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- PDB-3r2c: Crystal Structure of Antitermination Factors NusB and NusE in com... -

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Basic information

Entry
Database: PDB / ID: 3r2c
TitleCrystal Structure of Antitermination Factors NusB and NusE in complex with BoxA RNA
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 signature. / Ribosomal protein S10 ...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 signature. / Ribosomal protein S10 / 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
ACETATE ION / 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: 1.902 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: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...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 / 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_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)62,07618
Polymers60,8976
Non-polymers1,17912
Water4,306239
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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,14410
Polymers30,4483
Non-polymers6967
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N utilization substance protein B
K: 30S ribosomal protein S10
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)30,9328
Polymers30,4483
Non-polymers4845
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.530, 113.008, 65.763
Angle α, β, γ (deg.)90.000, 102.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABJK

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


Mass: 17142.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_133, nusB / Plasmid: pDest42 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66530
#2: Protein 30S ribosomal protein S10 / protein nusE


Mass: 9501.236 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: pDest42 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66430

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RNA chain , 1 types, 2 molecules RS

#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)

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Non-polymers , 3 types, 251 molecules

#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, 25% PEG8000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 310K

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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 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 42602 / % possible obs: 94.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.102 / Χ2: 1.6 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.972.80.5233541.25174.5
1.97-2.053.40.53738381.231185.1
2.05-2.1440.44741631.28192.2
2.14-2.254.70.35543611.422196.5
2.25-2.395.50.28844011.406197.9
2.39-2.585.90.22344181.299198.6
2.58-2.8460.16244991.43199.1
2.84-3.255.90.11144681.703199.1
3.25-4.095.80.06445282.109199.3
4.09-405.60.04745722.229199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.8 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.56 Å
Translation2.5 Å37.56 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
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 3R2D

3r2d


Resolution: 1.902→35.663 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8686 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 2160 5.08 %
Rwork0.1693 --
obs0.171 42498 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.845 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso max: 122.21 Å2 / Biso mean: 37.7366 Å2 / Biso min: 7.19 Å2
Baniso -1Baniso -2Baniso -3
1-3.9657 Å20 Å2-6.5546 Å2
2---1.126 Å20 Å2
3----2.8397 Å2
Refinement stepCycle: LAST / Resolution: 1.902→35.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 376 78 239 4218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074126
X-RAY DIFFRACTIONf_angle_d1.0285605
X-RAY DIFFRACTIONf_chiral_restr0.061639
X-RAY DIFFRACTIONf_plane_restr0.005638
X-RAY DIFFRACTIONf_dihedral_angle_d15.5161680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9022-1.94640.292980.2582052215071
1.9464-1.99510.26551240.23122259238379
1.9951-2.04910.25231320.23052466259886
2.0491-2.10930.26041420.21542588273091
2.1093-2.17740.25511380.18872700283895
2.1774-2.25520.20571380.16692791292997
2.2552-2.34550.20981400.15142788292898
2.3455-2.45220.20581510.15752784293598
2.4522-2.58150.19811620.1612796295898
2.5815-2.74320.20861690.1612831300099
2.7432-2.95490.19861380.15432835297399
2.9549-3.25210.22171600.17352829298999
3.2521-3.72220.20161670.16252851301899
3.7222-4.68790.16131650.13992850301599
4.6879-35.66940.18011360.18252918305499
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)
10.4572-0.1150.28230.34220.01340.56440.0253-0.0127-0.0171-0.02560.010.01410.0293-0.018300.00850.00470.0220.04760.00110.04772.0473-24.693220.0385
20.4437-0.17790.22890.4380.11080.7587-0.0854-0.0360.008-0.0610.02710.0242-0.0757-0.021600.05990.0075-0.0150.04860.00290.050214.1246-18.288551.6574
30.2007-0.0921-0.03270.3114-0.10860.2087-0.08470.06340.04070.0628-0.0063-0.0793-0.22370.009400.1538-0.0204-0.02220.07160.0220.10028.8483-3.337524.5805
40.13370.1106-0.06330.1151-0.16650.23960.10180.0391-0.09080.00050.035-0.00720.30820.18700.19740.0765-0.06220.0872-0.03280.127418.3832-38.903942.1543
50.034-0.0731-0.02440.083-0.09290.17660.17510.0951-0.1039-0.5796-0.06250.23480.05110.060400.08670.00520.06320.1181-0.0190.00982.4505-27.26045.951
60.1365-0.00650.22380.2307-0.19820.1403-0.1428-0.0332-0.00740.080.0114-0.13880.05520.1309-00.1109-0.0033-0.00390.1507-0.01070.134127.0264-15.854557.5873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:137)A1 - 137
2X-RAY DIFFRACTION2(chain B and resid 1:140)B1 - 140
3X-RAY DIFFRACTION3(chain J and resid 3:82)J3 - 82
4X-RAY DIFFRACTION4(chain K and resid 3:81)K3 - 81
5X-RAY DIFFRACTION5(chain R and resid 1:9)R1 - 9
6X-RAY DIFFRACTION6(chain S and resid 1:10)S1 - 10

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