4PNO

Escherichia coli Hfq-RNA complex at 0.97 A Resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Structure of an Escherichia coli Hfq:RNA complex at 0.97 angstrom resolution.

Schulz, E.C., Barabas, O.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1492-1497

  • DOI: 10.1107/S2053230X14020044
  • Primary Citation of Related Structures:  
    4PNO

  • PubMed Abstract: 

    • In bacteria, small RNAs (sRNAs) silence or activate target genes through base pairing with the mRNA, thereby modulating its translation. A central player in this process is the RNA chaperone Hfq, which facilitates the annealing of sRNAs with their target mRNAs ...

    In bacteria, small RNAs (sRNAs) silence or activate target genes through base pairing with the mRNA, thereby modulating its translation. A central player in this process is the RNA chaperone Hfq, which facilitates the annealing of sRNAs with their target mRNAs. Hfq has two RNA-binding surfaces that recognize A-rich and U-rich sequences, and is believed to bind an sRNA-mRNA pair simultaneously. However, how Hfq promotes annealing remains unclear. Here, the crystal structure of Escherichia coli Hfq is presented in complex with U6-RNA bound to its proximal binding site at 0.97 Å resolution, revealing the Hfq-RNA interaction in exceptional detail.

    Organizational Affiliation: 

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein HfqA72Escherichia coliMutation(s): 0 
Gene Names: 
hfq, BN17_41491, BU34_16545, ECs5148, LF82_0993, A6581_02980, A6592_09715, A6V01_16650, A8C65_01735, A9819_23875, A9P13_23645, A9R57_13690, A9X72_22810, AAW05_14615, AC067_05655, AC789_1c45860, ACN002_4398, ACN68_17970, ACN81_01555, ACU57_19145, ACU90_12775, AJ318_17360, AM270_14645, AM446_25205, AM464_15620, AM465_01995, AMK83_03565, AML07_13370, AML35_20850, APT94_02395, APU18_25480, APZ14_20385, ARC77_18135, AU473_28000, AUQ13_10455, AUS26_23815, AW059_20310, AW106_17090, AWB10_23575, AWE53_001885, AWF59_005725, AWG78_009705, AWP75_27270, AZZ83_002809, B6V57_24395, B7C53_13980, B9N33_15755, B9T59_10095, BANRA_00139, BANRA_00176, BANRA_02756, BANRA_02861, BB545_04045, BE963_12375, BER14_11560, BFD68_08600, BHF03_14290, BHF46_15770, BHJ80_02485, BHS81_24965, BHS87_23370, BIQ87_24055, BIU72_05950, BIZ41_02855, BJJ90_23305, BK292_24845, BK296_26410, BK334_08150, BK373_03285, BK375_06710, BK383_13085, BMA87_06185, BMT49_19335, BMT91_05635, BOH76_10880, BON63_12710, BON65_22460, BON66_25580, BON69_04835, BON71_15710, BON72_19735, BON75_25110, BON76_04130, BON83_17390, BON86_07250, BON87_01840, BON91_13125, BON92_18425, BON94_18215, BON95_14980, BON96_04075, BON98_15480, BTQ04_18280, BTQ06_07280, BUE81_24160, BvCms12BK_04170, BvCms2454_04357, BvCms28BK_05184, BvCms35BK_01961, BvCmsC61A_01682, BvCmsHHP001_00651, BvCmsHHP019_00837, BvCmsHHP056_01643, BvCmsKKP036_00106, BvCmsKKP061_03353, BvCmsKSNP073_03476, BvCmsKSNP081_01966, BvCmsKSNP120_00851, BvCmsKSP011_04672, BvCmsKSP024_01263, BvCmsKSP026_01545, BvCmsKSP045_02479, BvCmsKSP058_02575, BvCmsKSP067_03846, BvCmsKSP076_04392, BvCmsNSNP036_02337, BvCmsNSP006_05651, BvCmsNSP007_04866, BvCmsNSP047_02023, BvCmsNSP072_05317, BvCmsOUP014_01611, BvCmsSINP011_01446, BvCmsSINP022_02384, BvCmsSIP019_03100, BvCmsSIP044_02445, BVL39_04265, BW690_00560, BWI89_16315, BWP17_13460, BXT93_16395, BZL31_13090, BZL69_06765, C2M16_07300, C2U48_11650, C4K41_15900, C4M78_05650, C5715_23380, C5F72_23650, C5F73_05820, C5N07_07170, C5P01_11630, C5P44_18700, C6669_06540, C6B13_11605, C7235_22640, C7B02_22720, C7B06_19470, C7B07_19490, C7B08_13170, C7B18_21970, C9098_20170, C9114_00825, C9141_20360, C9160_19980, C9162_14305, C9201_17665, C9306_16035, C9E25_08130, C9E67_27590, C9Z03_11050, C9Z23_18495, C9Z28_08950, C9Z29_19815, C9Z37_19325, C9Z39_09965, C9Z43_18110, C9Z68_08580, C9Z70_21945, C9Z78_15760, C9Z89_19795, CA593_04950, CCZ14_19805, CCZ17_16445, CDC27_22665, CF006_04835, CG692_00205, CI641_014385, CI693_12805, CI694_17300, CIG45_09925, CJU63_24695, CJU64_24905, CMR93_01180, CO706_20795, COD30_21550, COD46_22225, CQB02_20430, CQP61_24625, CR538_23110, CR539_02810, CRD98_04140, CRE06_02220, CRJUMX01_550007, CRM83_17345, CRT43_25140, CRX46_11480, CSB64_24410, CT146_11350, CUB99_10530, CV83915_01857, CVH05_06830, CWM24_06280, CWS33_03540, D0X26_12940, D1912_13955, D2184_07725, D2185_07795, D3821_07060, D3C88_29195, D3M98_16415, D3O91_01560, D3P02_10130, D3Y67_00705, D4011_02185, D4023_24305, D4074_23020, D4628_06590, D4636_22460, D4638_06370, D4660_23075, D4718_16185, D4L91_22935, D4M06_23370, D4M76_01495, D4U49_22015, D4U85_22755, D5H35_20680, D5I97_22270, D6004_16415, D6C36_22875, D6D43_22955, D6T60_21940, D6T98_03800, D6W00_07645, D6X36_01210, D6X63_00480, D6X76_08925, D7K33_08080, D7K63_02145, D7K66_01495, D7W70_13015, D7Y10_19435, D7Z75_22410, D8Y65_09490, D9610_19230, D9C99_08635, D9D20_08270, D9D31_07900, D9D33_02675, D9D43_14570, D9D44_05770, D9D94_05545, D9E13_11950, D9E19_02065, D9E34_14865, D9E35_09765, D9E49_11815, D9E73_04405, D9F17_02025, D9F32_10410, D9F87_11810, D9G11_21475, D9G29_02210, D9G42_20200, D9G48_11610, D9G69_11260, D9G95_09230, D9H10_23475, D9H36_10495, D9H53_05295, D9H68_15695, D9H70_08700, D9H94_06305, D9I18_04380, D9I20_17985, D9I87_10900, D9I88_12145, D9I97_14630, D9J03_08455, D9J11_13485, D9J44_09415, D9J46_20870, D9J52_05785, D9J58_20445, D9J63_13380, D9J78_18895, D9K02_08605, D9K48_15160, D9K54_26500, D9L89_02140, D9L99_19735, D9S45_09245, D9X77_21425, D9X97_13455, D9Z28_12365, DAH18_07410, DAH26_05195, DAH30_09270, DAH32_17610, DAH34_17735, DAH37_06210, DAH43_08785, DB359_11850, DBQ99_23500, DD762_20790, DEN86_00555, DEN89_23340, DEN97_13950, DEO04_15040, DEO20_13760, DIV22_15570, DJ487_19990, DJ492_19600, DJ503_09195, DK132_01000, DL251_17245, DL257_13280, DL292_04280, DL326_12570, DL455_22085, DL479_09720, DL530_20025, DL545_22570, DL705_08055, DL800_29060, DL979_11460, DLT82_15060, DLU50_02130, DLU67_01045, DLU82_19930, DLW60_20490, DLW88_17915, DLX38_18940, DLX40_22295, DLY41_23715, DLY44_22350, DM102_09025, DM155_20465, DM267_22100, DM272_21920, DM280_21580, DM296_19415, DM382_18770, DM820_22735, DM962_21190, DM973_03290, DMC44_08075, DMI04_22150, DMI53_04230, DMO02_24505, DMY83_06235, DMZ50_17400, DN627_22590, DN660_13980, DN700_22760, DN703_23685, DN808_04115, DNB37_06840, DNC98_05575, DND79_22930, DNI21_07215, DNJ62_09600, DNK12_21295, DNQ45_06700, DNR35_19090, DNR41_18375, DNW42_15595, DNX19_17790, DNX30_17555, DOE35_23430, DOM23_20870, DOS18_22550, DOT81_15640, DOU81_22325, DOY22_05285, DOY56_08260, DOY61_22110, DOY67_18770, DP258_23185, DP265_18575, DP277_02580, DQE91_09030, DQF36_19875, DQF57_15710, DQF71_21270, DQF72_18915, DQG35_15630, DQO13_23520, DQP61_08495, DRP48_15920, DRW19_23370, DS143_20965, DS721_07060, DS732_02645, DS966_08170, DT034_15370, DTL43_02335, DTL90_17260, DTM10_04685, DTM45_20960, DTZ20_26580, DU309_07950, DU333_08305, DVB38_20785, DW236_18585, DXT69_21905, DXT71_04250, DXT73_07380, DXX80_015215, E0I42_01070, E0K84_22240, E0L04_15180, E2112_14650, E2119_06475, E2127_06870, E2128_01920, E2129_04000, E2134_14005, E2135_09650, E2148_16690, E2855_05256, E2863_05042, E4A44_09080, E4K51_09075, E4K55_08600, E4K59_02050, E4K60_10930, E4K61_05680, E5P22_06630, E5P24_09310, E5P28_02915, E5P37_09910, E5S42_20025, E5S56_11835, E5S58_08500, E5S61_21825, E5S62_12230, EA159_10720, EA164_20540, EA167_13160, EA184_15845, EA189_18120, EA191_15165, EA198_11805, EA200_16495, EA203_13040, EA213_12025, EA214_14465, EA218_07380, EA222_17920, EA223_01060, EA231_14455, EA232_12645, EA235_13940, EA239_16885, EA242_18850, EA245_16635, EA247_17700, EA250_13645, EA410_11515, EA429_17195, EA433_08650, EA434_08510, EA435_16510, EA834_13355, EAI42_08070, EAI46_08365, EAI52_08670, EAM59_16345, EAN70_16345, EAN77_04035, EAX79_02910, EB476_05855, EB509_04095, EB510_02700, EB515_02095, EB525_RS07235, EBA46_03070, EBA84_09220, EBJ06_01155, EBM08_18790, EC1094V2_4083, EC3234A_108c00180, EC3426_00507, EC382_18635, EC95NR1_03792, ECONIH1_24830, ECTO124_04522, ECTO6_04311, ED178_01135, ED225_08495, ED307_02400, ED600_08235, ED607_06830, ED611_08765, ED648_13775, ED903_06980, ED944_02095, EEA45_03660, EEP23_07460, EF082_10350, EF173_02090, EG075_07965, EG599_16905, EG796_08800, EG808_10255, EGC26_01550, EGT48_17780, EGU87_19900, EH186_16230, EH412_13960, EHD63_02095, EHD79_20030, EHH55_18940, EHJ36_13950, EHJ66_01155, EHV81_18915, EHV90_18405, EHW09_20325, EHX09_21120, EI021_09680, EI028_05160, EI032_02905, EI041_05000, EIA08_19995, EIA21_18645, EIZ93_17485, EJ366_20580, EJC75_20620, EKI52_12660, EL75_3993, EL79_4171, EL80_4086, ELT20_09145, ELT22_12100, ELT23_15080, ELT33_15105, ELT48_15240, ELT49_00905, ELU82_07795, ELU85_14515, ELU96_21560, ELV00_12045, ELV05_12875, ELV08_11380, ELV13_19755, ELV15_00985, ELV22_09115, ELV24_17275, ELV28_07685, ELX56_19320, ELX70_15675, ELX76_15750, ELX79_17070, ELX83_07055, ELY05_00535, ELY23_03665, ELY24_03205, ELY41_00530, ELY48_02805, ELY50_08385, EO241_14865, EPS76_03625, EPS91_15880, EPS94_17880, EPT01_09965, EPU41_23530, EQ820_09225, EQ823_13665, EQ825_10885, EQO00_23375, ERL57_16230, ERS085365_01202, ERS085366_02337, ERS085374_02966, ERS085379_04135, ERS085383_01581, ERS085386_00994, ERS085404_01377, ERS085406_00106, ERS085411_03208, ERS139211_03911, ERS150873_01318, ERS150876_03898, EST51_22870, EVY14_02170, EWK56_08685, EXM29_20675, ExPECSC019_02738, ExPECSC038_04681, ExPECSC065_03220, EXX06_20735, EXX13_20210, EXX23_18985, EXX24_09325, EXX53_17405, EXX55_21270, EXX71_14685, EXX78_19430, EXX87_19015, EYD11_20570, EYX82_10025, EYX99_04095, EYY27_20025, EYY34_13915, EYY78_08690, F1E13_09495, F1E19_03535, F7F00_14720, F7F11_04380, F7F18_09850, F7F23_18570, F7F26_20100, F7F29_02090, F7F56_08500, F7G01_00685, F7G03_07025, F9040_07485, F9225_22790, F9B07_06005, F9X20_07225, F9Z53_12890, F9Z74_03130, FAF34_023265, FE846_00275, FKO60_18280, FNJ67_23945, FNJ69_20100, FORC82_4319, FPI65_25680, FQ021_22065, FQ022_21790, FQ915_09970, FQR64_20860, FQU83_24145, FQZ46_21960, FRV13_14645, FTV90_07315, FTV92_15610, FTV93_15975, FV293_00855, FV295_12375, FV438_02260, FVB16_06390, FWK02_31065, FY127_03740, FZ043_02100, FZC17_09895, FZN06_22340, FZN26_04235, FZN30_05660, G3565_21795, G3V64_12550, G5603_09605, G5608_12375, G5616_05800, G5632_13660, G5668_17850, G5670_14890, G5675_06950, G5680_17175, G5686_17255, G5688_12950, G5696_13875, G5697_19765, GFU40_15085, GFU45_12570, GFU47_24140, GHR40_02600, GII67_18845, GIJ01_09530, GIY19_13285, GJ11_26175, GJ638_00715, GJD97_24910, GKE92_06895, GKE98_14005, GKF21_05745, GKF28_05010, GKF34_05805, GKF39_06470, GKF47_05805, GKF52_07960, GKF74_12900, GKF86_05490, GKF89_03445, GKG08_03650, GKG09_04440, GKG11_04445, GKG12_11665, GKG22_04445, GKG29_04445, GN312_12115, GNZ03_04890, GNZ05_12090, GP650_21105, GP654_08815, GP661_15910, GP662_06515, GP664_20715, GP666_16345, GP671_01325, GP678_11390, GP689_08280, GP698_02270, GP700_05720, GP711_17935, GP720_11570, GP727_04055, GP892_05540, GP912_07665, GP935_18170, GP950_01055, GP979_12070, GQA06_06285, GQA23_06890, GQA63_14700, GQA64_16110, GQE22_08115, GQE30_17840, GQE33_09245, GQE34_01705, GQE36_16410, GQE42_10415, GQE47_08780, GQE51_12530, GQE58_16055, GQE64_09115, GQE87_16250, GQE88_08575, GQE93_06705, GQF59_13905, GQL64_02200, GQM04_15810, GQM06_01925, GQM09_08015, GQM10_00825, GQM13_10750, GQM17_02090, GQM18_03810, GQM28_21740, GQN16_16315, GQN24_16735, GQN33_18120, GQS26_11040, GQY14_08900, GRW05_08875, GRW12_08130, GRW27_04355, GRW30_20640, GRW42_14605, GRW57_18725, GRW80_01325, GRW81_08400, GUB08_01700, GUB85_10765, GUB91_12735, GUB95_12395, GUC01_09045, GUC12_13425, GUC40_22145, GUI16_13115, GUI33_10855, GZS12_21090, HmCms169_03358, HmCms184_03238, HmCmsJML074_01363, HmCmsJML079_00389, HmCmsJML146_00663, HmCmsJML204_04002, HW43_02560, MJ49_08105, MS6198_48930, MS8345_04802, NCTC10082_01826, NCTC10089_04530, NCTC10090_02575, NCTC10418_06678, NCTC10429_04712, NCTC10766_05014, NCTC10767_00433, NCTC10865_05618, NCTC10963_04582, NCTC10974_05100, NCTC11022_04509, NCTC11126_02279, NCTC11181_01758, NCTC11341_03055, NCTC12650_04781, NCTC12950_04915, NCTC13216_02306, NCTC7922_05244, NCTC7927_04997, NCTC7928_03955, NCTC8009_07950, NCTC8179_00931, NCTC8450_00607, NCTC8500_05054, NCTC8621_04650, NCTC8622_02063, NCTC8959_04286, NCTC8960_02018, NCTC8985_03740, NCTC9001_04851, NCTC9007_00891, NCTC9036_04403, NCTC9044_02656, NCTC9045_05321, NCTC9050_02521, NCTC9055_01394, NCTC9058_02407, NCTC9062_03652, NCTC9073_03942, NCTC9075_06145, NCTC9081_01534, NCTC9111_04690, NCTC9117_05603, NCTC9119_04705, NCTC9434_02205, NCTC9701_04792, NCTC9702_05280, NCTC9703_03881, NCTC9706_01790, NCTC9777_00918, NCTC9962_01826, NCTC9969_04621, PGD_03354, PU06_09650, RG28_05880, RK56_012400, RX35_04433, SAMEA3472043_02152, SAMEA3472044_01525, SAMEA3472047_01688, SAMEA3472055_02993, SAMEA3472056_01692, SAMEA3472070_02769, SAMEA3472080_00096, SAMEA3472090_00989, SAMEA3472108_01562, SAMEA3472110_03214, SAMEA3472112_03403, SAMEA3472114_01878, SAMEA3472147_02931, SAMEA3484427_02083, SAMEA3484429_03123, SAMEA3484434_04172, SAMEA3485101_04739, SAMEA3752372_02987, SAMEA3752553_03659, SAMEA3752557_01671, SAMEA3752559_00150, SAMEA3752620_03485, SAMEA3753064_01610, SAMEA3753097_01239, SAMEA3753164_04006, SAMEA3753290_02099, SAMEA3753300_00650, SK85_04535, SY51_24045, U12A_04578, U14A_04572, UC41_03410, UN86_20815, UN91_24810, WQ89_21920, WR15_07030, YDC107_2895

UniProt
Find proteins for C1IFD2 (Escherichia coli)
Explore C1IFD2 
Go to UniProtKB:  C1IFD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1IFD2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U5P
Query on U5P
Download Ideal Coordinates CCD File 
B [auth A]URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.11α = 90
b = 61.11β = 90
c = 27.86γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
EU FP7 - Marie Curie IEFGermanyPIEF-GA-2011-301489

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Data collection
  • Version 1.2: 2018-03-07
    Changes: Advisory, Data collection, Derived calculations, Other, Source and taxonomy