL, strA, b3342, JW3304 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7S3
#14: Protein 30S ribosomal protein S13 / Small ribosomal subunit protein uS13


Mass: 13128.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsM, b3298, JW3260 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7S9
#15: Protein 30S ribosomal protein S14 / Small ribosomal subunit protein uS14


Mass: 11606.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsN, b3307, JW3269 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG59
#17: Protein 30S ribosomal protein S16 / 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 K-12 (bacteria) / Gene: rpsP, b2609, JW2590 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7T3
#18: Protein 30S ribosomal protein S17 / Small ribosomal subunit protein uS17


Mass: 9724.491 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsQ, neaA, b3311, JW3273 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG63
#19: Protein 30S ribosomal protein S18 / Small ribosomal subunit protein bS18


Mass: 9005.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsR, b4202, JW4160 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7T7
#20: Protein 30S ribosomal protein S19 / Small ribosomal subunit protein uS19


Mass: 10455.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsS, b3316, JW3278 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7U3
#21: Protein 30S ribosomal protein S20 / Small ribosomal subunit protein bS20


Mass: 9708.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsT, b0023, JW0022 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7U7
#22: Protein 30S ribosomal protein S21 / Small ribosomal subunit protein bS21


Mass: 8524.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsU, b3065, JW3037 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P68679

-
Small ribosomal subunit protein ... , 4 types, 4 molecules DEGP

#4: Protein Small ribosomal subunit protein uS3


Mass: 26031.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: rpsC, A5U30_004548, A8502_004027, ACN81_25500, ACU57_20980, AW118_24880, AWP47_12665, B6R15_004073, B6R31_004972, BANRA_01945, BANRA_04324, BCB93_004289, BE932_15515, BER14_25170, BG944_001129, ...Gene: rpsC, A5U30_004548, A8502_004027, ACN81_25500, ACU57_20980, AW118_24880, AWP47_12665, B6R15_004073, B6R31_004972, BANRA_01945, BANRA_04324, BCB93_004289, BE932_15515, BER14_25170, BG944_001129, BGM66_003597, BGZ_02594, BGZ_04121, BJI68_08695, BK292_20485, BK383_24665, BKL28_004547, BR158_003786, BTB68_004360, BTQ06_10670, BvCmsKKP061_03026, BvCmsSIP010_02681, BXT93_05495, C0P57_002664, C1Q91_004908, C2121_004166, C2M16_25425, C2R31_004629, C3F40_19740, C9Z68_22615, CF22_004853, CG704_20890, CIG67_10695, CQ842_14345, CQ842_22325, CTR35_003626, CV83915_02784, D3C88_13310, D3G36_23070, D4M65_20635, D4N09_20235, D9D43_22570, D9E49_05220, D9J61_16715, DD762_23610, DIV22_15195, DNQ45_03820, DNX30_25415, DS732_24325, DTL43_20935, DU321_12065, E2865_04467, E4K51_21555, E5H86_24460, E6D34_21695, EAI46_07540, ECs4179, EIA08_24020, EIZ93_12405, EN85_004353, EPS76_07150, EPS97_20030, EWK56_25060, ExPECSC038_03644, F7F11_22660, F7N46_23945, F9413_21170, F9461_25590, F9B07_24620, FGAF848_25890, FIJ20_21130, FJQ40_18370, FKO60_25700, FOI11_019195, FOI11_03985, FPI65_20370, FPS11_25365, FVB16_04935, FWK02_12630, FZU14_21885, G3V95_19910, G3W53_21020, G4A38_21575, G4A47_20845, G5603_24650, GAI89_24765, GAJ12_24655, GFY48_21635, GGB84_004455, GKF66_21610, GNW61_16695, GNZ05_25920, GOP25_22770, GP711_23370, GP954_00880, GP965_04360, GP975_01250, GP979_01940, GQA06_03885, GQE86_20145, GQM04_10630, GQM13_25265, GQM21_11295, GQN34_23330, GQW07_21485, GRO95_20750, GRW05_09125, GRW24_04690, GUC01_21245, H0O53_20765, H0O72_19480, HEP30_018700, HEP34_004758, HHH44_004523, HI055_004152, HIE29_005199, HJQ60_004999, HLX92_10010, HLZ50_22115, HMV95_19670, HMW38_23170, HV109_02125, HV209_14650, HVV39_09330, HVW04_17470, HVW43_18605, HVY77_02110, I6H00_20860, I6H02_12055, J0541_004409, J5U05_004075, JNP96_25370, NCTC10082_02827, NCTC10089_00490, NCTC10429_01082, NCTC10764_03851, NCTC10767_01504, NCTC10974_00537, NCTC11126_02758, NCTC11181_02726, NCTC11341_01901, NCTC7922_04054, NCTC7927_00539, NCTC7928_02529, NCTC8009_01498, NCTC8179_05929, NCTC8333_00477, NCTC8500_00322, NCTC8621_00496, NCTC8622_00518, NCTC8959_03273, NCTC8960_03058, NCTC9001_04242, NCTC9045_00553, NCTC9075_00712, NCTC9077_00592, NCTC9081_00905, NCTC9117_00744, NCTC9702_00525, NCTC9706_02725, NCTC9962_06785, OGM49_22395, P6223_003995, QDW62_02130, RZR61_12955, SAMEA3472112_00681, SAMEA3752557_01964, WR15_19670
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: C3SQX2
#5: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsD, BWG_2987 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: C4ZUF1
#7: Protein Small ribosomal subunit protein bS6


Mass: 15197.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: rpsF, BANRA_02890, BGM66_001638, BJI68_10200, C0P57_000210, CIG67_23060, CTR35_001516, CV83915_01828, E6D34_03615, G4A38_03220, G4A47_10770, GNW61_00195, GQM21_23655, GRW05_28450, HVY77_22975, ...Gene: rpsF, BANRA_02890, BGM66_001638, BJI68_10200, C0P57_000210, CIG67_23060, CTR35_001516, CV83915_01828, E6D34_03615, G4A38_03220, G4A47_10770, GNW61_00195, GQM21_23655, GRW05_28450, HVY77_22975, J0541_002297, JNP96_03175, NCTC8500_05020, NCTC9045_05184, NCTC9706_01764, P6223_000651, SAMEA3752557_01699
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: W8T6F0
#16: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsO, secC, b3165, JW3134 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ADZ4

-
Non-polymers , 1 types, 86 molecules

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


Mass: 24.305 Da / Num. of mol.: 86 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 30S ribosomal subunit / Type: RIBOSOME / Entity ID: #2-#23 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 49.95 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52113 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00757879
ELECTRON MICROSCOPYf_angle_d0.72985838
ELECTRON MICROSCOPYf_dihedral_angle_d13.07131298
ELECTRON MICROSCOPYf_chiral_restr0.09310857
ELECTRON MICROSCOPYf_plane_restr0.0075134

+
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