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- PDB-7yla: Cryo-EM structure of 50S-HflX complex -

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Basic information

Entry
Database: PDB / ID: 7yla
TitleCryo-EM structure of 50S-HflX complex
Components
  • (50S ribosomal protein ...) x 29
  • 5S rRNA
  • Escherichia coli strain K-12 substr. MG1655_TMP32XR1 chromosome, complete genome
  • GTPase HflX
KeywordsRIBOSOME / HflX
Function / homology
Function and homology information


ribosome disassembly / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination ...ribosome disassembly / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / translation repressor activity / ribosome assembly / rescue of stalled ribosome / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / transferase activity / response to heat / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
HflX, C-terminal domain / HflX C-terminal domain / GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. ...HflX, C-terminal domain / HflX C-terminal domain / GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / EF-G domain III/V-like / Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / 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 L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L36 signature. / 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 L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L16 / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / GTPase HflX / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsDamu, W. / Ning, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31725007 China
CitationJournal: Biorxiv / Year: 2022
Title: Cryo-EM Structure of the 50S-HflX Complex Reveals a Novel Mechanism of Antibiotic Resistance in E. coli
Authors: Wu, D. / Dai, Y. / Gao, N.
History
DepositionJul 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
6: GTPase HflX
I: Escherichia coli strain K-12 substr. MG1655_TMP32XR1 chromosome, complete genome
J: 5S rRNA
K: 50S ribosomal protein L2
L: 50S ribosomal protein L3
M: 50S ribosomal protein L4
N: 50S ribosomal protein L5
O: 50S ribosomal protein L6
P: 50S ribosomal protein L9
Q: 50S ribosomal protein L11
R: 50S ribosomal protein L13
S: 50S ribosomal protein L14
T: 50S ribosomal protein L15
U: 50S ribosomal protein L16
V: 50S ribosomal protein L17
W: 50S ribosomal protein L18
X: 50S ribosomal protein L19
Y: 50S ribosomal protein L20
Z: 50S ribosomal protein L21
a: 50S ribosomal protein L22
b: 50S ribosomal protein L23
c: 50S ribosomal protein L24
d: 50S ribosomal protein L25
e: 50S ribosomal protein L27
f: 50S ribosomal protein L28
g: 50S ribosomal protein L29
h: 50S ribosomal protein L30
i: 50S ribosomal protein L32
j: 50S ribosomal protein L33
k: 50S ribosomal protein L34
l: 50S ribosomal protein L35
m: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,400,14938
Polymers1,399,46532
Non-polymers6846
Water00
1


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

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Components

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Protein , 1 types, 1 molecules 6

#1: Protein GTPase HflX / GTP-binding protein HflX


Mass: 48362.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hflX, b4173, JW4131 / Production host: Escherichia coli (E. coli) / References: UniProt: P25519

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RNA chain , 2 types, 2 molecules IJ

#2: RNA chain Escherichia coli strain K-12 substr. MG1655_TMP32XR1 chromosome, complete genome / 23S rRNA


Mass: 941612.375 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: 937521852
#3: RNA chain 5S rRNA


Mass: 38177.762 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: 1727529157

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50S ribosomal protein ... , 29 types, 29 molecules KLMNOPQRSTUVWXYZabcdefghijklm

#4: Protein 50S ribosomal protein L2


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, EAZG_04115 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LPI5
#5: Protein 50S ribosomal protein L3


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, rplC_1, A5U30_004554, A6592_25805, A8499_003334, A8502_004021, A9X72_02175, AAG43_004444, AAS29_002160, ACN68_01905, ACN81_25530, ACU57_20950, AF998_005044, AM464_09230, APX88_16065, ...Gene: rplC, rplC_1, A5U30_004554, A6592_25805, A8499_003334, A8502_004021, A9X72_02175, AAG43_004444, AAS29_002160, ACN68_01905, ACN81_25530, ACU57_20950, AF998_005044, AM464_09230, APX88_16065, AT335_004245, AT845_004376, AW118_24910, AW119_26720, AWP47_12635, B6R12_002805, B6R15_004067, B6R31_004966, B6R48_005033, B6R87_004943, BANRA_04330, BANRA_04478, BEA19_23435, BER14_25200, BF481_004928, BG944_001135, BGM66_003591, BHS81_19845, BJI68_08665, BJJ90_02115, BK292_20515, BK383_24635, BKL28_004541, BLM69_000042, BMC79_004417, BMT49_24970, BMT50_12205, BMT91_20080, BN17_32541, BO068_004021, BOB65_004252, BOH76_10300, BON63_16650, BON64_02020, BON65_18050, BON66_26160, BON67_18880, BON68_24750, BON69_09885, BON70_00130, BON71_23175, BON72_13515, BON73_23855, BON74_04615, BON75_18755, BON76_15795, BON77_05670, BON78_22665, BON79_17330, BON80_14605, BON81_00485, BON82_23230, BON83_10090, BON84_09820, BON86_14480, BON87_22970, BON88_17700, BON89_16080, BON90_18925, BON91_16820, BON92_01280, BON93_00960, BON94_10910, BON95_01970, BON96_04520, BON97_10055, BON98_13405, BR158_003792, BR331_19070, BRV02_004595, BRV34_003968, BRV41_004356, BSR05_22800, BTB68_004354, BTQ06_10700, BUO55_004695, BvCmsF30A_00536, BvCmsHHP019_04150, BvCmsHHP056_02722, BvCmsKKP036_04791, BvCmsKKP061_03032, BvCmsKSNP073_02074, BVL39_09465, BXT93_05465, BZL69_26040, C0P57_002670, C1Q91_004902, C2121_004160, C2M16_25395, C2R31_004635, C2U48_16885, C3F40_19710, C5N07_23480, C5Y87_24355, C9114_23900, C9160_24410, C9E67_02715, C9Z68_22645, CA593_09640, CCS08_00225, CCV12_002919, CDC27_17755, CDL36_25500, CDL37_18685, CF22_004847, CG831_003651, CHM61_002989, CIG67_10665, CO706_15295, CQ986_004879, CQB02_00720, CR538_02410, CR539_21910, CR628_001368, CSE52_004332, CTR35_003632, CV83915_02778, CWS33_24950, CX938_003833, CXJ73_004407, CY655_21330, D0X26_24590, D1H34_002944, D3822_13385, D3C88_31160, D3G36_23040, D3Y67_24485, D4N09_20265, D4U49_16240, D9D43_22540, D9D77_24765, D9E34_23515, D9E49_05250, D9H94_20740, D9J03_20145, D9J61_16745, DAH17_20625, DAH18_25830, DAH19_23775, DAH20_24960, DAH21_04325, DAH22_07570, DAH23_26045, DAH24_26530, DAH25_10220, DAH26_26195, DAH27_08515, DAH28_09130, DAH29_12635, DAH30_24525, DAH31_24575, DAH32_04050, DAH33_05990, DAH34_23375, DAH35_26770, DAH36_23945, DAH37_14780, DAH38_04660, DAH40_11295, DAH41_02685, DAH42_05785, DAH43_07620, DAH45_06625, DAH46_07610, DAH47_06860, DAH48_25915, DAH49_06250, DAH50_22825, DD762_23640, DEN86_25710, DEN87_25115, DEN88_25025, DEN89_26920, DEN90_26120, DEN91_25670, DEN92_25260, DEN93_25395, DEN94_25060, DEN95_25535, DEN96_24490, DEN97_24555, DEN98_24370, DEN99_24050, DEO00_23745, DEO01_24140, DEO02_24550, DEO03_23465, DEO04_24850, DEO05_24720, DEO06_25035, DEO07_25275, DEO08_24815, DEO09_24800, DEO10_24835, DEO11_24485, DEO12_25760, DEO13_24900, DEO14_24930, DEO15_25560, DEO17_25290, DEO19_25310, DEO20_25430, DIV22_15165, DKP82_26155, DM870_23850, DN627_24275, DNQ45_03850, DNX30_25385, DRW19_24990, DS732_24355, DTL43_20905, DTL90_24785, DTM45_24460, DU321_12095, DXT69_23845, DXT70_20105, DXT71_20625, DXT73_21180, E0I42_22285, E2112_22050, E2113_03705, E2114_23425, E2115_22225, E2116_22695, E2117_23015, E2118_22205, E2119_19545, E2120_23465, E2121_21545, E2122_18945, E2123_21645, E2124_22245, E2125_23050, E2127_22005, E2128_19230, E2129_22280, E2130_23045, E2131_16935, E2132_21170, E2133_20125, E2134_21975, E2135_06090, E2136_22520, E2646_17875, E3N34_07255, E3O05_13890, E4K51_21585, E4T14_17190, E4T84_22775, E5H86_24430, E5M02_22195, E5P22_10575, E5P23_18270, E5P24_20790, E5P25_23480, E5P26_15700, E5P27_18105, E5P28_20780, E5P29_17690, E5P30_23040, E5P31_16840, E5P32_11705, E5P33_08980, E5P34_20380, E5P35_16020, E5P36_06820, E5P37_20795, E5P39_20305, E5P40_15190, E5P41_17280, E5P42_07455, E5P43_17755, E5P44_19020, E5P45_14030, E5P46_16940, E5P47_16665, E5P48_15985, E5P49_19740, E5P50_20825, E5P51_15750, E5P52_20390, E5S34_21770, E5S35_22550, E5S36_21060, E5S38_21955, E5S39_21710, E5S42_21790, E5S43_21540, E5S44_22800, E5S45_22935, E5S46_21670, E5S47_23275, E5S48_23215, E5S51_20910, E5S52_23140, E5S53_22850, E5S54_24660, E5S55_22910, E5S56_23115, E5S57_20250, E5S58_20935, E5S59_22515, E5S61_22770, E5S62_22400, E6C80_04260, E6D34_21665, EA239_22885, EA435_23125, EAI46_07570, EAN77_23430, EAX79_10805, EBP16_21780, EC1094V2_335, EC95NR1_02711, ECs4185, ED648_20425, EHD79_24145, EI021_21125, EIA08_24050, EIZ93_12375, EKI52_17570, EL79_0396, EL80_0388, ELT16_22425, ELT17_22345, ELT20_19075, ELT21_19060, ELT22_22590, ELT23_23200, ELT24_21815, ELT25_21770, ELT26_21745, ELT27_21655, ELT28_22740, ELT29_23005, ELT30_21030, ELT31_10320, ELT32_22730, ELT33_23515, ELT34_21725, ELT35_21180, ELT36_21870, ELT38_22650, ELT39_22215, ELT40_22100, ELT41_20840, ELT44_23170, ELT45_22690, ELT46_22780, ELT48_23015, ELT49_22970, ELT50_22965, ELT51_23840, ELT52_22220, ELT54_08510, ELT55_20145, ELT56_22890, ELT58_22145, ELT59_22310, ELT60_23010, ELT61_22580, ELT63_20870, ELT72_22275, ELU07_18705, ELU82_21805, ELU83_22925, ELU85_15865, ELU88_22880, ELU89_17475, ELU90_22325, ELU91_21450, ELU94_19155, ELU95_22685, ELU96_23485, ELU97_23540, ELU98_18150, ELU99_24045, ELV00_23405, ELV01_23770, ELV02_22800, ELV03_22315, ELV04_22810, ELV05_20095, ELV07_23660, ELV08_15755, ELV09_19390, ELV10_17970, ELV11_24730, ELV12_18320, ELV13_17640, ELV15_19655, ELV16_22775, ELV20_22490, ELV21_17705, ELV22_19090, ELV23_23300, ELV26_24050, ELV28_23020, ELV29_21190, ELV40_23840, ELX48_21575, ELX61_21805, ELX66_23305, ELX68_21395, ELX69_24375, ELX76_23035, ELX79_21270, ELX85_16835, ELX96_16900, ELY02_08085, ELY31_21655, ELY32_12770, ELY36_23250, ELY39_19505, ELY41_18815, ELY48_23255, EN85_004347, EPS76_07120, ERS085406_04388, ERS139208_04336, EWK56_25090, ExPECSC038_03638, EXX13_24635, EYV17_11500, EYV18_18495, EYX47_21135, F0L67_25410, F2N20_22060, F2N31_23540, F3N40_22270, F7F11_22630, F7N46_23915, F9413_21140, F9461_25560, F9B07_24590, F9S83_19085, F9V24_19050, F9X20_02055, FA849_13265, FA868_22840, FDM60_20745, FE584_05435, FE587_06325, FEJ01_22420, FEL34_20830, FFF58_25360, FGG80_25040, FHD44_21360, FHO90_04645, FHQ91_21910, FIJ20_21100, FJQ40_18400, FJQ51_22090, FJQ53_22820, FKO60_25730, FOI11_019165, FOI11_04015, FPI65_20400, FPJ29_20960, FPS11_25335, FQF29_19275, FV293_22370, FVB16_04965, FY127_21635, FZC17_14865, FZN31_02540, FZU14_21915, G3565_26410, G3813_004621, G3V95_19940, G3W53_21050, G4A38_21605, G4A47_20875, G5603_24680, G7630_004348, G9448_16980, GAI66_20425, GAI89_24735, GAJ12_24625, GAJ26_22105, GF147_24610, GF699_19830, GFY34_22805, GIB53_19305, GJ11_21480, GJO56_22830, GKF66_21640, GKF89_18565, GNW61_16725, GNZ05_25890, GOP25_22800, GP711_23400, GP944_18885, GP954_00850, GP965_04390, GP975_01280, GP979_01910, GQA06_03855, GQM04_10660, GQM13_25295, GQM21_11325, GQN34_23360, GQW07_21455, GQW68_22815, GQW80_23060, GRC73_21655, GRO95_20720, GRW05_09155, GRW24_04660, GRW56_00390, GRW57_03445, GSM54_23235, GSY44_20095, GTP88_23085, GUC01_21275, GUI33_20140, H0O37_13895, H0O39_19195, H0O51_24830, H0O53_20735, H0O72_19510, HCQ42_003930, HEP30_018730, HEP34_004752, HHH44_004517, HI055_004158, HIE29_005205, HIN64_004180, HJ942_004420, HJQ60_004993, HJS37_004719, HJU54_004673, HKA49_005017, HL563_21455, HL601_22260, HLV18_23245, HLX92_09980, HLZ50_22085, HmCms169_03512, HMJ82_26095, HMU06_24615, HMV95_19700, HMW38_23200, HNC36_20285, HNC59_23020, HNC66_24755, HNC99_22445, HND12_26325, HV109_02095, HV146_21765, HV209_14620, HVV39_09360, HVW04_17440, HVW19_19380, HVW43_18575, HVX31_01875, HVX32_19140, HVY77_02080, HVZ29_19190, HVZ30_01960, HVZ71_02265, HX136_02100, I6H00_20830, I6H01_10815, IA00_004106, IFB95_004824, IH768_14175, IH772_23920, IT029_004935, J0541_004415, J4S20_004784, J5U05_004069, JE86ST02C_37880, JE86ST05C_37910, JFD_03731, JNP96_25400, NCTC10082_02821, NCTC10089_00484, NCTC10090_03509, NCTC10418_00672, NCTC10429_01075, NCTC10764_03845, NCTC10767_01498, NCTC10865_00640, NCTC10974_00531, NCTC11126_02752, NCTC11341_01907, NCTC12950_00461, NCTC13127_00766, NCTC13148_03458, NCTC13216_01370, NCTC4450_02457, NCTC7927_00533, NCTC7928_02535, NCTC8008_05364, NCTC8009_01491, NCTC8179_05923, NCTC8333_00471, NCTC8450_04919, NCTC8500_00315, NCTC8621_00490, NCTC8959_03279, NCTC8960_03052, NCTC8985_04963, NCTC9036_00521, NCTC9037_00645, NCTC9044_01378, NCTC9077_00586, NCTC9081_00899, NCTC9111_00849, NCTC9117_00738, NCTC9702_00519, NCTC9706_02719, NCTC9775_03984, NCTC9777_01873, NCTC9962_06779, ND22_005138, RG28_21705, SAMEA3472044_01144, SAMEA3472056_05429, SAMEA3472147_04274, SAMEA3751407_00042, SAMEA3752557_01970, SAMEA3753106_04616, TUM18780_04180, WP4S18E07_04240, WR15_19700, XU56_003421
Production host: Escherichia coli (E. coli) / References: UniProt: C3SQU2
#6: Protein 50S ribosomal protein L4 / Large ribosomal subunit protein uL4


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
#7: Protein 50S ribosomal protein L5 / Large ribosomal subunit protein uL5


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, b3308, JW3270 / Production host: Escherichia coli (E. coli) / References: UniProt: P62399
#8: Protein 50S ribosomal protein L6


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


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
#10: Protein 50S ribosomal protein L11 / Large ribosomal subunit protein uL11


Mass: 14020.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplK, relC, b3983, JW3946 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7J7
#11: Protein 50S ribosomal protein L13 / Large ribosomal subunit protein uL13


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
#12: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: C3SQZ2
#13: Protein 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 K-12 (bacteria) / Gene: rplO / Production host: Escherichia coli (E. coli) / References: UniProt: P02413
#14: 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
#15: Protein 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, EAXG_02993 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LC97
#16: Protein 50S ribosomal protein L18 / Large ribosomal subunit protein uL18


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
#17: Protein 50S ribosomal protein L19 / Large ribosomal subunit protein bL19


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, b2606, JW2587 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7K6
#18: Protein 50S ribosomal protein L20 / 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) / Gene: rplT, pdzA, b1716, JW1706 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L3
#19: Protein 50S ribosomal protein L21 / Large ribosomal subunit protein bL21


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, b3186, JW3153 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG48
#20: Protein 50S ribosomal protein L22 / Large ribosomal subunit protein uL22


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, eryB, b3315, JW3277 / Production host: Escherichia coli (E. coli) / References: UniProt: P61175
#21: Protein 50S ribosomal protein L23 / 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) / Gene: rplW, b3318, JW3280 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#22: Protein 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, ECJG_02968 / Production host: Escherichia coli (E. coli) / References: UniProt: F4TL32
#23: Protein 50S ribosomal protein L25 / 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, b2185, JW2173 / Production host: Escherichia coli (E. coli) / References: UniProt: P68919
#24: Protein 50S ribosomal protein L27 / Large ribosomal subunit protein bL27


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, b3185, JW3152 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L8
#25: Protein 50S ribosomal protein L28 / Large ribosomal subunit protein bL28


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, b3637, JW3612 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7M2
#26: Protein 50S ribosomal protein L29 / Large ribosomal subunit protein uL29


Mass: 7155.267 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmC, b3312, JW3274 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7M6
#27: 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
#28: 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, HMPREF9536_00655 / Production host: Escherichia coli (E. coli) / References: UniProt: D7XI28
#29: Protein/peptide 50S ribosomal protein L33 / Large ribosomal subunit protein bL33


Mass: 5814.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmG, b3636, JW3611 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7N9
#30: Protein/peptide 50S ribosomal protein L34 / Large ribosomal subunit protein bL34


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, rimA, ssaF, b3703, JW3680 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7P5
#31: Protein 50S ribosomal protein L35 / Large ribosomal subunit protein bL35 / Ribosomal protein A


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, b1717, JW1707 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#32: Protein/peptide 50S ribosomal protein L36 / Large ribosomal subunit protein bL36-A / Ribosomal protein B


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, b3299, JW3261 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Q6

-
Non-polymers , 4 types, 6 molecules

#33: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#34: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Cryo-EM structure of 50S-HflXCOMPLEX#1-#320RECOMBINANT
250S ribosomeCOMPLEX#2-#321NATURAL
3GTPase HflXCOMPLEX#11RECOMBINANT
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

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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: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 1200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 1.8 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93913 / Symmetry type: POINT

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