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- PDB-5m9n: Crystal structure of human TDRD1 extended Tudor domain in complex... -

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Basic information

Entry
Database: PDB / ID: 5m9n
TitleCrystal structure of human TDRD1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide
Components
  • E2F peptide
  • Tudor domain-containing protein 1
KeywordsSTRUCTURAL PROTEIN / RNA-mediated gene silencing / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


transposable element silencing by siRNA-mediated heterochromatin formation / negative regulation of fat cell proliferation / pi-body / Rb-E2F complex / lens fiber cell apoptotic process / P granule organization / piRNA processing / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA binding / Inhibition of replication initiation of damaged DNA by RB1/E2F1 ...transposable element silencing by siRNA-mediated heterochromatin formation / negative regulation of fat cell proliferation / pi-body / Rb-E2F complex / lens fiber cell apoptotic process / P granule organization / piRNA processing / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA binding / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / chromatoid body / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to fatty acid / Activation of NOXA and translocation to mitochondria / Transcription of E2F targets under negative control by DREAM complex / P granule / anoikis / Activation of PUMA and translocation to mitochondria / mRNA stabilization / DNA-binding transcription activator activity / nuclear chromosome / G2 Phase / negative regulation of fat cell differentiation / G1/S-Specific Transcription / Transcriptional Regulation by E2F6 / forebrain development / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / PIWI-interacting RNA (piRNA) biogenesis / germ cell development / 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 / DNA damage checkpoint signaling / meiotic cell cycle / 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 / response to lipopolysaccharide / Oxidative Stress Induced Senescence / spermatogenesis / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / ribonucleoprotein complex / negative regulation of DNA-templated transcription / synapse / positive regulation of gene expression / centrosome / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / : / : / 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 ...: / : / : / 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. / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Tudor domain / Tudor domain / SNase-like, OB-fold superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
N3, N4-DIMETHYLARGININE / Transcription factor E2F1 / Tudor domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTallant, C. / Savitsky, P. / Moehlenbrink, J. / Chan, C. / Nunez-Alonso, G. / Newman, J.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Tallant, C. / Savitsky, P. / Moehlenbrink, J. / Chan, C. / Nunez-Alonso, G. / Newman, J.A. / 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 TDRD1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide
Authors: Tallant, C. / Savitsky, P. / Moehlenbrink, J. / Chan, C. / Nunez-Alonso, G. / Newman, J.A. / 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 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tudor domain-containing protein 1
B: Tudor domain-containing protein 1
C: E2F peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7737
Polymers50,3843
Non-polymers3884
Water1,42379
1
A: Tudor domain-containing protein 1
C: E2F peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1984
Polymers26,0742
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tudor domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5743
Polymers24,3101
Non-polymers2642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.910, 52.962, 59.619
Angle α, β, γ (deg.)64.94, 88.85, 67.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tudor domain-containing protein 1 / Cancer/testis antigen 41.1 / CT41.1


Mass: 24310.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDRD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXT4
#2: Protein/peptide E2F peptide


Mass: 1764.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 2MR: dimethylated arginine / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01094*PLUS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-2MR / N3, N4-DIMETHYLARGININE


Type: L-peptide linking / Mass: 202.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG4000, 0.2M MgCl2, 0.1 M Tris pH 8.5 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0282 Å / Relative weight: 1
ReflectionResolution: 1.95→29.34 Å / Num. obs: 30788 / % possible obs: 96.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.712 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.025 / Net I/σ(I): 16.7
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.3 / % possible all: 89.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B9X

4b9x


Resolution: 1.95→29.34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.633 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26035 1600 5.2 %RANDOM
Rwork0.21222 ---
obs0.21482 29186 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.441 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å21.66 Å20.06 Å2
2---3.11 Å20.17 Å2
3---3.97 Å2
Refinement stepCycle: 1 / Resolution: 1.95→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 25 79 3236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193226
X-RAY DIFFRACTIONr_bond_other_d0.0020.023199
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9984366
X-RAY DIFFRACTIONr_angle_other_deg0.96937402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7635404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71625.92125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71815574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.824158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213546
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02643
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_it1.4272.2741619
X-RAY DIFFRACTIONr_mcbond_other1.4242.2711618
X-RAY DIFFRACTIONr_mcangle_it2.4063.3842016
X-RAY DIFFRACTIONr_mcangle_other2.4073.3882017
X-RAY DIFFRACTIONr_scbond_it1.4092.4191607
X-RAY DIFFRACTIONr_scbond_other1.4092.4191607
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3253.5512349
X-RAY DIFFRACTIONr_long_range_B_refined6.13317.8653431
X-RAY DIFFRACTIONr_long_range_B_other6.12717.7613412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.946→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 113 -
Rwork0.293 2004 -
obs--91.29 %
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)
11.06890.47610.62761.1965-0.34910.7740.04480.02680.101-0.0275-0.0420.11130.07990.0544-0.00280.2042-0.0651-0.05560.33030.020.062838.080241.85345.5552
20.05030.2312-0.00781.5141-0.06481.64440.0474-0.0642-0.03620.03380.011-0.0817-0.0717-0.1439-0.05840.2308-0.0859-0.08730.38710.090.048146.479126.843727.3675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A474 - 675
2X-RAY DIFFRACTION2B473 - 672

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