+Open data
-Basic information
Entry | Database: PDB / ID: 9gup | |||||||||||||||||||||
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Title | 30S mRNA delivery complex (open head) | |||||||||||||||||||||
Components |
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Keywords | RIBOSOME / Transcription / translation / coupling / Ribosome. | |||||||||||||||||||||
Function / homology | Function and homology information RNA secondary structure unwinding / 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 ...RNA secondary structure unwinding / 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 / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / negative regulation of translation / single-stranded RNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Escherichia coli K-12 (bacteria) synthetic construct (others) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||||||||
Authors | Rahil, H. / Weixlbaumer, A. / Webster, M.W. | |||||||||||||||||||||
Funding support | European Union, France, United States, United Kingdom, 6items
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Citation | Journal: Science / Year: 2024 Title: Molecular basis of mRNA delivery to the bacterial ribosome Authors: Webster, M.W. / Chauvier, A. / Rahil, H. / Graziadei, A. / Miropolskaya, N. / Charles, K. / Takacs, M. / Saintandre, C. / Rappsilber, J. / Walter, N.G. / Weixlbaumer, A. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9gup.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9gup.ent.gz | 942.4 KB | Display | PDB format |
PDBx/mmJSON format | 9gup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9gup_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 9gup_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9gup_validation.xml.gz | 102.1 KB | Display | |
Data in CIF | 9gup_validation.cif.gz | 167.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/9gup ftp://data.pdbj.org/pub/pdb/validation_reports/gu/9gup | HTTPS FTP |
-Related structure data
Related structure data | 51615MC 9gr1C 9guqC 9gurC 9gusC 9gutC 9guuC 9guvC 9guwC 9guxC 51572 51573 51574 51575 M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 2 types, 2 molecules AX
#1: RNA chain | 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 |
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#23: RNA chain | 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 | 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 |
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#3: Protein | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 |
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#5: Protein | 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 | 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 | 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 / |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 30S ribosomal subunit / Type: RIBOSOME / Entity ID: #2-#23 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 49.95 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52113 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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