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- PDB-7w2p: Tudor domain of SMN in complex with a small molecule -

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Basic information

Entry
Database: PDB / ID: 7w2p
TitleTudor domain of SMN in complex with a small molecule
ComponentsSurvival motor neuron protein
KeywordsRNA BINDING PROTEIN / SMN / Tudor / 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
Chem-8AI / Survival motor neuron protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsLi, W. / Arrowsmith, C.H. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,68317
Polymers7,3521
Non-polymers33116
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-8 kcal/mol
Surface area4460 Å2
Unit cell
Length a, b, c (Å)35.893, 35.893, 92.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 7352.253 Da / Num. of mol.: 1
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-8AI / 2-[(4-fluorophenyl)methyl]-2-azatricyclo[7.3.0.0^{3,7}]dodeca-1(9),3(7)-dien-8-imine


Mass: 282.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19FN2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.02 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8 M sodium acetate, pH 7.0, 0.1 M Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.15→46 Å / Num. obs: 22319 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 21.5
Reflection shellResolution: 1.15→1.17 Å / Num. unique obs: 1064 / CC1/2: 0.785

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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: 1.15→33.44 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.818 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1496 1144 5.1 %RANDOM
Rwork0.1278 ---
obs0.1288 21099 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.12 Å2 / Biso mean: 11.864 Å2 / Biso min: 6.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 1.15→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms484 0 36 38 558
Biso mean--15.73 21.54 -
Num. residues----64
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.013595
X-RAY DIFFRACTIONr_bond_other_d0.0050.018523
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.7832
X-RAY DIFFRACTIONr_angle_other_deg1.8591.6231239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.096583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1324.82829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9531597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.536152
X-RAY DIFFRACTIONr_chiral_restr0.120.282
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02120
X-RAY DIFFRACTIONr_rigid_bond_restr2.77731117
LS refinement shellResolution: 1.15→1.179 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 95 -
Rwork0.234 1508 -
all-1603 -
obs--99.69 %

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