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- PDB-8jy0: Crystal structure of RhoBAST complexed with TMR-DN -

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Basic information

Entry
Database: PDB / ID: 8jy0
TitleCrystal structure of RhoBAST complexed with TMR-DN
Components
  • RhoBAST
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA / RhoBAST / TMR-DN
Function / homology
Function and homology information


RNA-binding region-containing protein RBM41/RNPC3 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / TRIETHYLENE GLYCOL / : / : / RNA / RNA (> 10) / Small nuclear ribonucleoprotein polypeptide A
Similarity search - Component
Biological speciesHomo sapiens (human)
artificial sequences (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsZhang, Y. / Xiao, Y. / Xu, Z. / Fang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST.
Authors: Zhang, Y. / Xu, Z. / Xiao, Y. / Jiang, H. / Zuo, X. / Li, X. / Fang, X.
History
DepositionJul 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U1 small nuclear ribonucleoprotein A
B: RhoBAST
C: U1 small nuclear ribonucleoprotein A
E: U1 small nuclear ribonucleoprotein A
D: RhoBAST
F: RhoBAST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,11118
Polymers97,0626
Non-polymers3,04912
Water1,74797
1
A: U1 small nuclear ribonucleoprotein A
B: RhoBAST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6098
Polymers32,3542
Non-polymers1,2556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-24 kcal/mol
Surface area15730 Å2
MethodPISA
2
C: U1 small nuclear ribonucleoprotein A
D: RhoBAST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2756
Polymers32,3542
Non-polymers9214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-31 kcal/mol
Surface area15820 Å2
MethodPISA
3
E: U1 small nuclear ribonucleoprotein A
F: RhoBAST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2274
Polymers32,3542
Non-polymers8732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-10 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.531, 158.936, 182.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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Protein / RNA chain , 2 types, 6 molecules ACEBDF

#1: Protein U1 small nuclear ribonucleoprotein A


Mass: 11744.777 Da / Num. of mol.: 3 / Mutation: Y31H,Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M0R2B8
#2: RNA chain RhoBAST


Mass: 20609.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial sequences (others)
Production host: in vitro transcription vector pT7-TP(deltai) (others)

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Non-polymers , 6 types, 109 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-V8C / 5-aminocarbonyl-2-[3-(dimethylamino)-6-dimethylazaniumylidene-xanthen-9-yl]benzoate


Mass: 429.468 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H23N3O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-V7U / 2,4-dinitroaniline


Mass: 183.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5N3O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.97 Å3/Da / Density % sol: 69.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 40161 / % possible obs: 97.4 % / Redundancy: 5.4 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.043 / Rrim(I) all: 0.105 / Χ2: 1.185 / Net I/σ(I): 8.2 / Num. measured all: 216661
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.75-2.84.90.89719270.6790.8990.4361.0041.00295.8
2.8-2.8550.72419410.7140.9130.3490.8091.00695.1
2.85-2.94.90.60719160.7840.9380.2920.6790.98494.2
2.9-2.964.90.5219300.8570.9610.250.5811.02394.5
2.96-3.035.40.40219970.910.9760.1870.4461.04496.9
3.03-3.15.40.31219650.940.9840.1450.3461.08597
3.1-3.175.40.23519930.9580.9890.1080.261.10797.7
3.17-3.265.50.17219950.9840.9960.0780.191.08697.7
3.26-3.365.40.14119930.9870.9970.0640.1551.13598.1
3.36-3.465.10.15620140.9740.9940.0740.1741.7198
3.46-3.595.10.11320310.9910.9980.0530.1251.18198.9
3.59-3.735.20.13220310.9790.9950.0620.1471.69598.8
3.73-3.95.40.09820410.990.9970.0450.1081.58198.3
3.9-4.115.40.07119700.9970.9990.0320.0781.22896.9
4.11-4.3660.0620490.9980.9990.0260.0661.298.8
4.36-4.76.10.05320470.9980.9990.0220.0571.1798.8
4.7-5.175.90.04820580.99910.020.0521.13998.9
5.17-5.925.40.04520660.99810.020.0491.05198.9
5.92-7.465.60.0420590.99910.0180.0441.09897.3
7.46-505.60.03121380.99910.0140.0341.12796.7

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DRZ

1drz


Resolution: 2.75→28.95 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1998 4.99 %
Rwork0.2016 --
obs0.2031 40072 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 4301 2 97 6861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097304
X-RAY DIFFRACTIONf_angle_d1.36810824
X-RAY DIFFRACTIONf_dihedral_angle_d18.4212766
X-RAY DIFFRACTIONf_chiral_restr0.061346
X-RAY DIFFRACTIONf_plane_restr0.009644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.35451370.32682592X-RAY DIFFRACTION94
2.82-2.90.36521360.31282603X-RAY DIFFRACTION94
2.9-2.980.36581380.31452612X-RAY DIFFRACTION94
2.98-3.080.32211390.27542694X-RAY DIFFRACTION97
3.08-3.190.29321420.2342700X-RAY DIFFRACTION97
3.19-3.310.26271440.22792730X-RAY DIFFRACTION98
3.31-3.460.29341410.24622697X-RAY DIFFRACTION98
3.46-3.650.2541460.22192760X-RAY DIFFRACTION99
3.65-3.880.23551440.21032752X-RAY DIFFRACTION99
3.88-4.170.21381420.18322702X-RAY DIFFRACTION97
4.17-4.590.19381460.15482784X-RAY DIFFRACTION99
4.59-5.250.16951460.14982784X-RAY DIFFRACTION99
5.25-6.610.18981480.172814X-RAY DIFFRACTION98
6.61-28.950.17351490.16492850X-RAY DIFFRACTION96

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