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- PDB-8bvh: Cryo-EM structure of the Hfq-Crc-amiE translation repression assembly. -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bvh | ||||||
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Title | Cryo-EM structure of the Hfq-Crc-amiE translation repression assembly. | ||||||
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![]() | RNA BINDING PROTEIN / co-transcriptional RNA folding / Crc / metabolic regulation / ribonucleoprotein assembly / RNA chaperone Hfq / translational regulation | ||||||
Function / homology | ![]() double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA repair / regulation of DNA-templated transcription / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
![]() | Dendooven, T. / Luisi, B.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Translational regulation by Hfq-Crc assemblies emerges from polymorphic ribonucleoprotein folding. Authors: Tom Dendooven / Elisabeth Sonnleitner / Udo Bläsi / Ben F Luisi / ![]() ![]() Abstract: The widely occurring bacterial RNA chaperone Hfq is a key factor in the post-transcriptional control of hundreds of genes in Pseudomonas aeruginosa. How this broadly acting protein can contribute to ...The widely occurring bacterial RNA chaperone Hfq is a key factor in the post-transcriptional control of hundreds of genes in Pseudomonas aeruginosa. How this broadly acting protein can contribute to the regulatory requirements of many different genes remains puzzling. Here, we describe cryo-EM structures of higher order assemblies formed by Hfq and its partner protein Crc on control regions of different P. aeruginosa target mRNAs. Our results show that these assemblies have mRNA-specific quaternary architectures resulting from the combination of multivalent protein-protein interfaces and recognition of patterns in the RNA sequence. The structural polymorphism of these ribonucleoprotein assemblies enables selective translational repression of many different target mRNAs. This system elucidates how highly complex regulatory pathways can evolve with a minimal economy of proteinogenic components in combination with RNA sequence and fold. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 780.3 KB | Display | ![]() |
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PDB format | ![]() | 659.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 66.7 KB | Display | |
Data in CIF | ![]() | 101.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 16264MC ![]() 8bvjC ![]() 8bvmC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 9114.487 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 30101.869 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: crc, exoA, ALP65_01013, CAZ10_32350, CGU42_22755, DT376_09125, E4V10_18585, E5D53_27785, E5Z62_16095, E5Z63_23405, ECC04_031800, GNQ48_25180, GUL26_21635, IPC111_12165, IPC112_13745, IPC113_ ...Gene: crc, exoA, ALP65_01013, CAZ10_32350, CGU42_22755, DT376_09125, E4V10_18585, E5D53_27785, E5Z62_16095, E5Z63_23405, ECC04_031800, GNQ48_25180, GUL26_21635, IPC111_12165, IPC112_13745, IPC113_22800, IPC114_17225, IPC115_20105, IPC116_23795, IPC117_25625, IPC118_26680, IPC119_29495, IPC120_26430, IPC121_21355, IPC122_22810, IPC123_28525, IPC124_13695, IPC125_17530, IPC126_13890, IPC127_14855, IPC128_10355, IPC1295_10410, IPC129_12605, IPC1306_08360, IPC1307_28280, IPC1308_08250, IPC1309_21675, IPC130_13760, IPC1310_18070, IPC1311_27715, IPC1312_27760, IPC1313_12995, IPC1314_23305, IPC1315_13925, IPC1316_03820, IPC1317_21325, IPC1319_28440, IPC131_02850, IPC1320_21925, IPC1321_13670, IPC1322_08030, IPC1323_08650, IPC1324_08655, IPC1325_28715, IPC1326_03390, IPC1327_03390, IPC1329_17010, IPC132_06970, IPC1330_11465, IPC1331_28200, IPC1332_29425, IPC1333_11845, IPC1334_25345, IPC1335_28860, IPC1336_09225, IPC1337_29545, IPC1339_28790, IPC133_03360, IPC1340_28180, IPC1341_12600, IPC1342_25815, IPC1343_28125, IPC1345_26635, IPC1346_12480, IPC1347_06540, IPC1349_02495, IPC134_02845, IPC135_03360, IPC137_05170, IPC139_09290, IPC140_06730, IPC141_03365, IPC142_07260, IPC143_27785, IPC144_27850, IPC145_26565, IPC146_07875, IPC1474_29365, IPC1476_04745, IPC1477_00205, IPC1478_21530, IPC1479_05830, IPC147_27530, IPC1480_09320, IPC1481_08100, IPC1482_03390, IPC1485_09070, IPC1486_00200, IPC1487_09730, IPC1488_23420, IPC1489_30180, IPC148_13460, IPC1490_30060, IPC1491_03590, IPC1492_29195, IPC1494_10055, IPC1496_07955, IPC1498_13815, IPC1499_04620, IPC149_07870, IPC1500_13950, IPC1501_16685, IPC1502_17430, IPC1503_12005, IPC1504_12415, IPC1505_29825, IPC1506_17410, IPC1507_24155, IPC1508_30170, IPC1509_28695, IPC150_28080, IPC1510_28915, IPC1511_30420, IPC1512_29660, IPC1515_25380, IPC1516_25030, IPC1517_08725, IPC1518_07355, IPC1519_08150, IPC151_23655, IPC1521_08375, IPC1522_08210, IPC1523_29925, IPC152_28760, IPC153_23345, IPC154_17265, IPC155_18160, IPC156_17280, IPC157_20765, IPC1583_04500, IPC1584_21700, IPC1585_03355, IPC1586_12135, IPC1587_07630, IPC1588_00205, IPC1589_12850, IPC158_22475, IPC1590_04505, IPC1591_26650, IPC1592_03360, IPC1593_28620, IPC1594_08340, IPC1595_28610, IPC1596_08050, IPC1597_07705, IPC1598_07535, IPC1599_12520, IPC159_19675, IPC1600_03625, IPC1601_25405, IPC1602_28860, IPC1603_04480, IPC1604_17280, IPC1605_06980, IPC1606_28085, IPC161_21475, IPC168_27215, IPC172_03365, IPC173_03365, IPC174_04115, IPC175_27990, IPC176_00200, IPC177_23820, IPC178_12645, IPC179_03225, IPC180_03440, IPC181_03440, IPC182_27410, IPC183_07620, IPC184_23205, IPC26_03230, IPC27_25570, IPC29_25820, IPC30_25775, IPC31_26330, IPC32_23895, IPC33_16805, IPC34_07650, IPC35_07645, IPC36_11985, IPC37_11015, IPC38_07925, IPC40_27470, IPC41_03360, IPC42_03360, IPC43_23085, IPC44_22815, IPC45_21905, IPC46_07155, IPC47_03385, IPC48_27355, IPC49_03360, IPC50_30570, IPC51_28835, IPC54_18710, IPC55_30750, IPC56_25845, IPC574_05650, IPC575_13820, IPC576_07870, IPC577_30530, IPC578_05650, IPC579_06085, IPC57_11625, IPC580_13610, IPC582_05645, IPC584_14310, IPC586_05655, IPC589_14875, IPC58_27585, IPC596_07850, IPC597_03535, IPC598_09625, IPC599_08585, IPC59_11860, IPC600_09330, IPC601_08240, IPC602_08660, IPC603_03370, IPC604_03350, IPC605_03350, IPC606_24980, IPC607_31450, IPC608_28595, IPC609_14300, IPC60_11070, IPC610_25045, IPC611_03630, IPC612_03625, IPC613_03625, IPC614_10255, IPC615_03650, IPC616_03650, IPC618_03645, IPC61_27990, IPC620_03665, IPC621_02265, IPC622_09600, IPC623_28715, IPC624_03390, IPC625_10215, IPC627_06380, IPC629_12080, IPC630_04660, IPC632_00200, IPC633_27305, IPC634_00200, IPC64_27165, IPC65_28585, IPC66_27855, IPC67_03650, IPC68_03420, IPC70_17275, IPC71_27005, IPC737_07685, IPC73_27875, IPC74_28395, IPC75_18330, IPC76_17335, IPC77_23945, IPC78_12120, NCTC13621_05232, PA52Ts2_6132, PAMH19_3299 Production host: ![]() ![]() #3: RNA chain | | Mass: 33720.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Complex of RNA chaperone Hfq and helper protein Crc assembled on a fragment of amiE mRNA Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.26 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18rc5_3822: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63000 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||
Refine LS restraints |
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