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 7YLA | pdb_00007yla

Cryo-EM structure of 50S-HflX complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7YLA

This is version 1.1 of the entry. See complete history. 

Literature

Cryo-EM Structure of the 50S-HflX Complex Reveals a Novel Mechanism of Antibiotic Resistance in E. coli

Wu, D., Dai, Y., Gao, N.

(2022) bioRxiv 

Macromolecule Content 

  • Total Structure Weight: 1,400.15 kDa 
  • Atom Count: 93,732 
  • Modeled Residue Count: 6,769 
  • Deposited Residue Count: 6,804 
  • Unique protein chains: 30
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GTPase HflXA [auth 6]426Escherichia coliMutation(s): 0 
Gene Names: hflX, b4173, JW4131
UniProt
Find proteins for P25519 (Escherichia coli (strain K12))
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Go to UniProtKB:  P25519
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UniProt GroupP25519
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth K]271Escherichia coliMutation(s): 0 
Gene Names: rplB, EAZG_04115
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth L]209Escherichia coliMutation(s): 0 
Gene Names: 
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

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Find proteins for C3SQU2 (Escherichia coli)
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth M]201Escherichia coliMutation(s): 0 
Gene Names: rplD, eryA, b3319, JW3281
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Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 7
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50S ribosomal protein L5G [auth N]177Escherichia coliMutation(s): 0 
Gene Names: rplE, b3308, JW3270
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Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 8
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50S ribosomal protein L6H [auth O]176Escherichia coliMutation(s): 0 
Gene Names: rplF
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Entity ID: 9
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50S ribosomal protein L9I [auth P]149Escherichia coliMutation(s): 0 
Gene Names: rplI, b4203, JW4161
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Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 10
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50S ribosomal protein L11J [auth Q]134Escherichia coliMutation(s): 0 
Gene Names: rplK, relC, b3983, JW3946
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50S ribosomal protein L13K [auth R]142Escherichia coliMutation(s): 0 
Gene Names: rplM, b3231, JW3200
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Entity ID: 12
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50S ribosomal protein L14L [auth S]122Escherichia coliMutation(s): 0 
Gene Names: rplN
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50S ribosomal protein L15M [auth T]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplO
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Entity ID: 14
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50S ribosomal protein L16N [auth U]136Escherichia coliMutation(s): 0 
Gene Names: rplP, b3313, JW3275
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Entity ID: 15
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50S ribosomal protein L17O [auth V]120Escherichia coliMutation(s): 0 
Gene Names: rplQ, EAXG_02993
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Entity ID: 16
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50S ribosomal protein L18P [auth W]116Escherichia coliMutation(s): 0 
Gene Names: rplR, b3304, JW3266
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Entity ID: 17
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50S ribosomal protein L19Q [auth X]114Escherichia coliMutation(s): 0 
Gene Names: rplS, b2606, JW2587
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Entity ID: 18
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50S ribosomal protein L20R [auth Y]117Escherichia coliMutation(s): 0 
Gene Names: rplT, pdzA, b1716, JW1706
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L21S [auth Z]103Escherichia coliMutation(s): 0 
Gene Names: rplU, b3186, JW3153
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22T [auth a]110Escherichia coliMutation(s): 0 
Gene Names: rplV, eryB, b3315, JW3277
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23U [auth b]93Escherichia coliMutation(s): 0 
Gene Names: rplW, b3318, JW3280
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Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth c]102Escherichia coliMutation(s): 0 
Gene Names: rplX, ECJG_02968
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L25W [auth d]94Escherichia coliMutation(s): 0 
Gene Names: rplY, b2185, JW2173
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27X [auth e]75Escherichia coliMutation(s): 0 
Gene Names: rpmA, b3185, JW3152
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Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Y [auth f]77Escherichia coliMutation(s): 0 
Gene Names: rpmB, b3637, JW3612
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Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Z [auth g]62Escherichia coliMutation(s): 0 
Gene Names: rpmC, b3312, JW3274
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Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AA [auth h]58Escherichia coliMutation(s): 0 
Gene Names: rpmD, b3302, JW3264
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Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BA [auth i]56Escherichia coliMutation(s): 0 
Gene Names: rpmF, HMPREF9536_00655
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L33CA [auth j]50Escherichia coliMutation(s): 0 
Gene Names: rpmG, b3636, JW3611
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Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L34DA [auth k]46Escherichia coliMutation(s): 0 
Gene Names: rpmH, rimA, ssaF, b3703, JW3680
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Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35EA [auth l]64Escherichia coliMutation(s): 0 
Gene Names: rpmI, b1717, JW1707
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Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FA [auth m]38Escherichia coliMutation(s): 0 
Gene Names: rpmJ, b3299, JW3261
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Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 2
MoleculeChains LengthOrganismImage
Escherichia coli strain K-12 substr. MG1655_TMP32XR1 chromosome, complete genomeB [auth I]2,904Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth J]118Escherichia coli
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Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
(Subject of Investigation/LOI)

Query on GNP


Download:Ideal Coordinates CCD File
GA [auth 6]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN


Download:Ideal Coordinates CCD File
LA [auth m]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG


Download:Ideal Coordinates CCD File
HA [auth 6],
IA [auth K],
KA [auth L]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
(Subject of Investigation/LOI)

Query on NA


Download:Ideal Coordinates CCD File
JA [auth K]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31725007

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-04
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references