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- PDB-4eya: Crystal Structure of a Plectonemic RNA Supercoil -

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Basic information

Entry
Database: PDB / ID: 4eya
TitleCrystal Structure of a Plectonemic RNA Supercoil
Components
  • N utilization substance protein B homolog
  • RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
Keywordstranscription/RNA / transcription elongation / ssRNA / dsRNA / NusE protein / TRANSCRIPTION / transcription-RNA complex
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / RNA binding / cytosol
Similarity search - Function
N-utilizing Substance Protein B Homolog; Chain A / NusB-like / NusB antitermination factor / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Transcription antitermination protein NusB
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsStagno, J.R. / Ji, X.
CitationJournal: Nat Commun / Year: 2012
Title: Crystal structure of a plectonemic RNA supercoil.
Authors: Stagno, J.R. / Ma, B. / Li, J. / Altieri, A.S. / Byrd, R.A. / Ji, X.
History
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software / Item: _pdbx_entity_src_syn.organism_scientific
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_ncs_dom_lim / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N utilization substance protein B homolog
B: N utilization substance protein B homolog
C: N utilization substance protein B homolog
D: N utilization substance protein B homolog
E: N utilization substance protein B homolog
F: N utilization substance protein B homolog
G: N utilization substance protein B homolog
H: N utilization substance protein B homolog
a: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
c: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
e: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
g: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
i: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
j: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
h: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
f: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
d: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
b: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
k: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
m: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
o: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
q: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
s: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
t: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
r: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
p: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
n: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
l: RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,71844
Polymers213,22828
Non-polymers1,48916
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.424, 126.264, 144.131
Angle α, β, γ (deg.)90.000, 89.980, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H
13a
23n
14i
24l

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHRchain A and (resseq 1:136 )AA1 - 1361 - 136
21METMETTHRTHRchain C and (resseq 1:136 )CC1 - 1361 - 136
31METMETTHRTHRchain E and (resseq 1:136 )EE1 - 1361 - 136
41METMETTHRTHRchain G and (resseq 1:136 )GG1 - 1361 - 136
12TYRTYRSERSERchain B and (resseq 3:138 )BB3 - 1383 - 138
22TYRTYRSERSERchain D and (resseq 3:138 )DD3 - 1383 - 138
32TYRTYRSERSERchain F and (resseq 3:138 )FF3 - 1383 - 138
42TYRTYRSERSERchain H and (resseq 3:138 )HH3 - 1383 - 138
13GGAAchain a or chain c or chain e or chain g or chain h or chain f or chain d or chain baI1 - 121 - 12
23GGAAchain m or chain o or chain q or chain s or chain t or chain r or chain p or chain nnAA1 - 121 - 12
14GGAAchain i or chain jiM1 - 121 - 12
24GGAAchain k or chain llBA1 - 121 - 12

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.999999, 0.001259, -0.00045), (-0.001259, -0.999999, 0.000419), (-0.000449, 0.000419, 1)63.226501, -62.0383, 72.097801
2given(1.49255, 0.001259, -0.00045), (-1, 1.5575, 0.000419), (0.000839, 0.000774, 0.999999)62.561699, 0.588667, 108.109001
3given(-0.00036, -0.999999, -0.001001), (0.999999, -0.000359, -0.000948), (0.000947, -0.001002, 0.999999)0.516366, -62.662701, 36.003899
4given(-0.999999, 0.001364, 0.000791), (-0.001365, -0.999999, -0.000453), (0.000791, -0.000454, 1)63.244701, -62.084499, 72.025497
5given(7.13255, 0.001364, 0.000791), (-1, 7.12205, -0.000453), (0.000183, -0.000573, 1)62.675999, 0.573941, 108.058998
6given(0.000104, -1, 0.000535), (1, 0.000104, 0.000183), (-0.000183, 0.000535, 1)0.516977, -62.629799, 36.040699
7given(0.000692, 1, 0.000256), (-1, 0.000692, 0.000432), (0.000432, -0.000256, 1)62.6325, 0.569882, -36.055801
8given(6.88643, 1, 0.000256), (-1, 6.88064, 0.000432), (0.000369, -0.000157, 1)62.684799, 0.532509, 108.096001

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Components

#1: Protein
N utilization substance protein B homolog / Protein NusB


Mass: 17142.789 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_133, nusB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66530
#2: RNA chain
RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')


Mass: 3804.296 Da / Num. of mol.: 20 / Source method: obtained synthetically
Details: Synthetic RNA representing the BoxA RNA from Aquifex aeolicus
Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium sulfate, 26% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.0622 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2009
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0622 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 37610 / Num. obs: 37610 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.095 / Χ2: 0.979 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.213.90.45722120.986153.1
3.21-3.344.20.35427840.977167.9
3.34-3.494.80.40635940.972188.3
3.49-3.685.90.36340860.99198.9
3.68-3.917.10.26741360.9581100
3.91-4.217.70.19441081.0061100
4.21-4.637.80.1241490.9761100
4.63-5.37.80.09241780.9581100
5.3-6.677.80.09441330.9691100
6.67-507.50.03442300.9971100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.12
Highest resolutionLowest resolution
Rotation2.99 Å44.75 Å
Translation2.99 Å44.75 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R2D

3r2d


Resolution: 3.2→39.974 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.87 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.272 972 2.74 %Random
Rwork0.2282 ---
all0.2316 35471 --
obs0.2295 35471 94.77 %-
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.045 Å2 / ksol: 0.294 e/Å3
Displacement parametersBiso max: 205.97 Å2 / Biso mean: 89.9411 Å2 / Biso min: 33.64 Å2
Baniso -1Baniso -2Baniso -3
1-14.0351 Å2-0 Å2-0.5838 Å2
2--8.2663 Å20 Å2
3----22.3014 Å2
Refinement stepCycle: LAST / Resolution: 3.2→39.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8948 5020 92 0 14060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214784
X-RAY DIFFRACTIONf_angle_d0.54920976
X-RAY DIFFRACTIONf_chiral_restr0.0492516
X-RAY DIFFRACTIONf_plane_restr0.0031772
X-RAY DIFFRACTIONf_dihedral_angle_d15.8926288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1116X-RAY DIFFRACTIONPOSITIONAL0.014
12C1116X-RAY DIFFRACTIONPOSITIONAL0.014
13E1116X-RAY DIFFRACTIONPOSITIONAL0.003
14G1116X-RAY DIFFRACTIONPOSITIONAL0.014
21B1109X-RAY DIFFRACTIONPOSITIONAL0.002
22D1109X-RAY DIFFRACTIONPOSITIONAL0.002
23F1109X-RAY DIFFRACTIONPOSITIONAL0.002
24H1109X-RAY DIFFRACTIONPOSITIONAL0.002
31a2008X-RAY DIFFRACTIONPOSITIONAL0.002
32n2008X-RAY DIFFRACTIONPOSITIONAL0.002
41i502X-RAY DIFFRACTIONPOSITIONAL0.002
42l502X-RAY DIFFRACTIONPOSITIONAL0.002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.36870.34171110.28823626373771
3.3687-3.57960.29971380.29264869500794
3.5796-3.85580.33321410.247151505291100
3.8558-4.24340.27561390.235152455384100
4.2434-4.85650.24551480.201651555303100
4.8565-6.11520.29251450.238551865331100
6.1152-39.97680.22991500.20335268541899

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