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

ID or keywords:

Entry

Database: PDB / ID: 8bvm

Title

Cryo-EM structure of Hfq-Crc-rbsB translation repression complex

Components

Catabolite repression control protein
RNA-binding protein Hfq
rbsB mRNA

Keywords

RNA BINDING PROTEIN / co-transcriptional RNA folding / Crc / metabolic regulation / ribonucleoprotein assembly / RNA chaperone Hfq / translational regulation

Function / homology

Function and homology information

exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / DNA repair / regulation of DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å

Authors

Dendooven, T. / Luisi, B.F.

Funding support

United Kingdom, 1items

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 ...

History

Deposition	Dec 4, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 25, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2	Jul 24, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / refine / struct_ncs_dom_lim Item: _em_admin.last_update / _refine.ls_d_res_high ..._em_admin.last_update / _refine.ls_d_res_high / _refine.ls_d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bvm.cif.gz	317.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8bvm.ent.gz	253.7 KB	Display	PDB format
PDBx/mmJSON format	8bvm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8bvm_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8bvm_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8bvm_validation.xml.gz	51.6 KB	Display
Data in CIF	8bvm_validation.cif.gz	77.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bv/8bvm ftp://data.pdbj.org/pub/pdb/validation_reports/bv/8bvm	HTTPS FTP

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Related structure data

Related structure data	16266MC 16264C 16265C 8bvhC 8bvjC C: citing same article (ref.) M: map data used to model this data
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (2) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (2) #253 - Jan 2021 Expressome similarity (2) #260 - Aug 2021 Ribonuclease P similarity (2) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (2) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #245 - May 2020 Spliceosomes similarity (3) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (2) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #161 - May 2013 Ricin similarity (2) #227 - Nov 2018 Telomerase similarity (2) #266 - Feb 2022 Oligosaccharyltransferase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #18 - Jun 2001 Myosin similarity (3) #19 - Jul 2001 Actin similarity (3) #107 - Nov 2008 Mechanosensitive Channels similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (2)
#130 - Oct 2010
Riboswitches
similarity (2)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (2)
#253 - Jan 2021
Expressome
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#260 - Aug 2021
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#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
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#87 - Mar 2007
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#245 - May 2020
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#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (2)
#262 - Oct 2021
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similarity (2)
#65 - May 2005
Self-splicing RNA
similarity (2)
#105 - Sep 2008
Ribonuclease A
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Selenocysteine Synthase
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Poly(A) Polymerase
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Toll-like Receptors
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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

235 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: electron microscopy

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	ILE	ILE	A	A	1 - 262	1 - 262
2	1	GLY	GLY	ILE	ILE	H	H	1 - 262	1 - 262
1	2	GLY	GLY	ILE	ILE	A	A	1 - 262	1 - 262
2	2	GLY	GLY	ILE	ILE	N	N	1 - 262	1 - 262
1	3	HIS	HIS	VAL	VAL	B	B	5 - 68	5 - 68
2	3	HIS	HIS	VAL	VAL	C	C	5 - 68	5 - 68
1	4	SER	SER	ARG	ARG	B	B	6 - 69	6 - 69
2	4	SER	SER	ARG	ARG	D	D	6 - 69	6 - 69
1	5	HIS	HIS	ARG	ARG	B	B	5 - 69	5 - 69
2	5	HIS	HIS	ARG	ARG	E	E	5 - 69	5 - 69
1	6	HIS	HIS	LEU	LEU	B	B	5 - 70	5 - 70
2	6	HIS	HIS	LEU	LEU	F	F	5 - 70	5 - 70
1	7	SER	SER	ARG	ARG	B	B	6 - 69	6 - 69
2	7	SER	SER	ARG	ARG	G	G	6 - 69	6 - 69
1	8	HIS	HIS	LEU	LEU	B	B	5 - 70	5 - 70
2	8	HIS	HIS	LEU	LEU	I	I	5 - 70	5 - 70
1	9	HIS	HIS	VAL	VAL	B	B	5 - 68	5 - 68
2	9	HIS	HIS	VAL	VAL	J	J	5 - 68	5 - 68
1	10	SER	SER	ARG	ARG	B	B	6 - 69	6 - 69
2	10	SER	SER	ARG	ARG	K	K	6 - 69	6 - 69
1	11	HIS	HIS	ARG	ARG	B	B	5 - 69	5 - 69
2	11	HIS	HIS	ARG	ARG	L	L	5 - 69	5 - 69
1	12	HIS	HIS	LEU	LEU	B	B	5 - 70	5 - 70
2	12	HIS	HIS	LEU	LEU	M	M	5 - 70	5 - 70
1	13	SER	SER	ARG	ARG	B	B	6 - 69	6 - 69
2	13	SER	SER	ARG	ARG	O	O	6 - 69	6 - 69
1	14	SER	SER	VAL	VAL	C	C	6 - 68	6 - 68
2	14	SER	SER	VAL	VAL	D	D	6 - 68	6 - 68
1	15	HIS	HIS	VAL	VAL	C	C	5 - 68	5 - 68
2	15	HIS	HIS	VAL	VAL	E	E	5 - 68	5 - 68
1	16	HIS	HIS	VAL	VAL	C	C	5 - 68	5 - 68
2	16	HIS	HIS	VAL	VAL	F	F	5 - 68	5 - 68
1	17	SER	SER	VAL	VAL	C	C	6 - 68	6 - 68
2	17	SER	SER	VAL	VAL	G	G	6 - 68	6 - 68
1	18	HIS	HIS	VAL	VAL	C	C	5 - 68	5 - 68
2	18	HIS	HIS	VAL	VAL	I	I	5 - 68	5 - 68
1	19	HIS	HIS	ARG	ARG	C	C	5 - 69	5 - 69
2	19	HIS	HIS	ARG	ARG	J	J	5 - 69	5 - 69
1	20	SER	SER	VAL	VAL	C	C	6 - 68	6 - 68
2	20	SER	SER	VAL	VAL	K	K	6 - 68	6 - 68
1	21	HIS	HIS	VAL	VAL	C	C	5 - 68	5 - 68
2	21	HIS	HIS	VAL	VAL	L	L	5 - 68	5 - 68
1	22	HIS	HIS	VAL	VAL	C	C	5 - 68	5 - 68
2	22	HIS	HIS	VAL	VAL	M	M	5 - 68	5 - 68
1	23	SER	SER	VAL	VAL	C	C	6 - 68	6 - 68
2	23	SER	SER	VAL	VAL	O	O	6 - 68	6 - 68
1	24	SER	SER	LEU	LEU	D	D	6 - 70	6 - 70
2	24	SER	SER	LEU	LEU	E	E	6 - 70	6 - 70
1	25	SER	SER	ARG	ARG	D	D	6 - 69	6 - 69
2	25	SER	SER	ARG	ARG	F	F	6 - 69	6 - 69
1	26	SER	SER	PRO	PRO	D	D	6 - 71	6 - 71
2	26	SER	SER	PRO	PRO	G	G	6 - 71	6 - 71
1	27	SER	SER	ARG	ARG	D	D	6 - 69	6 - 69
2	27	SER	SER	ARG	ARG	I	I	6 - 69	6 - 69
1	28	SER	SER	VAL	VAL	D	D	6 - 68	6 - 68
2	28	SER	SER	VAL	VAL	J	J	6 - 68	6 - 68
1	29	SER	SER	PRO	PRO	D	D	6 - 71	6 - 71
2	29	SER	SER	PRO	PRO	K	K	6 - 71	6 - 71
1	30	SER	SER	LEU	LEU	D	D	6 - 70	6 - 70
2	30	SER	SER	LEU	LEU	L	L	6 - 70	6 - 70
1	31	SER	SER	ARG	ARG	D	D	6 - 69	6 - 69
2	31	SER	SER	ARG	ARG	M	M	6 - 69	6 - 69
1	32	SER	SER	PRO	PRO	D	D	6 - 71	6 - 71
2	32	SER	SER	PRO	PRO	O	O	6 - 71	6 - 71
1	33	HIS	HIS	ARG	ARG	E	E	5 - 69	5 - 69
2	33	HIS	HIS	ARG	ARG	F	F	5 - 69	5 - 69
1	34	SER	SER	LEU	LEU	E	E	6 - 70	6 - 70
2	34	SER	SER	LEU	LEU	G	G	6 - 70	6 - 70
1	35	HIS	HIS	ARG	ARG	E	E	5 - 69	5 - 69
2	35	HIS	HIS	ARG	ARG	I	I	5 - 69	5 - 69
1	36	HIS	HIS	VAL	VAL	E	E	5 - 68	5 - 68
2	36	HIS	HIS	VAL	VAL	J	J	5 - 68	5 - 68
1	37	SER	SER	LEU	LEU	E	E	6 - 70	6 - 70
2	37	SER	SER	LEU	LEU	K	K	6 - 70	6 - 70
1	38	LYS	LYS	PRO	PRO	E	E	3 - 71	3 - 71
2	38	LYS	LYS	PRO	PRO	L	L	3 - 71	3 - 71
1	39	HIS	HIS	ARG	ARG	E	E	5 - 69	5 - 69
2	39	HIS	HIS	ARG	ARG	M	M	5 - 69	5 - 69
1	40	SER	SER	LEU	LEU	E	E	6 - 70	6 - 70
2	40	SER	SER	LEU	LEU	O	O	6 - 70	6 - 70
1	41	SER	SER	ARG	ARG	F	F	6 - 69	6 - 69
2	41	SER	SER	ARG	ARG	G	G	6 - 69	6 - 69
1	42	HIS	HIS	LEU	LEU	F	F	5 - 70	5 - 70
2	42	HIS	HIS	LEU	LEU	I	I	5 - 70	5 - 70
1	43	HIS	HIS	VAL	VAL	F	F	5 - 68	5 - 68
2	43	HIS	HIS	VAL	VAL	J	J	5 - 68	5 - 68
1	44	SER	SER	ARG	ARG	F	F	6 - 69	6 - 69
2	44	SER	SER	ARG	ARG	K	K	6 - 69	6 - 69
1	45	HIS	HIS	ARG	ARG	F	F	5 - 69	5 - 69
2	45	HIS	HIS	ARG	ARG	L	L	5 - 69	5 - 69
1	46	HIS	HIS	LEU	LEU	F	F	5 - 70	5 - 70
2	46	HIS	HIS	LEU	LEU	M	M	5 - 70	5 - 70
1	47	SER	SER	ARG	ARG	F	F	6 - 69	6 - 69
2	47	SER	SER	ARG	ARG	O	O	6 - 69	6 - 69
1	48	SER	SER	ARG	ARG	G	G	6 - 69	6 - 69
2	48	SER	SER	ARG	ARG	I	I	6 - 69	6 - 69
1	49	SER	SER	VAL	VAL	G	G	6 - 68	6 - 68
2	49	SER	SER	VAL	VAL	J	J	6 - 68	6 - 68
1	50	SER	SER	PRO	PRO	G	G	6 - 71	6 - 71
2	50	SER	SER	PRO	PRO	K	K	6 - 71	6 - 71
1	51	SER	SER	LEU	LEU	G	G	6 - 70	6 - 70
2	51	SER	SER	LEU	LEU	L	L	6 - 70	6 - 70
1	52	SER	SER	ARG	ARG	G	G	6 - 69	6 - 69
2	52	SER	SER	ARG	ARG	M	M	6 - 69	6 - 69
1	53	SER	SER	PRO	PRO	G	G	6 - 71	6 - 71
2	53	SER	SER	PRO	PRO	O	O	6 - 71	6 - 71
1	54	GLY	GLY	ILE	ILE	H	H	1 - 262	1 - 262
2	54	GLY	GLY	ILE	ILE	N	N	1 - 262	1 - 262
1	55	HIS	HIS	VAL	VAL	I	I	5 - 68	5 - 68
2	55	HIS	HIS	VAL	VAL	J	J	5 - 68	5 - 68
1	56	SER	SER	ARG	ARG	I	I	6 - 69	6 - 69
2	56	SER	SER	ARG	ARG	K	K	6 - 69	6 - 69
1	57	HIS	HIS	ARG	ARG	I	I	5 - 69	5 - 69
2	57	HIS	HIS	ARG	ARG	L	L	5 - 69	5 - 69
1	58	HIS	HIS	LEU	LEU	I	I	5 - 70	5 - 70
2	58	HIS	HIS	LEU	LEU	M	M	5 - 70	5 - 70
1	59	SER	SER	ARG	ARG	I	I	6 - 69	6 - 69
2	59	SER	SER	ARG	ARG	O	O	6 - 69	6 - 69
1	60	SER	SER	VAL	VAL	J	J	6 - 68	6 - 68
2	60	SER	SER	VAL	VAL	K	K	6 - 68	6 - 68
1	61	HIS	HIS	VAL	VAL	J	J	5 - 68	5 - 68
2	61	HIS	HIS	VAL	VAL	L	L	5 - 68	5 - 68
1	62	HIS	HIS	VAL	VAL	J	J	5 - 68	5 - 68
2	62	HIS	HIS	VAL	VAL	M	M	5 - 68	5 - 68
1	63	SER	SER	VAL	VAL	J	J	6 - 68	6 - 68
2	63	SER	SER	VAL	VAL	O	O	6 - 68	6 - 68
1	64	SER	SER	LEU	LEU	K	K	6 - 70	6 - 70
2	64	SER	SER	LEU	LEU	L	L	6 - 70	6 - 70
1	65	SER	SER	ARG	ARG	K	K	6 - 69	6 - 69
2	65	SER	SER	ARG	ARG	M	M	6 - 69	6 - 69
1	66	SER	SER	PRO	PRO	K	K	6 - 71	6 - 71
2	66	SER	SER	PRO	PRO	O	O	6 - 71	6 - 71
1	67	HIS	HIS	ARG	ARG	L	L	5 - 69	5 - 69
2	67	HIS	HIS	ARG	ARG	M	M	5 - 69	5 - 69
1	68	SER	SER	LEU	LEU	L	L	6 - 70	6 - 70
2	68	SER	SER	LEU	LEU	O	O	6 - 70	6 - 70
1	69	SER	SER	ARG	ARG	M	M	6 - 69	6 - 69
2	69	SER	SER	ARG	ARG	O	O	6 - 69	6 - 69

NCS ensembles :

#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)

-
Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component

ID	Name	Type	Entity ID	Parent-ID	Source
1	Complex of the RNA chaperone Hfq and helper protein Crc assembled on a rbsB mRNA fragment	COMPLEX	all	0	RECOMBINANT
2	Catabolite repression control protein	COMPLEX	#1	1	RECOMBINANT
3	rbsB mRNA	COMPLEX	#3	1	RECOMBINANT
4	RNA-binding protein Hfq	COMPLEX	#2	1	RECOMBINANT

Molecular weight

Value: 0.180 MDa / Experimental value: NO

Source (natural)

ID	Entity assembly-ID	Organism	Ncbi tax-ID
2	2	Pseudomonas aeruginosa (bacteria)	287
3	3	Pseudomonas aeruginosa (bacteria)	287
4	4	Pseudomonas aeruginosa (bacteria)	287

Source (recombinant)

ID	Entity assembly-ID	Organism	Ncbi tax-ID
2	2	Pseudomonas aeruginosa (bacteria)	287
3	3	Synthetic construct (others)	32630
4	4	Escherichia coli (E. coli)	562

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

Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
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

EM software

ID	Name	Version	Category
2	EPU		image acquisition
4	CTFFIND	4.1	CTF correction
7	UCSF Chimera	1.13.1	model fitting
9	cryoSPARC	2.15	initial Euler assignment
10	cryoSPARC	2.15	final Euler assignment
12	cryoSPARC	2.15	3D reconstruction
13	REFMAC		model refinement
14	PHENIX		model refinement

CTF correction

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

3D reconstruction

Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148700 / Symmetry type: POINT

Atomic model building

Protocol: RIGID BODY FIT

Refinement

Resolution: 3.8→3.8 Å / Cor.coef. F_o:F_c: 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

	R_factor	Num. reflection	% reflection
R_work	0.39935	-	-
obs	0.39935	471805	100 %

Solvent computation

Solvent model: PARAMETERS FOR MASK CACLULATION

Displacement parameters

B_iso mean: 251.902 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	11.97 Å²	3.08 Å²	-5.64 Å²
2-	-	-5.23 Å²	-1.64 Å²
3-	-	-	-6.73 Å²

Refinement step

Cycle: 1 / Total: 14008

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
ELECTRON MICROSCOPY	f_bond_d	0.001	14342
ELECTRON MICROSCOPY	f_angle_d	0.38	19692
ELECTRON MICROSCOPY	f_dihedral_angle_d	15.142	2352
ELECTRON MICROSCOPY	f_chiral_restr	0.04	2226
ELECTRON MICROSCOPY	f_plane_restr	0.003	2351

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	17576	0.09
1	2	H	17576	0.09
2	1	A	17432	0.09
2	2	N	17432	0.09
3	1	B	3640	0.14
3	2	C	3640	0.14
4	1	B	3628	0.13
4	2	D	3628	0.13
5	1	B	3684	0.12
5	2	E	3684	0.12
6	1	B	3754	0.13
6	2	F	3754	0.13
7	1	B	3656	0.13
7	2	G	3656	0.13
8	1	B	3894	0.08
8	2	I	3894	0.08
9	1	B	3686	0.12
9	2	J	3686	0.12
10	1	B	3616	0.12
10	2	K	3616	0.12
11	1	B	3688	0.11
11	2	L	3688	0.11
12	1	B	3722	0.14
12	2	M	3722	0.14
13	1	B	3668	0.13
13	2	O	3668	0.13
14	1	C	3526	0.14
14	2	D	3526	0.14
15	1	C	3532	0.15
15	2	E	3532	0.15
16	1	C	3656	0.12
16	2	F	3656	0.12
17	1	C	3526	0.15
17	2	G	3526	0.15
18	1	C	3616	0.14
18	2	I	3616	0.14
19	1	C	3786	0.1
19	2	J	3786	0.1
20	1	C	3504	0.14
20	2	K	3504	0.14
21	1	C	3550	0.14
21	2	L	3550	0.14
22	1	C	3612	0.13
22	2	M	3612	0.13
23	1	C	3546	0.15
23	2	O	3546	0.15
24	1	D	3684	0.11
24	2	E	3684	0.11
25	1	D	3624	0.12
25	2	F	3624	0.12
26	1	D	3810	0.12
26	2	G	3810	0.12
27	1	D	3658	0.12
27	2	I	3658	0.12
28	1	D	3548	0.13
28	2	J	3548	0.13
29	1	D	3846	0.08
29	2	K	3846	0.08
30	1	D	3688	0.1
30	2	L	3688	0.1
31	1	D	3588	0.13
31	2	M	3588	0.13
32	1	D	3758	0.12
32	2	O	3758	0.12
33	1	E	3704	0.12
33	2	F	3704	0.12
34	1	E	3692	0.13
34	2	G	3692	0.13
35	1	E	3716	0.12
35	2	I	3716	0.12
36	1	E	3586	0.14
36	2	J	3586	0.14
37	1	E	3692	0.11
37	2	K	3692	0.11
38	1	E	3934	0.09
38	2	L	3934	0.09
39	1	E	3652	0.13
39	2	M	3652	0.13
40	1	E	3702	0.13
40	2	O	3702	0.13
41	1	F	3676	0.13
41	2	G	3676	0.13
42	1	F	3792	0.12
42	2	I	3792	0.12
43	1	F	3694	0.1
43	2	J	3694	0.1
44	1	F	3624	0.12
44	2	K	3624	0.12
45	1	F	3712	0.11
45	2	L	3712	0.11
46	1	F	3848	0.08
46	2	M	3848	0.08
47	1	F	3664	0.12
47	2	O	3664	0.12
48	1	G	3706	0.12
48	2	I	3706	0.12
49	1	G	3574	0.14
49	2	J	3574	0.14
50	1	G	3796	0.12
50	2	K	3796	0.12
51	1	G	3698	0.12
51	2	L	3698	0.12
52	1	G	3632	0.14
52	2	M	3632	0.14
53	1	G	3874	0.08
53	2	O	3874	0.08
54	1	H	17746	0.09
54	2	N	17746	0.09
55	1	I	3686	0.12
55	2	J	3686	0.12
56	1	I	3654	0.12
56	2	K	3654	0.12
57	1	I	3722	0.11
57	2	L	3722	0.11
58	1	I	3732	0.14
58	2	M	3732	0.14
59	1	I	3696	0.12
59	2	O	3696	0.12
60	1	J	3542	0.13
60	2	K	3542	0.13
61	1	J	3616	0.13
61	2	L	3616	0.13
62	1	J	3682	0.11
62	2	M	3682	0.11
63	1	J	3564	0.13
63	2	O	3564	0.13
64	1	K	3704	0.1
64	2	L	3704	0.1
65	1	K	3582	0.13
65	2	M	3582	0.13
66	1	K	3766	0.12
66	2	O	3766	0.12
67	1	L	3658	0.12
67	2	M	3658	0.12
68	1	L	3702	0.12
68	2	O	3702	0.12
69	1	M	3622	0.14
69	2	O	3622	0.14

LS refinement shell

Resolution: 3.6→3.693 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0	0	-
R_work	1.883	34782	-
obs	-	-	100 %

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