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- PDB-7afo: Bacterial 30S ribosomal subunit assembly complex state B (body domain) -

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Basic information

Entry
Database: PDB / ID: 7afo
TitleBacterial 30S ribosomal subunit assembly complex state B (body domain)
Components
  • (30S ribosomal protein ...) x 12
  • 16SrRNA (body domain of the 30S ribosome)
  • Ribosomal RNA small subunit methyltransferase A
  • Ribosome maturation factor RimP
KeywordsRIBOSOME / Cryo-EM / 30S biogenesis / ribosome assembly / RbfA / RsgA / YjeQ / RimP / KsgA / RsmA
Function / homology
Function and homology information


16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding ...16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / translation / RNA binding / cytosol / cytoplasm
Similarity search - Function
Ribosome maturation factor RimP / Ribosome maturation factor RimP, N-terminal / Ribosome maturation factor RimP, C-terminal / RimP, N-terminal domain superfamily / Ribosome maturation factor RimP, C-terminal domain superfamily / RimP N-terminal domain / RimP C-terminal SH3 domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site ...Ribosome maturation factor RimP / Ribosome maturation factor RimP, N-terminal / Ribosome maturation factor RimP, C-terminal / RimP, N-terminal domain superfamily / Ribosome maturation factor RimP, C-terminal domain superfamily / RimP N-terminal domain / RimP C-terminal SH3 domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / 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 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 / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / 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 S5, C-terminal domain / 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 S15 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11 / S4 RNA-binding domain / S4 domain / Ribosomal protein S11 / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosome maturation factor RimP / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosome maturation factor RimP / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Ribosomal RNA small subunit methyltransferase A / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsSchedlbauer, A. / Iturrioz, I. / Ochoa-Lizarralde, B. / Diercks, T. / Kaminishi, T. / Capuni, R. / Astigarraga, E. / Gil-Carton, D. / Fucini, P. / Connell, S.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)CTQ2017-82222-R Spain
European CommissionPCIG14-GA-2013-632072 Spain
CitationJournal: Sci Adv / Year: 2021
Title: A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit.
Authors: Andreas Schedlbauer / Idoia Iturrioz / Borja Ochoa-Lizarralde / Tammo Diercks / Jorge Pedro López-Alonso / José Luis Lavin / Tatsuya Kaminishi / Retina Çapuni / Neha Dhimole / Elisa de ...Authors: Andreas Schedlbauer / Idoia Iturrioz / Borja Ochoa-Lizarralde / Tammo Diercks / Jorge Pedro López-Alonso / José Luis Lavin / Tatsuya Kaminishi / Retina Çapuni / Neha Dhimole / Elisa de Astigarraga / David Gil-Carton / Paola Fucini / Sean R Connell /
Abstract: While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high- ...While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30 ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16 ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.
History
DepositionSep 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model / struct_conn
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

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Assembly

Deposited unit
A: 16SrRNA (body domain of the 30S ribosome)
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
H: 30S ribosomal protein S8
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
T: 30S ribosomal protein S20
U: 30S ribosomal protein S21
X: Ribosome maturation factor RimP
Y: Ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)702,35335
Polymers701,86715
Non-polymers48620
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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30S ribosomal protein ... , 12 types, 12 molecules DEFHKLOPQRTU

#2: Protein 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR62
#3: Protein 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR27
#4: Protein 30S ribosomal protein S6 / Small ribosomal subunit protein bS6


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#5: Protein 30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR12
#6: Protein 30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR57
#7: Protein 30S ribosomal protein S12


Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQR7
#8: Protein 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SSQ7
#9: Protein 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SYP2
#10: Protein 30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQY7
#11: Protein 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SFP7
#12: Protein 30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TRH7
#13: Protein 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3STZ7

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Protein , 2 types, 2 molecules XY

#14: Protein Ribosome maturation factor RimP


Mass: 16737.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: rimP, yhbC, A6581_13520, A6592_14330, A6V01_00515, A8C65_02275, A9819_18200, A9P13_03050, A9R57_12705, A9X72_02945, AC067_23780, AC789_1c35400, ACN002_3263, ACU57_14550, ACU90_11670, AJ318_ ...Gene: rimP, yhbC, A6581_13520, A6592_14330, A6V01_00515, A8C65_02275, A9819_18200, A9P13_03050, A9R57_12705, A9X72_02945, AC067_23780, AC789_1c35400, ACN002_3263, ACU57_14550, ACU90_11670, AJ318_05135, AM270_15615, AM446_04425, AM464_08475, AM465_07740, AMK83_06445, AML07_19235, AML35_13990, APT94_23095, APU18_16510, APZ14_04190, ARC77_12300, AU473_05840, AUQ13_02970, AUS26_18365, AW059_15280, AW106_13165, AWB10_02960, AWE53_007750, AWF59_011795, AWG78_015830, AWG90_020515, AZZ83_001444, B6V57_17915, B7C53_06465, B9M99_10360, B9N33_16975, B9T59_16360, BANRA_01790, BANRA_03978, BANRA_04186, BB545_09885, BEN53_19595, BFD68_02460, BHF03_08615, BHF46_07210, BHS81_19095, BHS87_17860, BIQ87_17930, BIU72_05300, BIZ41_14495, BJJ90_02875, BK248_21925, BK292_10325, BK296_12945, BK334_09665, BK373_10280, BK375_17180, BK383_15860, BMA87_01190, BMT49_25700, BMT91_09135, BvCms12BK_01026, BvCms2454_04843, BvCms28BK_03353, BvCms35BK_01522, BvCmsC61A_01482, BvCmsHHP019_03132, BvCmsHHP056_02505, BvCmsKKP036_00265, BvCmsKKP061_00867, BvCmsKSNP073_02141, BvCmsKSNP081_00265, BvCmsKSNP120_03551, BvCmsKSP011_02071, BvCmsKSP024_00304, BvCmsKSP026_00481, BvCmsKSP045_01629, BvCmsKSP058_01861, BvCmsKSP067_01443, BvCmsKSP076_01609, BvCmsNSNP036_02130, BvCmsNSP006_04619, BvCmsNSP007_02230, BvCmsNSP047_04139, BvCmsNSP072_03166, BvCmsOUP014_03611, BvCmsSINP011_04479, BvCmsSINP022_03542, BvCmsSIP019_00386, BvCmsSIP044_00116, BWI89_22175, C2M16_04320, C2U48_17655, C4K41_03675, C4M78_03215, C5715_22690, C5N07_18175, C5P01_18940, C5P44_00535, C6669_12125, C6B13_18120, C7235_03330, C7B02_15770, C7B06_16695, C7B07_10705, C7B08_03460, C7B18_13725, C9098_07895, C9114_15350, C9141_00495, C9160_02445, C9162_04215, C9201_13770, C9306_00520, C9E25_11375, C9E67_03480, C9Z03_07385, C9Z23_02310, C9Z28_00490, C9Z29_07085, C9Z37_14765, C9Z39_14380, C9Z43_00485, C9Z69_11070, C9Z70_06870, C9Z78_03420, C9Z89_09170, CA593_10450, CCZ14_12150, CCZ17_15250, CDC27_16980, CDL37_12105, CF006_16775, CG692_07190, CI641_009150, CI693_03565, CI694_20945, CIG45_16155, CJU63_19030, CJU64_18910, CMR93_08945, CO706_14525, COD30_12805, COD46_10650, CQB02_14455, CQP61_03755, CR538_03180, CR539_21140, CRD98_04820, CRE06_06720, CRJUMX01_260087, CRM83_23605, CRT43_19210, CRX46_03850, CSB64_06490, CT146_02950, CUB99_16240, CVH05_10885, CWM24_22975, CWS33_08270, D0X26_08985, D1912_12210, D2184_10400, D2185_00550, D2188_02685, D3821_08430, D3822_14680, D3M98_06670, D3O91_07730, D3P01_09055, D3P02_05570, D3Y67_18395, D4011_13620, D4074_02330, D4628_02550, D4636_02785, D4638_00685, D4660_02725, D4718_08975, D4L91_11845, D4M06_11120, D4U49_10465, D4U85_14225, D4V08_01260, D5H35_09675, D5I97_10565, D6004_08020, D6C36_14055, D6D43_15405, D6T60_15285, D6T98_02305, D6W00_13910, D6X36_05255, D6X63_01325, D6X76_04230, D7K33_12750, D7K63_12115, D7K66_04390, D7W70_15750, D7Y10_03485, D7Z75_02840, D8Y65_13370, D9610_07705, D9C99_05015, D9D31_09850, D9D33_00515, D9D43_03510, D9D44_04305, D9D94_03385, D9E13_09760, D9E19_10295, D9E34_10730, D9E49_09490, D9E73_12375, D9F17_07095, D9F32_01135, D9G11_02975, D9G29_06920, D9G42_16795, D9G48_22395, D9G69_00995, D9G95_16980, D9H10_06565, D9H36_12500, D9H53_01090, D9H68_07455, D9H70_01525, D9H94_03415, D9I18_07070, D9I20_02730, D9I37_14605, D9I87_04955, D9I88_16545, D9I97_11395, D9J11_01025, D9J44_07745, D9J46_20545, D9J52_07810, D9J58_06005, D9J60_11080, D9J63_16805, D9J78_05025, D9K02_05975, D9K48_12150, D9K54_17935, D9L89_05265, D9L99_02555, D9S45_00150, D9X77_02225, D9X97_03015, D9Z28_03265, DAH18_20505, DAH26_17210, DAH30_12980, DAH32_14080, DAH34_01875, DAH37_04360, DAH43_16675, DB359_10675, DBQ99_04145, DD762_19135, DEN86_08165, DEN89_09300, DEN97_16030, DEO04_19500, DEO19_06325, DEO20_07555, DIV22_03080, DJ487_12870, DJ492_21815, DJ503_10870, DK132_15395, DL251_15040, DL257_05545, DL292_14605, DL326_05955, DL455_12595, DL479_06485, DL530_21135, DL545_03765, DL705_01195, DL800_23160, DL979_03350, DLT82_02550, DLU50_08445, DLU67_08270, DLU82_10225, DLW60_07385, DLW88_04690, DLX38_07775, DLY41_08050, DLY44_02205, DM102_15060, DM129_03900, DM155_07540, DM267_13960, DM272_02325, DM280_08950, DM296_04730, DM382_07255, DM820_04520, DM962_02535, DM973_04545, DMC44_07025, DMI04_04165, DMI53_12610, DMO02_15300, DMY83_09815, DMZ50_12315, DN660_01225, DN700_04490, DN703_00975, DN808_01785, DNB37_13600, DNC98_07055, DND16_06430, DND79_01225, DNI21_14825, DNJ62_11965, DNK12_02730, DNQ45_19755, DNR35_05290, DNR41_11080, DNW42_05300, DNX19_05475, DNX30_11260, DOE35_12505, DOM23_01535, DOS18_12925, DOT81_04150, DOU81_12270, DOY22_13980, DOY56_12140, DOY61_04590, DOY67_01180, DP265_06450, DP277_10000, DQE91_01160, DQF36_20850, DQF57_03510, DQF71_07055, DQF72_06355, DQG35_02725, DQO13_01190, DQP61_01665, DRP48_13805, DRW19_01190, DS143_06665, DS721_10985, DS732_23590, DS966_19175, DT034_01165, DTL43_04190, DTM10_07090, DTM45_14405, DTZ20_11985, DU309_11240, DU321_08565, DU333_16815, DVB38_07290, DW236_11980, DWB25_03315, DXT69_05625, DXT71_00545, DXT73_13265, DXX80_009485, E0I42_14235, E0K84_20585, E0L04_19770, E0L12_03810, E2112_05640, E2114_08285, E2115_05735, E2119_05765, E2127_02470, E2128_02600, E2129_05655, E2134_15700, E2135_07975, E2148_12390, E2855_04121, E2863_03946, E4K55_06555, E4K60_03320, E4K61_09175, E5P22_12890, E5P28_13015, E5P37_13240, E5S42_11910, E5S46_04245, E5S47_02865, E5S56_15530, E5S58_02830, E5S61_05810, EA159_13410, EA167_07035, EA189_10710, EA191_13025, EA198_19520, EA200_07260, EA203_14945, EA213_02390, EA214_08705, EA218_15110, EA222_06430, EA225_06975, EA231_14825, EA232_14625, EA233_06070, EA242_07640, EA245_09665, EA250_06530, EA410_15875, EA429_03180, EA434_19670, EA435_15260, EA834_14920, EAI42_15040, EAI46_15085, EAI52_09995, EAM59_00915, EAN70_10640, EAN77_10380, EAX79_13125, EB476_09145, EB509_07095, EB510_12300, EB515_06920, EBA46_01560, EBA84_05725, EBJ06_06030, EBM08_05350, EC3234A_53c00490, EC3426_04319, EC382_14550, EC95NR1_02552, ECONIH1_18750, ECTO124_00619, ECTO6_00586, ED225_04165, ED307_11680, ED600_09295, ED607_10320, ED611_04175, ED648_02810, ED903_04550, ED944_07155, EEA45_06835, EEP23_06195, EF082_03885, EF173_16900, EG075_10005, EG599_06060, EG796_01085, EG808_04740, EGC26_04810, EGT48_12345, EGU87_04110, EH186_10365, EH412_00890, EHD45_09310, EHD63_05170, EHD79_19375, EHH55_24255, EHJ36_00890, EHJ66_05985, EHV81_00450, EHV90_06065, EHW09_05495, EHX09_11690, EI021_03960, EI028_15155, EI032_08700, EI041_02105, EIA08_12605, EIA21_02775, EIZ93_15760, EJ366_26100, EJC75_15120, EKI52_18340, ELT17_03400, ELT20_05150, ELT22_04740, ELT23_06870, ELT33_08790, ELT48_07015, ELT49_04545, ELT58_00540, ELU82_09410, ELU85_07030, ELU96_15070, ELV05_02170, ELV08_03090, ELV13_06450, ELV15_01725, ELV22_10740, ELV24_06460, ELV28_06240, ELX56_11845, ELX70_11310, ELX76_04020, ELX79_02845, ELX83_01980, ELY05_03155, ELY23_12930, ELY24_06190, ELY41_02060, ELY48_01080, ELY50_10975, EO241_09475, EPS76_01470, EPS91_00535, EPS94_08350, EPT01_00520, EPU41_18025, EQ823_04945, EQ825_16430, EQ830_04625, ERL57_13330, ERS085365_00561, ERS085366_00575, ERS085374_01907, ERS085379_00394, ERS085383_00718, ERS085386_00509, ERS085404_02208, ERS085406_02910, ERS085416_00333, ERS139211_00574, ERS150873_04325, ERS150876_01006, EST51_02850, EVY14_07620, EWK56_02880, EXM29_19890, ExPECSC019_00733, ExPECSC038_02681, ExPECSC065_00152, EXX06_09585, EXX13_07220, EXX23_07435, EXX24_06255, EXX53_05215, EXX55_08940, EXX71_13295, EXX78_16835, EXX87_04485, EYD11_02750, EYX82_02350, EYX99_26670, EYY27_17450, EYY34_08680, EYY78_15515, F1E13_04755, F1E19_22160, F7F00_12275, F7F11_09140, F7F18_01100, F7F23_11550, F7F26_00510, F7F29_05220, F7G01_14085, F7G03_16255, F9059_01215, F9Z74_11735, FAF34_018990, FE846_13840, FKO60_06135, FNJ67_03680, FNJ69_14760, FNJ83_20460, FQ022_08085, FQ915_16575, FQR64_03140, FQU83_04615, FQZ46_16235, FRV13_20650, FV293_08480, FV295_10420, FV438_11005, FVB16_12900, FWK02_30950, FY127_14860, FZ043_21930, GFU40_08290, GFU45_16445, GFU47_23645, GHR40_07700, GII67_12855, GII91_02620, GIY13_09410, GIY19_08440, GJ11_20705, GJ638_05280, GJD97_02990, GKE15_04560, GKE22_12100, GKE24_04550, GKE26_04235, GKE29_02570, GKE31_04515, GKE39_10640, GKE46_11105, GKE58_04470, GKE60_04205, GKE64_10430, GKE77_04900, GKE87_00805, GKE92_01045, GKE93_06080, GKF00_04240, GKF03_05185, GKF28_11940, GKF34_04535, GKF47_04530, GKF74_09325, GKF86_04155, GKF89_14480, GKG08_09990, GKG09_10130, GKG11_10335, GKG12_08430, GKG22_10250, GKG29_10290, GN312_06535, GNZ00_04975, GNZ02_01185, GNZ03_06215, GP654_17605, GP661_13150, GP664_11975, GP666_12855, GP689_13980, GP700_08285, GP712_11280, GP720_14900, GP727_07890, GP912_13015, GP935_13235, GP946_08565, GP950_18120, GQA06_13100, GQE22_11445, GQE30_02675, GQE34_11815, GQE42_06055, GQE47_10010, GQE51_04775, GQE58_09360, GQE64_09830, GQE68_06305, GQE88_18540, GQE93_14745, GQL64_21185, GQM06_01810, GQM09_10960, GQM13_09315, GQM17_12990, GQN16_09395, GQN33_10425, GQS26_10800, GRW42_15825, GRW80_12150, HmCms169_01197, HmCms184_00230, HmCmsJML074_04857, HmCmsJML079_04423, HmCmsJML146_01154, HmCmsJML204_02229, HmCmsJML236_03431, HW43_20810, MJ49_14450, MS6198_36560, MS8345_03519, NCTC10082_02969, NCTC10089_00628, NCTC10090_03661, NCTC10764_04007, NCTC10766_02930, NCTC10767_01659, NCTC10865_00812, NCTC10963_00588, NCTC11022_03335, NCTC11181_02870, NCTC12650_00863, NCTC13216_01221, NCTC13846_00637, NCTC7927_00693, NCTC7928_02343, NCTC8009_01696, NCTC8179_06096, NCTC8621_00648, NCTC8959_03135, NCTC8960_03211, NCTC9001_05629, NCTC9007_04393, NCTC9036_00679, NCTC9044_01214, NCTC9045_00716, NCTC9050_03744, NCTC9055_02513, NCTC9058_01245, NCTC9062_02553, NCTC9111_00997, NCTC9119_00654, NCTC9434_00565, NCTC9701_00708, NCTC9703_05099, NCTC9706_02867, NCTC9777_02133, NCTC9969_00790, PGD_03946, PU06_19955, RG28_20970, RK56_014715, RX35_04257, SAMEA3472043_01802, SAMEA3472044_03331, SAMEA3472047_01873, SAMEA3472055_00399, SAMEA3472056_03073, SAMEA3472070_01171, SAMEA3472080_00946, SAMEA3472090_00549, SAMEA3472108_00101, SAMEA3472110_01542, SAMEA3472112_01526, SAMEA3472114_00482, SAMEA3472147_01879, SAMEA3484427_00607, SAMEA3484429_00735, SAMEA3484434_03594, SAMEA3485101_01711, SAMEA3752372_01780, SAMEA3752553_01186, SAMEA3752557_01874, SAMEA3752559_03272, SAMEA3752620_02342, SAMEA3753064_02937, SAMEA3753097_03303, SAMEA3753164_02301, SAMEA3753290_00147, SAMEA3753300_02130, SK85_03483, SY51_18280, U12A_03406, U14A_03403, UC41_24430, UN86_15485, UN91_15510, WQ89_06745, WR15_24545, YDC107_1843
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J3VRH1
#15: Protein Ribosomal RNA small subunit methyltransferase A / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine ...16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine transferase / 16S rRNA dimethylase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 30452.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rsmA, ksgA, EC54115_03242 / Production host: Escherichia coli (E. coli)
References: UniProt: I4T5U1, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase

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RNA chain / Non-polymers , 2 types, 21 molecules A

#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#1: RNA chain 16SrRNA (body domain of the 30S ribosome)


Mass: 499513.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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Details

Has ligand of interestN

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Bacterial 30S ribosomal subunit assembly complex state B (body domain)RIBOSOME30S body from multibody refinement#1-#150MULTIPLE SOURCES
2Bacterial 30S ribosomal subunit assembly complex state B (body domain)COMPLEX#1-#151NATURAL
3Bacterial 30S ribosomal subunit assembly complex state B (body domain)RIBOSOME#14-#151RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 27

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Processing

SoftwareName: PHENIX / Version: 1.18rc1_3777: / Classification: refinement
EM software
IDNameVersionCategory
4Gctf1.06CTF correction
7PHENIX1.18model fitting
9PHENIX1.18model refinement
10Coot0.9model refinement
11RELION3initial Euler assignment
12RELION3final Euler assignment
13RELION3classification
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 406522
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23278 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
Atomic model buildingPDB-ID: 4YBB

4ybb


Accession code: 4YBB / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01537148
ELECTRON MICROSCOPYf_angle_d1.81755073
ELECTRON MICROSCOPYf_dihedral_angle_d17.90213682
ELECTRON MICROSCOPYf_chiral_restr0.186964
ELECTRON MICROSCOPYf_plane_restr0.0143339

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