+Open data
-Basic information
Entry | Database: PDB / ID: 8bvj | ||||||
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Title | Hfq-Crc-estA translation repression complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / co-transcriptional RNA folding / Crc / metabolic regulation / ribonucleoprotein assembly / RNA chaperone Hfq / translational regulation | ||||||
Function / homology | Function and homology information regulation of translation, ncRNA-mediated / regulation of RNA stability / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA repair / regulation of DNA-templated transcription / RNA binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Dendooven, T. / Luisi, B.F. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: EMBO J / Year: 2023 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bvj.cif.gz | 781.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bvj.ent.gz | 658.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/8bvj ftp://data.pdbj.org/pub/pdb/validation_reports/bv/8bvj | HTTPS FTP |
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-Related structure data
Related structure data | 16265MC 8bvhC 8bvmC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Pseudomonas aeruginosa (bacteria) / Gene: hfq, PSPA7_5673 / Production host: Escherichia coli (E. coli) / References: UniProt: A6VD57 #2: Protein | Mass: 30101.869 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) 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: Escherichia coli (E. coli) / References: UniProt: Q51380, exodeoxyribonuclease III #3: RNA chain | | Mass: 37997.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) |
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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 |
-Sample preparation
Component |
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Molecular weight | Value: 0.26 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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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 R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
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) |
-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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46800 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.5 Å | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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