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- PDB-3r2d: Crystal Structure of Antitermination Factors NusB and NusE in com... -

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Basic information

Entry
Database: PDB / ID: 3r2d
TitleCrystal Structure of Antitermination Factors NusB and NusE in complex with dsRNA
Components
  • 30S ribosomal protein S10
  • 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
  • N utilization substance protein B
KeywordsTRANSCRIPTION/RNA / cross species NusB-NusE-RNA interaction / transcription elongation / gene regulation / protein-RNA interaction / TRANSCRIPTION-RNA complex
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / small ribosomal subunit / tRNA binding / structural constituent of ribosome / translation / 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 / Ribosomal protein S10 / Ribosomal protein S10, conserved site / Ribosomal protein S10 / Ribosomal protein S10 signature. ...N-utilizing Substance Protein B Homolog; Chain A / NusB-like / NusB antitermination factor / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily / Ribosomal protein S10 / Ribosomal protein S10, conserved site / Ribosomal protein S10 / Ribosomal protein S10 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / RNA / RNA (> 10) / Small ribosomal subunit protein uS10 / Transcription antitermination protein NusB
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.199 Å
AuthorsStagno, J.R. / Ji, X.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination.
Authors: Stagno, J.R. / Altieri, A.S. / Bubunenko, M. / Tarasov, S.G. / Li, J. / Court, D.L. / Byrd, R.A. / Ji, X.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Jul 26, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N utilization substance protein B
B: N utilization substance protein B
J: 30S ribosomal protein S10
K: 30S ribosomal protein S10
R: 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
S: 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,80411
Polymers61,2736
Non-polymers5315
Water1,76598
1
A: N utilization substance protein B
J: 30S ribosomal protein S10
R: 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
S: 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5475
Polymers34,4414
Non-polymers1061
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N utilization substance protein B
K: 30S ribosomal protein S10
R: 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
S: 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8658
Polymers34,4414
Non-polymers4244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.786, 79.940, 106.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOMOLECULES 1 AND 2 REPRESENT SLIGHTLY DIFFERENT BINDING MODES OF NUSB/NUSE TO DOUBLE-STRANDED RNA

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Components

#1: Protein N utilization substance protein B / protein nusB


Mass: 17273.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_133, nusB / Plasmid: pDest527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66530
#2: Protein 30S ribosomal protein S10 / / protein nusE


Mass: 9558.287 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_008, NUSE, rpsJ / Plasmid: pDest527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66430
#3: RNA chain 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'


Mass: 3804.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: BoxA RNA / Source: (synth.) Aquifex aeolicus (bacteria)
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RIBOSOME BINDING LOOP (UNP RESIDUES 47-68) OF CHAINS J AND K (NUSE) HAS BEEN REPLACED WITH A ...THE RIBOSOME BINDING LOOP (UNP RESIDUES 47-68) OF CHAINS J AND K (NUSE) HAS BEEN REPLACED WITH A SERINE (SER47)

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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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M diammonium phosphate, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MAR 225 / Detector: CCD / Date: Feb 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.199→50 Å / Num. obs: 32257 / % possible obs: 94.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.285.50.542194.5
2.28-2.375.60.391194.9
2.37-2.485.70.24194.9
2.48-2.615.90.177194.5
2.61-2.775.90.127194.9
2.77-2.995.90.089196.8
2.99-3.295.80.072198.1
3.29-3.765.80.066198.4
3.76-4.745.60.047192.5
4.74-505.50.033187.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.84 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.17 Å
Translation2.5 Å38.17 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.1phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D3B

3d3b


Resolution: 2.199→33.642 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1659 5.15 %
Rwork0.2013 --
obs0.2033 32201 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.159 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8884 Å2-0 Å2-0 Å2
2---5.3617 Å20 Å2
3----0.5266 Å2
Refinement stepCycle: LAST / Resolution: 2.199→33.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 419 35 98 4032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044028
X-RAY DIFFRACTIONf_angle_d0.7235486
X-RAY DIFFRACTIONf_dihedral_angle_d16.4261638
X-RAY DIFFRACTIONf_chiral_restr0.056636
X-RAY DIFFRACTIONf_plane_restr0.003614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1991-2.26380.35731350.27322499X-RAY DIFFRACTION94
2.2638-2.33680.29931370.25982493X-RAY DIFFRACTION95
2.3368-2.42030.28841370.22582505X-RAY DIFFRACTION94
2.4203-2.51720.28011470.23592506X-RAY DIFFRACTION95
2.5172-2.63170.28681380.21762501X-RAY DIFFRACTION95
2.6317-2.77040.28851230.22692558X-RAY DIFFRACTION95
2.7704-2.94390.26331580.2232556X-RAY DIFFRACTION97
2.9439-3.1710.27811290.21832639X-RAY DIFFRACTION98
3.171-3.48980.27621350.2132668X-RAY DIFFRACTION98
3.4898-3.99410.23621330.18742643X-RAY DIFFRACTION98
3.9941-5.02950.19161450.16482461X-RAY DIFFRACTION90
5.0295-33.64620.20691420.19672513X-RAY DIFFRACTION88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3722-0.66392.3124.5761-1.84865.95210.52170.125-0.707-0.2322-0.08710.06110.86660.2541-0.00030.43960.1096-0.14450.45610.0440.412336.21966.3249-6.44
23.8932-0.7649-0.09565.06380.23223.05380.0202-0.16890.15460.3872-0.139-0.34420.0060.2295-00.4044-0.00410.00950.3243-0.00110.347744.313325.132230.0477
33.6498-1.24961.57873.4486-0.98182.5272-0.4653-0.14420.44460.09180.1083-0.1946-0.3812-0.23320.00010.410.0998-0.07940.65430.05690.440127.236226.7596-12.664
42.9719-1.7373-0.92043.0937-0.97793.38020.1762-0.10470.07940.3382-0.11870.4038-0.0604-0.1445-0.00020.5285-0.06870.17290.3594-0.12110.592625.268238.895432.6479
50.66690.80610.0131.6808-1.09091.576-1.84740.01513.29660.25210.7603-0.1861-1.2690.42630.00091.12710.2045-0.26770.8025-0.03331.117641.264832.02146.2397
60.1585-0.16330.101-0.09450.05370.5109-0.00020.39660.5763-0.1041-0.1949-0.1761-0.70180.35950.00040.67750.0615-0.0290.60670.0460.59541.014724.45697.8162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain J
4X-RAY DIFFRACTION4chain K
5X-RAY DIFFRACTION5chain R
6X-RAY DIFFRACTION6chain S

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