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- PDB-4v2s: Crystal structure of Hfq in complex with the sRNA RydC -

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Basic information

Entry
Database: PDB / ID: 4v2s
TitleCrystal structure of Hfq in complex with the sRNA RydC
Components
  • RNA-BINDING PROTEIN HFQ
  • RYDC
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / NATIVELY UNSTRUCTURED PROTEIN / PROTEIN-RNA RECOGNITION
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / regulation of translation, ncRNA-mediated / RNA folding chaperone / bent DNA binding / regulation of RNA stability / regulation of DNA-templated transcription / DNA binding / RNA binding / cytosol
Similarity search - Function
RNA-binding protein Hfq / Hfq protein / SH3 type barrels. - #100 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA-binding protein Hfq
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.48 Å
AuthorsDimastrogiovanni, D. / Frohlich, K.S. / Bruce, H.A. / Bandyra, K.J. / Hohensee, S. / Vogel, J. / Luisi, B.F.
CitationJournal: Elife / Year: 2014
Title: Recognition of the small regulatory RNA RydC by the bacterial Hfq protein.
Authors: Dimastrogiovanni, D. / Frohlich, K.S. / Bandyra, K.J. / Bruce, H.A. / Hohensee, S. / Vogel, J. / Luisi, B.F.
History
DepositionOct 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / pdbx_database_proc / pdbx_database_status
Item: _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.recvd_author_approval
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 30-STRANDED BARREL THIS IS REPRESENTED BY A 31-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-BINDING PROTEIN HFQ
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
Q: RYDC


Theoretical massNumber of molelcules
Total (without water)87,7757
Polymers87,7757
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13250 Å2
ΔGint-106.2 kcal/mol
Surface area28270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.940, 73.356, 137.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYSERSERAA4 - 694 - 69
21GLYGLYSERSERBB4 - 694 - 69
12GLYGLYSERSERAA4 - 694 - 69
22GLYGLYSERSERCC4 - 694 - 69
13GLYGLYHISHISAA4 - 714 - 71
23GLYGLYHISHISDD4 - 714 - 71
14GLNGLNHISHISAA5 - 705 - 70
24GLNGLNHISHISEE5 - 705 - 70
15GLYGLYHISHISAA4 - 704 - 70
25GLYGLYHISHISFF4 - 704 - 70
16LYSLYSSERSERBB3 - 693 - 69
26LYSLYSSERSERCC3 - 693 - 69
17ALAALASERSERBB2 - 692 - 69
27ALAALASERSERDD2 - 692 - 69
18GLNGLNSERSERBB5 - 695 - 69
28GLNGLNSERSEREE5 - 695 - 69
19ALAALASERSERBB2 - 692 - 69
29ALAALASERSERFF2 - 692 - 69
110LYSLYSSERSERCC3 - 693 - 69
210LYSLYSSERSERDD3 - 693 - 69
111GLNGLNSERSERCC5 - 695 - 69
211GLNGLNSERSEREE5 - 695 - 69
112LYSLYSSERSERCC3 - 693 - 69
212LYSLYSSERSERFF3 - 693 - 69
113GLNGLNHISHISDD5 - 705 - 70
213GLNGLNHISHISEE5 - 705 - 70
114ALAALAHISHISDD2 - 702 - 70
214ALAALAHISHISFF2 - 702 - 70
115GLNGLNHISHISEE5 - 705 - 70
215GLNGLNHISHISFF5 - 705 - 70

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
RNA-BINDING PROTEIN HFQ / HF-1 / HOST FACTOR-I PROTEIN / HF-I / HFQ


Mass: 11179.354 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: RNA-BINDING PROTEIN / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PEH-10-(HFQ) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6X3
#2: RNA chain RYDC


Mass: 20699.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SMALL REGULATORY RNA
Source: (synth.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M TRI-SODIUM CITRATE, 0.1 M SODIUM CACODYLATE (PH 6.5), 15% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.48→24.47 Å / Num. obs: 9190 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 99.5 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.6
Reflection shellResolution: 3.48→3.69 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RER

3rer


Resolution: 3.48→24.32 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.842 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED CHAIN A 1-3 74- 102. CHAIN B 71-102. CHAIN C 1-2 71-102. CHAIN D 1 73-102. CHAIN E 1-4 72-102. CHAIN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED CHAIN A 1-3 74- 102. CHAIN B 71-102. CHAIN C 1-2 71-102. CHAIN D 1 73-102. CHAIN E 1-4 72-102. CHAIN F 1 72-102. THE FOLLOWING NUCLEOTIDES ARE DISORDERED 1-5 20-21.
RfactorNum. reflection% reflectionSelection details
Rfree0.28158 463 4.8 %RANDOM
Rwork0.21686 ---
obs0.21989 9190 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.089 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2---6.85 Å20 Å2
3---5.93 Å2
Refinement stepCycle: LAST / Resolution: 3.48→24.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 1187 0 45 4470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0174624
X-RAY DIFFRACTIONr_bond_other_d0.0010.023842
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.7576538
X-RAY DIFFRACTIONr_angle_other_deg3.34638869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08924.088137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8815570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9081521
X-RAY DIFFRACTIONr_chiral_restr0.0840.2765
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214345
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021036
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35060.16
12B35060.16
21A32730.18
22C32730.18
31A32980.16
32D32980.16
41A32740.18
42E32740.18
51A34640.17
52F34640.17
61B33290.16
62C33290.16
71B33260.14
72D33260.14
81B33570.15
82E33570.15
91B35140.15
92F35140.15
101C33830.19
102D33830.19
111C32210.18
112E32210.18
121C34410.17
122F34410.17
131D31660.17
132E31660.17
141D34070.17
142F34070.17
151E33260.17
152F33260.17
LS refinement shellResolution: 3.477→3.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 22 -
Rwork0.295 587 -
obs--87.37 %

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