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- PDB-5m9o: Crystal structure of human SND1 extended Tudor domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 5m9o
TitleCrystal structure of human SND1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide
Components
  • E2F peptide
  • Staphylococcal nuclease domain-containing protein 1
KeywordsTRANSCRIPTION / Transcriptional coactivator / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


RNAi effector complex / negative regulation of fat cell proliferation / Rb-E2F complex / lens fiber cell apoptotic process / regulation of cell cycle process / miRNA catabolic process / RISC complex binding / negative regulation of DNA binding / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / nuclease activity ...RNAi effector complex / negative regulation of fat cell proliferation / Rb-E2F complex / lens fiber cell apoptotic process / regulation of cell cycle process / miRNA catabolic process / RISC complex binding / negative regulation of DNA binding / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / nuclease activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / dense body / cellular response to fatty acid / mRNA stabilization / Transcription of E2F targets under negative control by DREAM complex / Activation of NOXA and translocation to mitochondria / : / micrococcal nuclease / regulatory ncRNA-mediated gene silencing / anoikis / Activation of PUMA and translocation to mitochondria / DNA-binding transcription activator activity / nuclear chromosome / G2 Phase / negative regulation of fat cell differentiation / G1/S-Specific Transcription / forebrain development / Transcriptional Regulation by E2F6 / mRNA catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of G1/S transition of mitotic cell cycle / positive regulation of glial cell proliferation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / cis-regulatory region sequence-specific DNA binding / RNA endonuclease activity / DNA damage checkpoint signaling / transcription coregulator activity / cellular response to nerve growth factor stimulus / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / RNA polymerase II transcription regulator complex / cellular response to xenobiotic stimulus / positive regulation of fibroblast proliferation / Transcriptional regulation of granulopoiesis / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / Cyclin D associated events in G1 / osteoblast differentiation / Signaling by BRAF and RAF1 fusions / melanosome / endonuclease activity / spermatogenesis / response to lipopolysaccharide / Oxidative Stress Induced Senescence / cellular response to hypoxia / sequence-specific DNA binding / DNA-binding transcription factor binding / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / positive regulation of apoptotic process / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / centrosome / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
RNA-induced silencing complex, nuclease component Tudor-SN / : / E2F transcription factor, CC-MB domain / E2F transcription factor CC-MB domain / E2F Family / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / Tudor domain ...RNA-induced silencing complex, nuclease component Tudor-SN / : / E2F transcription factor, CC-MB domain / E2F transcription factor CC-MB domain / E2F Family / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Transcription factor E2F1 / Staphylococcal nuclease domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTallant, C. / Savitsky, P. / Moehlenbrink, J. / Chan, C. / Nunez-Alonso, G. / Siejka, P. / Sorrell, F.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Tallant, C. / Savitsky, P. / Moehlenbrink, J. / Chan, C. / Nunez-Alonso, G. / Siejka, P. / Sorrell, F.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Fedorov, O. / La Thangue, N.B. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide
Authors: Tallant, C. / Savitsky, P. / Moehlenbrink, J. / Chan, C. / Nunez-Alonso, G. / Siejka, P. / Sorrell, F.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Fedorov, O. / La ...Authors: Tallant, C. / Savitsky, P. / Moehlenbrink, J. / Chan, C. / Nunez-Alonso, G. / Siejka, P. / Sorrell, F.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Fedorov, O. / La Thangue, N.B. / Knapp, S.
History
DepositionNov 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Derived calculations
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Staphylococcal nuclease domain-containing protein 1
B: E2F peptide


Theoretical massNumber of molelcules
Total (without water)26,3912
Polymers26,3912
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-6 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.243, 80.626, 39.289
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Staphylococcal nuclease domain-containing protein 1 / 100 kDa coactivator / EBNA2 coactivator p100 / Tudor domain-containing protein 11 / p100 co-activator


Mass: 25369.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SND1, TDRD11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7KZF4
#2: Protein/peptide E2F peptide


Mass: 1021.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01094*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10 % PEG 1000, 10% PEG 8000 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→28.14 Å / Num. obs: 38367 / % possible obs: 96 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 16.2
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.8 / % possible all: 69.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OMC

3omc


Resolution: 1.45→28.14 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.615 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 1920 5 %RANDOM
Rwork0.22892 ---
obs0.23039 36421 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.625 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å2-0.42 Å2
2---0.05 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.45→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 0 166 1918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191793
X-RAY DIFFRACTIONr_bond_other_d0.0020.021693
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9592431
X-RAY DIFFRACTIONr_angle_other_deg0.95933889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4395220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34423.97788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27615291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.251513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02421
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3642.043880
X-RAY DIFFRACTIONr_mcbond_other1.3652.039879
X-RAY DIFFRACTIONr_mcangle_it2.1963.0521097
X-RAY DIFFRACTIONr_mcangle_other2.1953.0561098
X-RAY DIFFRACTIONr_scbond_it1.6342.199913
X-RAY DIFFRACTIONr_scbond_other1.6332.203914
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6283.2321334
X-RAY DIFFRACTIONr_long_range_B_refined4.75916.8732068
X-RAY DIFFRACTIONr_long_range_B_other4.59616.5932009
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.449→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 124 -
Rwork0.303 1970 -
obs--71.61 %

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