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- PDB-7w30: Tudor domain of SMN in complex with a small molecule -

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Basic information

Entry
Database: PDB / ID: 7w30
TitleTudor domain of SMN in complex with a small molecule
ComponentsSurvival motor neuron protein
KeywordsRNA BINDING PROTEIN / SMN / Tudor domain / small molecule
Function / homology
Function and homology information


Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / cytoplasmic ribonucleoprotein granule / Z disc / nervous system development ...Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / cytoplasmic ribonucleoprotein granule / Z disc / nervous system development / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / perikaryon / nuclear body / neuron projection / axon / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
SMN complex subunit Smn1 / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain
Similarity search - Domain/homology
1,2-dimethylquinolin-4-imine / Survival motor neuron protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, W. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Liu, Y. / Min, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nat Commun / Year: 2022
Title: A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II.
Authors: Liu, Y. / Iqbal, A. / Li, W. / Ni, Z. / Wang, Y. / Ramprasad, J. / Abraham, K.J. / Zhang, M. / Zhao, D.Y. / Qin, S. / Loppnau, P. / Jiang, H. / Guo, X. / Brown, P.J. / Zhen, X. / Xu, G. / ...Authors: Liu, Y. / Iqbal, A. / Li, W. / Ni, Z. / Wang, Y. / Ramprasad, J. / Abraham, K.J. / Zhang, M. / Zhao, D.Y. / Qin, S. / Loppnau, P. / Jiang, H. / Guo, X. / Brown, P.J. / Zhen, X. / Xu, G. / Mekhail, K. / Ji, X. / Bedford, M.T. / Greenblatt, J.F. / Min, J.
History
DepositionNov 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Survival motor neuron protein
B: Survival motor neuron protein
C: Survival motor neuron protein
D: Survival motor neuron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,09837
Polymers29,4094
Non-polymers68933
Water1,982110
1
A: Survival motor neuron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,69713
Polymers7,3521
Non-polymers34412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Survival motor neuron protein


Theoretical massNumber of molelcules
Total (without water)7,3528
Polymers7,3521
Non-polymers07
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Survival motor neuron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,52410
Polymers7,3521
Non-polymers1729
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Survival motor neuron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5246
Polymers7,3521
Non-polymers1725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.725, 70.725, 119.931
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Survival motor neuron protein / Component of gems 1 / Gemin-1


Mass: 7352.253 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMN1, SMN, SMNT, SMN2, SMNC / Production host: Escherichia coli (E. coli) / References: UniProt: Q16637
#2: Chemical
ChemComp-8AT / 1,2-dimethylquinolin-4-imine


Mass: 172.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 29 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M Hepes, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→35.36 Å / Num. obs: 32704 / % possible obs: 99.4 % / Redundancy: 10.5 % / CC1/2: 1 / Net I/σ(I): 29.4
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 1857 / CC1/2: 0.774

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QQ6

4qq6


Resolution: 1.8→35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.187 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 1243 3.8 %RANDOM
Rwork0.21 ---
obs0.2118 31293 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.27 Å2 / Biso mean: 29.034 Å2 / Biso min: 5.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å2-0 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 1.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 94 110 1995
Biso mean--30.83 32.33 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131943
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171681
X-RAY DIFFRACTIONr_angle_refined_deg1.921.6582671
X-RAY DIFFRACTIONr_angle_other_deg1.5351.6123899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5055246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6625.30183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39815285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.311154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 84 -
Rwork0.267 2228 -
all-2312 -
obs--98.09 %
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)
12.5707-1.564-0.49863.41170.30713.1486-0.02970.09230.3211-0.0830.0596-0.3592-0.2243-0.0103-0.02990.17470.04190.00480.0649-0.02360.071825.616928.807925.6153
22.9362-0.82920.01133.4907-0.22812.47580.0064-0.18890.13530.21530.0929-0.4024-0.08160.2441-0.09930.1890.0904-0.07090.0899-0.05560.08914.008642.25741.0186
33.1338-0.64790.84973.823-0.53764.2701-0.038-0.1680.06860.09270.0596-0.0029-0.1347-0.0518-0.02160.09540.0861-0.02660.0893-0.02920.010226.599126.489348.868
42.2201-1.7069-0.0032.8947-0.21595.624-0.00390.25060.2509-0.4378-0.1371-0.391-0.12690.47240.14090.2596-0.01120.01650.14290.02550.100312.100444.046115.0093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 301
2X-RAY DIFFRACTION2B89 - 302
3X-RAY DIFFRACTION3C88 - 301
4X-RAY DIFFRACTION4D91 - 301

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