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- PDB-4qq6: Crystal Structure of tudor domain of SMN1 in complex with a small... -

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Basic information

Entry
Database: PDB / ID: 4qq6
TitleCrystal Structure of tudor domain of SMN1 in complex with a small organic molecule
ComponentsSurvival motor neuron proteinSurvival of motor neuron
KeywordsRNA BINDING PROTEIN / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / Cajal body / spliceosomal snRNP assembly / DNA-templated transcription termination / cytoplasmic ribonucleoprotein granule / Z disc / snRNP Assembly ...Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / Cajal body / spliceosomal snRNP assembly / DNA-templated transcription termination / cytoplasmic ribonucleoprotein granule / Z disc / snRNP Assembly / nervous system development / SARS-CoV-2 modulates host translation machinery / perikaryon / nuclear body / neuron projection / axon / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 ...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 / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-36X / Survival motor neuron protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLiu, Y. / Tempel, W. / Iqbal, A. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Min, J. / Structural Genomics Consortium (SGC)
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
DepositionJun 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 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)7,5985
Polymers7,4091
Non-polymers1884
Water46826
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.789, 27.789, 112.817
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsTHE BIOLOGICAL UNIT IS UNKNOWN

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Components

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


Mass: 7409.304 Da / Num. of mol.: 1 / Fragment: unp residues 82-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMN1, SMN, SMNT, SMN2, SMNC / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q16637
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#3: Chemical ChemComp-36X / 4-methyl-2,3,4,5,6,7-hexahydrodicyclopenta[b,e]pyridin-8(1H)-imine


Mass: 188.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 1.7 Å3/Da / Density % sol: 27.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2M ammonium sulfate, 0.2M potassium/sodium tartrate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→37.61 Å / Num. obs: 5006 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 19.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.75-1.7910.30.8062.92917283100
8.75-37.619.20.03253.94244699.1

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Processing

Software
NameVersionClassificationNB
Aimless0.3.3data scaling
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MHN

1mhn


Resolution: 1.75→24.07 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2294 / WRfactor Rwork: 0.1496 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7967 / SU B: 3.803 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1368 / SU Rfree: 0.1482 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Model is based on initial rigid body refinement of protein coordinates from PDB entry 1MHN. SMILES(CN1C2=C(CCC2)C(=N)C2=C1CCC2) represents the uncharged form of the ligand. Geometry ...Details: Model is based on initial rigid body refinement of protein coordinates from PDB entry 1MHN. SMILES(CN1C2=C(CCC2)C(=N)C2=C1CCC2) represents the uncharged form of the ligand. Geometry restraints for the inhibitor were prepared on the GRADE server with SMILES(C[n+]1c2CCCc2c(N)c2CCCc12). We note that mogul (CSD) inferred the type of the C1-C2 bond in refined ligand coordinates as double, which would be inconsistent with any traditional hybridization state of C1. COOT and MOLPROBITY were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 508 10.3 %RANDOM
Rwork0.1646 ---
obs0.1727 4942 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.38 Å2 / Biso mean: 26.6793 Å2 / Biso min: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å2-0 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms454 0 17 26 497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02489
X-RAY DIFFRACTIONr_bond_other_d0.0010.02443
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.965671
X-RAY DIFFRACTIONr_angle_other_deg0.87431027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.883561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26125.45522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.881578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7152
X-RAY DIFFRACTIONr_chiral_restr0.1140.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02107
X-RAY DIFFRACTIONr_mcbond_it3.2132.43236
X-RAY DIFFRACTIONr_mcbond_other3.2072.433237
X-RAY DIFFRACTIONr_mcangle_it4.473.601293
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 33 -
Rwork0.246 319 -
all-352 -
obs--100 %

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