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- PDB-8bvm: Cryo-EM structure of Hfq-Crc-rbsB translation repression complex -

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Basic information

Entry
Database: PDB / ID: 8bvm
TitleCryo-EM structure of Hfq-Crc-rbsB translation repression complex
Components
  • Catabolite repression control protein
  • RNA-binding protein Hfq
  • rbsB mRNA
KeywordsRNA BINDING PROTEIN / co-transcriptional RNA folding / Crc / metabolic regulation / ribonucleoprotein assembly / RNA chaperone Hfq / translational regulation
Function / homology
Function and homology information


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
Exodeoxyribonuclease III-like / RNA-binding protein Hfq / Hfq protein / AP endonuclease 1 / AP endonucleases family 1 profile. / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / : / Sm domain profile. / Endonuclease/exonuclease/phosphatase superfamily / LSM domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA-binding protein Hfq / Catabolite repression control protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDendooven, T. / Luisi, B.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: 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
DepositionDec 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catabolite repression control protein
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq
D: RNA-binding protein Hfq
E: RNA-binding protein Hfq
F: RNA-binding protein Hfq
G: RNA-binding protein Hfq
H: Catabolite repression control protein
I: RNA-binding protein Hfq
J: RNA-binding protein Hfq
K: RNA-binding protein Hfq
L: RNA-binding protein Hfq
M: RNA-binding protein Hfq
N: Catabolite repression control protein
O: RNA-binding protein Hfq
u: rbsB mRNA


Theoretical massNumber of molelcules
Total (without water)234,53016
Polymers234,53016
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area32480 Å2
ΔGint-182 kcal/mol
Surface area71750 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H
12A
22N
13B
23C
14B
24D
15B
25E
16B
26F
17B
27G
18B
28I
19B
29J
110B
210K
111B
211L
112B
212M
113B
213O
114C
214D
115C
215E
116C
216F
117C
217G
118C
218I
119C
219J
120C
220K
121C
221L
122C
222M
123C
223O
124D
224E
125D
225F
126D
226G
127D
227I
128D
228J
129D
229K
130D
230L
131D
231M
132D
232O
133E
233F
134E
234G
135E
235I
136E
236J
137E
237K
138E
238L
139E
239M
140E
240O
141F
241G
142F
242I
143F
243J
144F
244K
145F
245L
146F
246M
147F
247O
148G
248I
149G
249J
150G
250K
151G
251L
152G
252M
153G
253O
154H
254N
155I
255J
156I
256K
157I
257L
158I
258M
159I
259O
160J
260K
161J
261L
162J
262M
163J
263O
164K
264L
165K
265M
166K
266O
167L
267M
168L
268O
169M
269O

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 262
2010H1 - 262
1020A1 - 262
2020N1 - 262
1030B5 - 68
2030C5 - 68
1040B6 - 69
2040D6 - 69
1050B5 - 69
2050E5 - 69
1060B5 - 70
2060F5 - 70
1070B6 - 69
2070G6 - 69
1080B5 - 70
2080I5 - 70
1090B5 - 68
2090J5 - 68
10100B6 - 69
20100K6 - 69
10110B5 - 69
20110L5 - 69
10120B5 - 70
20120M5 - 70
10130B6 - 69
20130O6 - 69
10140C6 - 68
20140D6 - 68
10150C5 - 68
20150E5 - 68
10160C5 - 68
20160F5 - 68
10170C6 - 68
20170G6 - 68
10180C5 - 68
20180I5 - 68
10190C5 - 69
20190J5 - 69
10200C6 - 68
20200K6 - 68
10210C5 - 68
20210L5 - 68
10220C5 - 68
20220M5 - 68
10230C6 - 68
20230O6 - 68
10240D6 - 70
20240E6 - 70
10250D6 - 69
20250F6 - 69
10260D6 - 71
20260G6 - 71
10270D6 - 69
20270I6 - 69
10280D6 - 68
20280J6 - 68
10290D6 - 71
20290K6 - 71
10300D6 - 70
20300L6 - 70
10310D6 - 69
20310M6 - 69
10320D6 - 71
20320O6 - 71
10330E5 - 69
20330F5 - 69
10340E6 - 70
20340G6 - 70
10350E5 - 69
20350I5 - 69
10360E5 - 68
20360J5 - 68
10370E6 - 70
20370K6 - 70
10380E3 - 71
20380L3 - 71
10390E5 - 69
20390M5 - 69
10400E6 - 70
20400O6 - 70
10410F6 - 69
20410G6 - 69
10420F5 - 70
20420I5 - 70
10430F5 - 68
20430J5 - 68
10440F6 - 69
20440K6 - 69
10450F5 - 69
20450L5 - 69
10460F5 - 70
20460M5 - 70
10470F6 - 69
20470O6 - 69
10480G6 - 69
20480I6 - 69
10490G6 - 68
20490J6 - 68
10500G6 - 71
20500K6 - 71
10510G6 - 70
20510L6 - 70
10520G6 - 69
20520M6 - 69
10530G6 - 71
20530O6 - 71
10540H1 - 262
20540N1 - 262
10550I5 - 68
20550J5 - 68
10560I6 - 69
20560K6 - 69
10570I5 - 69
20570L5 - 69
10580I5 - 70
20580M5 - 70
10590I6 - 69
20590O6 - 69
10600J6 - 68
20600K6 - 68
10610J5 - 68
20610L5 - 68
10620J5 - 68
20620M5 - 68
10630J6 - 68
20630O6 - 68
10640K6 - 70
20640L6 - 70
10650K6 - 69
20650M6 - 69
10660K6 - 71
20660O6 - 71
10670L5 - 69
20670M5 - 69
10680L6 - 70
20680O6 - 70
10690M6 - 69
20690O6 - 69

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69

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Components

#1: Protein Catabolite repression control protein / Exodeoxyribonuclease III


Mass: 30101.869 Da / Num. of mol.: 3
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: Pseudomonas aeruginosa (bacteria) / References: UniProt: Q51380, exodeoxyribonuclease III
#2: Protein
RNA-binding protein Hfq


Mass: 9114.487 Da / Num. of mol.: 12
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
#3: RNA chain rbsB mRNA


Mass: 34850.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of the RNA chaperone Hfq and helper protein Crc assembled on a rbsB mRNA fragmentCOMPLEXall0RECOMBINANT
2Catabolite repression control proteinCOMPLEX#11RECOMBINANT
3rbsB mRNACOMPLEX#31RECOMBINANT
4RNA-binding protein HfqCOMPLEX#21RECOMBINANT
Molecular weightValue: 0.180 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Pseudomonas aeruginosa (bacteria)287
33Pseudomonas aeruginosa (bacteria)287
44Pseudomonas aeruginosa (bacteria)287
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Pseudomonas aeruginosa (bacteria)287
33Synthetic construct (others)32630
44Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18rc5_3822: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF Chimera1.13.1model fitting
9cryoSPARC2.15initial Euler assignment
10cryoSPARC2.15final Euler assignment
12cryoSPARC2.153D reconstruction
13REFMACmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148700 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementResolution: 3.6→240.7 Å / Cor.coef. Fo:Fc: 0.915 / SU B: 17.532 / SU ML: 0.247 / ESU R: 0.264
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.39935 --
obs0.39935 471805 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 251.902 Å2
Baniso -1Baniso -2Baniso -3
1-11.97 Å23.08 Å2-5.64 Å2
2---5.23 Å2-1.64 Å2
3----6.73 Å2
Refinement stepCycle: 1 / Total: 14008
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00114342
ELECTRON MICROSCOPYf_angle_d0.3819692
ELECTRON MICROSCOPYf_dihedral_angle_d15.1422352
ELECTRON MICROSCOPYf_chiral_restr0.042226
ELECTRON MICROSCOPYf_plane_restr0.0032351
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A175760.09
12H175760.09
21A174320.09
22N174320.09
31B36400.14
32C36400.14
41B36280.13
42D36280.13
51B36840.12
52E36840.12
61B37540.13
62F37540.13
71B36560.13
72G36560.13
81B38940.08
82I38940.08
91B36860.12
92J36860.12
101B36160.12
102K36160.12
111B36880.11
112L36880.11
121B37220.14
122M37220.14
131B36680.13
132O36680.13
141C35260.14
142D35260.14
151C35320.15
152E35320.15
161C36560.12
162F36560.12
171C35260.15
172G35260.15
181C36160.14
182I36160.14
191C37860.1
192J37860.1
201C35040.14
202K35040.14
211C35500.14
212L35500.14
221C36120.13
222M36120.13
231C35460.15
232O35460.15
241D36840.11
242E36840.11
251D36240.12
252F36240.12
261D38100.12
262G38100.12
271D36580.12
272I36580.12
281D35480.13
282J35480.13
291D38460.08
292K38460.08
301D36880.1
302L36880.1
311D35880.13
312M35880.13
321D37580.12
322O37580.12
331E37040.12
332F37040.12
341E36920.13
342G36920.13
351E37160.12
352I37160.12
361E35860.14
362J35860.14
371E36920.11
372K36920.11
381E39340.09
382L39340.09
391E36520.13
392M36520.13
401E37020.13
402O37020.13
411F36760.13
412G36760.13
421F37920.12
422I37920.12
431F36940.1
432J36940.1
441F36240.12
442K36240.12
451F37120.11
452L37120.11
461F38480.08
462M38480.08
471F36640.12
472O36640.12
481G37060.12
482I37060.12
491G35740.14
492J35740.14
501G37960.12
502K37960.12
511G36980.12
512L36980.12
521G36320.14
522M36320.14
531G38740.08
532O38740.08
541H177460.09
542N177460.09
551I36860.12
552J36860.12
561I36540.12
562K36540.12
571I37220.11
572L37220.11
581I37320.14
582M37320.14
591I36960.12
592O36960.12
601J35420.13
602K35420.13
611J36160.13
612L36160.13
621J36820.11
622M36820.11
631J35640.13
632O35640.13
641K37040.1
642L37040.1
651K35820.13
652M35820.13
661K37660.12
662O37660.12
671L36580.12
672M36580.12
681L37020.12
682O37020.12
691M36220.14
692O36220.14
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.883 34782 -
obs--100 %

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