7YLA

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


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 


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase HflXA [auth 6]426Escherichia coliMutation(s): 0 
Gene Names: hflXb4173JW4131
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth K]271Escherichia coliMutation(s): 0 
Gene Names: rplBEAZG_04115
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth L]209Escherichia coliMutation(s): 0 
Gene Names: 
rplCrplC_1A5U30_004554A6592_25805A8499_003334A8502_004021A9X72_02175AAG43_004444AAS29_002160ACN68_01905ACN81_25530ACU57_20950AF998_005044AM464_09230APX88_16065AT335_004245AT845_004376AW118_24910AW119_26720AWP47_12635B6R12_002805B6R15_004067B6R31_004966B6R48_005033B6R87_004943BANRA_04330BANRA_04478BEA19_23435BER14_25200BF481_004928BG944_001135BGM66_003591BHS81_19845BJI68_08665BJJ90_02115BK292_20515BK383_24635BKL28_004541BLM69_000042BMC79_004417BMT49_24970BMT50_12205BMT91_20080BN17_32541BO068_004021BOB65_004252BOH76_10300BON63_16650BON64_02020BON65_18050BON66_26160BON67_18880BON68_24750BON69_09885BON70_00130BON71_23175BON72_13515BON73_23855BON74_04615BON75_18755BON76_15795BON77_05670BON78_22665BON79_17330BON80_14605BON81_00485BON82_23230BON83_10090BON84_09820BON86_14480BON87_22970BON88_17700BON89_16080BON90_18925BON91_16820BON92_01280BON93_00960BON94_10910BON95_01970BON96_04520BON97_10055BON98_13405BR158_003792BR331_19070BRV02_004595BRV34_003968BRV41_004356BSR05_22800BTB68_004354BTQ06_10700BUO55_004695BvCmsF30A_00536BvCmsHHP019_04150BvCmsHHP056_02722BvCmsKKP036_04791BvCmsKKP061_03032BvCmsKSNP073_02074BVL39_09465BXT93_05465BZL69_26040C0P57_002670C1Q91_004902C2121_004160C2M16_25395C2R31_004635C2U48_16885C3F40_19710C5N07_23480C5Y87_24355C9114_23900C9160_24410C9E67_02715C9Z68_22645CA593_09640CCS08_00225CCV12_002919CDC27_17755CDL36_25500CDL37_18685CF22_004847CG831_003651CHM61_002989CIG67_10665CO706_15295CQ986_004879CQB02_00720CR538_02410CR539_21910CR628_001368CSE52_004332CTR35_003632CV83915_02778CWS33_24950CX938_003833CXJ73_004407CY655_21330D0X26_24590D1H34_002944D3822_13385D3C88_31160D3G36_23040D3Y67_24485D4N09_20265D4U49_16240D9D43_22540D9D77_24765D9E34_23515D9E49_05250D9H94_20740D9J03_20145D9J61_16745DAH17_20625DAH18_25830DAH19_23775DAH20_24960DAH21_04325DAH22_07570DAH23_26045DAH24_26530DAH25_10220DAH26_26195DAH27_08515DAH28_09130DAH29_12635DAH30_24525DAH31_24575DAH32_04050DAH33_05990DAH34_23375DAH35_26770DAH36_23945DAH37_14780DAH38_04660DAH40_11295DAH41_02685DAH42_05785DAH43_07620DAH45_06625DAH46_07610DAH47_06860DAH48_25915DAH49_06250DAH50_22825DD762_23640DEN86_25710DEN87_25115DEN88_25025DEN89_26920DEN90_26120DEN91_25670DEN92_25260DEN93_25395DEN94_25060DEN95_25535DEN96_24490DEN97_24555DEN98_24370DEN99_24050DEO00_23745DEO01_24140DEO02_24550DEO03_23465DEO04_24850DEO05_24720DEO06_25035DEO07_25275DEO08_24815DEO09_24800DEO10_24835DEO11_24485DEO12_25760DEO13_24900DEO14_24930DEO15_25560DEO17_25290DEO19_25310DEO20_25430DIV22_15165DKP82_26155DM870_23850DN627_24275DNQ45_03850DNX30_25385DRW19_24990DS732_24355DTL43_20905DTL90_24785DTM45_24460DU321_12095DXT69_23845DXT70_20105DXT71_20625DXT73_21180E0I42_22285E2112_22050E2113_03705E2114_23425E2115_22225E2116_22695E2117_23015E2118_22205E2119_19545E2120_23465E2121_21545E2122_18945E2123_21645E2124_22245E2125_23050E2127_22005E2128_19230E2129_22280E2130_23045E2131_16935E2132_21170E2133_20125E2134_21975E2135_06090E2136_22520E2646_17875E3N34_07255E3O05_13890E4K51_21585E4T14_17190E4T84_22775E5H86_24430E5M02_22195E5P22_10575E5P23_18270E5P24_20790E5P25_23480E5P26_15700E5P27_18105E5P28_20780E5P29_17690E5P30_23040E5P31_16840E5P32_11705E5P33_08980E5P34_20380E5P35_16020E5P36_06820E5P37_20795E5P39_20305E5P40_15190E5P41_17280E5P42_07455E5P43_17755E5P44_19020E5P45_14030E5P46_16940E5P47_16665E5P48_15985E5P49_19740E5P50_20825E5P51_15750E5P52_20390E5S34_21770E5S35_22550E5S36_21060E5S38_21955E5S39_21710E5S42_21790E5S43_21540E5S44_22800E5S45_22935E5S46_21670E5S47_23275E5S48_23215E5S51_20910E5S52_23140E5S53_22850E5S54_24660E5S55_22910E5S56_23115E5S57_20250E5S58_20935E5S59_22515E5S61_22770E5S62_22400E6C80_04260E6D34_21665EA239_22885EA435_23125EAI46_07570EAN77_23430EAX79_10805EBP16_21780EC1094V2_335EC95NR1_02711ECs4185ED648_20425EHD79_24145EI021_21125EIA08_24050EIZ93_12375EKI52_17570EL79_0396EL80_0388ELT16_22425ELT17_22345ELT20_19075ELT21_19060ELT22_22590ELT23_23200ELT24_21815ELT25_21770ELT26_21745ELT27_21655ELT28_22740ELT29_23005ELT30_21030ELT31_10320ELT32_22730ELT33_23515ELT34_21725ELT35_21180ELT36_21870ELT38_22650ELT39_22215ELT40_22100ELT41_20840ELT44_23170ELT45_22690ELT46_22780ELT48_23015ELT49_22970ELT50_22965ELT51_23840ELT52_22220ELT54_08510ELT55_20145ELT56_22890ELT58_22145ELT59_22310ELT60_23010ELT61_22580ELT63_20870ELT72_22275ELU07_18705ELU82_21805ELU83_22925ELU85_15865ELU88_22880ELU89_17475ELU90_22325ELU91_21450ELU94_19155ELU95_22685ELU96_23485ELU97_23540ELU98_18150ELU99_24045ELV00_23405ELV01_23770ELV02_22800ELV03_22315ELV04_22810ELV05_20095ELV07_23660ELV08_15755ELV09_19390ELV10_17970ELV11_24730ELV12_18320ELV13_17640ELV15_19655ELV16_22775ELV20_22490ELV21_17705ELV22_19090ELV23_23300ELV26_24050ELV28_23020ELV29_21190ELV40_23840ELX48_21575ELX61_21805ELX66_23305ELX68_21395ELX69_24375ELX76_23035ELX79_21270ELX85_16835ELX96_16900ELY02_08085ELY31_21655ELY32_12770ELY36_23250ELY39_19505ELY41_18815ELY48_23255EN85_004347EPS76_07120ERS085406_04388ERS139208_04336EWK56_25090ExPECSC038_03638EXX13_24635EYV17_11500EYV18_18495EYX47_21135F0L67_25410F2N20_22060F2N31_23540F3N40_22270F7F11_22630F7N46_23915F9413_21140F9461_25560F9B07_24590F9S83_19085F9V24_19050F9X20_02055FA849_13265FA868_22840FDM60_20745FE584_05435FE587_06325FEJ01_22420FEL34_20830FFF58_25360FGG80_25040FHD44_21360FHO90_04645FHQ91_21910FIJ20_21100FJQ40_18400FJQ51_22090FJQ53_22820FKO60_25730FOI11_019165FOI11_04015FPI65_20400FPJ29_20960FPS11_25335FQF29_19275FV293_22370FVB16_04965FY127_21635FZC17_14865FZN31_02540FZU14_21915G3565_26410G3813_004621G3V95_19940G3W53_21050G4A38_21605G4A47_20875G5603_24680G7630_004348G9448_16980GAI66_20425GAI89_24735GAJ12_24625GAJ26_22105GF147_24610GF699_19830GFY34_22805GIB53_19305GJ11_21480GJO56_22830GKF66_21640GKF89_18565GNW61_16725GNZ05_25890GOP25_22800GP711_23400GP944_18885GP954_00850GP965_04390GP975_01280GP979_01910GQA06_03855GQM04_10660GQM13_25295GQM21_11325GQN34_23360GQW07_21455GQW68_22815GQW80_23060GRC73_21655GRO95_20720GRW05_09155GRW24_04660GRW56_00390GRW57_03445GSM54_23235GSY44_20095GTP88_23085GUC01_21275GUI33_20140H0O37_13895H0O39_19195H0O51_24830H0O53_20735H0O72_19510HCQ42_003930HEP30_018730HEP34_004752HHH44_004517HI055_004158HIE29_005205HIN64_004180HJ942_004420HJQ60_004993HJS37_004719HJU54_004673HKA49_005017HL563_21455HL601_22260HLV18_23245HLX92_09980HLZ50_22085HmCms169_03512HMJ82_26095HMU06_24615HMV95_19700HMW38_23200HNC36_20285HNC59_23020HNC66_24755HNC99_22445HND12_26325HV109_02095HV146_21765HV209_14620HVV39_09360HVW04_17440HVW19_19380HVW43_18575HVX31_01875HVX32_19140HVY77_02080HVZ29_19190HVZ30_01960HVZ71_02265HX136_02100I6H00_20830I6H01_10815IA00_004106IFB95_004824IH768_14175IH772_23920IT029_004935J0541_004415J4S20_004784J5U05_004069JE86ST02C_37880JE86ST05C_37910JFD_03731JNP96_25400NCTC10082_02821NCTC10089_00484NCTC10090_03509NCTC10418_00672NCTC10429_01075NCTC10764_03845NCTC10767_01498NCTC10865_00640NCTC10974_00531NCTC11126_02752NCTC11341_01907NCTC12950_00461NCTC13127_00766NCTC13148_03458NCTC13216_01370NCTC4450_02457NCTC7927_00533NCTC7928_02535NCTC8008_05364NCTC8009_01491NCTC8179_05923NCTC8333_00471NCTC8450_04919NCTC8500_00315NCTC8621_00490NCTC8959_03279NCTC8960_03052NCTC8985_04963NCTC9036_00521NCTC9037_00645NCTC9044_01378NCTC9077_00586NCTC9081_00899NCTC9111_00849NCTC9117_00738NCTC9702_00519NCTC9706_02719NCTC9775_03984NCTC9777_01873NCTC9962_06779ND22_005138RG28_21705SAMEA3472044_01144SAMEA3472056_05429SAMEA3472147_04274SAMEA3751407_00042SAMEA3752557_01970SAMEA3753106_04616TUM18780_04180WP4S18E07_04240WR15_19700XU56_003421

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth M]201Escherichia coliMutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth N]177Escherichia coliMutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth O]176Escherichia coliMutation(s): 0 
Gene Names: rplF
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth P]149Escherichia coliMutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11J [auth Q]134Escherichia coliMutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13K [auth R]142Escherichia coliMutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14L [auth S]122Escherichia coliMutation(s): 0 
Gene Names: rplN
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15M [auth T]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplO
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16N [auth U]136Escherichia coliMutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17O [auth V]120Escherichia coliMutation(s): 0 
Gene Names: rplQEAXG_02993
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18P [auth W]116Escherichia coliMutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19Q [auth X]114Escherichia coliMutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20R [auth Y]117Escherichia coliMutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21S [auth Z]103Escherichia coliMutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22T [auth a]110Escherichia coliMutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23U [auth b]93Escherichia coliMutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth c]102Escherichia coliMutation(s): 0 
Gene Names: rplXECJG_02968
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25W [auth d]94Escherichia coliMutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27X [auth e]75Escherichia coliMutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Y [auth f]77Escherichia coliMutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Z [auth g]62Escherichia coliMutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AA [auth h]58Escherichia coliMutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BA [auth i]56Escherichia coliMutation(s): 0 
Gene Names: rpmFHMPREF9536_00655
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33CA [auth j]50Escherichia coliMutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34DA [auth k]46Escherichia coliMutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35EA [auth l]64Escherichia coliMutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FA [auth m]38Escherichia coliMutation(s): 0 
Gene Names: rpmJb3299JW3261
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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

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GA [auth 6]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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LA [auth m]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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HA [auth 6],
IA [auth K],
KA [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

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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

View Full Validation Report



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