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- PDB-4b9w: Structure of extended Tudor domain TD3 from mouse TDRD1 in comple... -

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Basic information

Entry
Database: PDB / ID: 4b9w
TitleStructure of extended Tudor domain TD3 from mouse TDRD1 in complex with MILI peptide containing dimethylarginine 45.
Components
  • PIWI-LIKE PROTEIN 2
  • TUDOR DOMAIN-CONTAINING PROTEIN 1
KeywordsREPLICATION
Function / homology
Function and homology information


perinucleolar chromocenter / PET complex / pi-body / secondary piRNA processing / transposable element silencing by mRNA destabilization / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / positive regulation of meiosis I / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing ...perinucleolar chromocenter / PET complex / pi-body / secondary piRNA processing / transposable element silencing by mRNA destabilization / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / positive regulation of meiosis I / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by heterochromatin formation / germ-line stem cell population maintenance / negative regulation of circadian rhythm / chromatoid body / dense body / positive regulation of cytoplasmic translation / regulatory ncRNA-mediated gene silencing / P granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / oogenesis / germ cell development / RNA endonuclease activity / meiotic cell cycle / rhythmic process / spermatogenesis / ribonucleoprotein complex / mRNA binding / synapse / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / : / : / Piwi, N-terminal domain / Tudor domain / Tudor domain profile. / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain ...: / : / : / : / Piwi, N-terminal domain / Tudor domain / Tudor domain profile. / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Piwi-like protein 2 / Tudor domain-containing protein 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMathioudakis, N. / Palencia, A. / Kadlec, J. / Round, A. / Tripsianes, K. / Sattler, M. / Pillai, R.S. / Cusack, S.
CitationJournal: Rna / Year: 2012
Title: The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors.
Authors: Mathioudakis, N. / Palencia, A. / Kadlec, J. / Round, A. / Tripsianes, K. / Sattler, M. / Pillai, R.S. / Cusack, S.
History
DepositionSep 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Apr 10, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn / struct_ref
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
P: PIWI-LIKE PROTEIN 2
S: PIWI-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0296
Polymers47,8454
Non-polymers1842
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-26.1 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.940, 53.960, 60.790
Angle α, β, γ (deg.)93.69, 98.56, 111.68
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999988, -0.000511, 0.004916), (-0.000503, -0.999998, -0.00167), (0.004917, 0.001667, -0.999987)-0.21223, 70.61587, 95.13131

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Components

#1: Protein TUDOR DOMAIN-CONTAINING PROTEIN 1 / TDRD1


Mass: 22578.844 Da / Num. of mol.: 2 / Fragment: EXTENDED TUDOR DOMAIN TD3, RESIDUES 692-892
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99MV1
#2: Protein/peptide PIWI-LIKE PROTEIN 2 / MILI


Mass: 1343.582 Da / Num. of mol.: 2
Fragment: N-TERMINAL PEPTIDE CONTAINING METHYLATED ARG45, RESIDUES 38-50
Source method: obtained synthetically / Details: ARG45 IS SYMMETRICALLY DIMETHYLATED / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q8CDG1
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsGLYCEROL (GOL): FROM CRYOPROTECTANT

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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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PROTEIN:PEPTIDE 1:5 RATIO, 0.2 M AMMONIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.5, 30 % PEG8000, 0.01 M MAGNESIUM ACETATE TETRAHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 25755 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.28
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.55 / % possible all: 95.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RESOLVEphasing
REFMAC5.6.0116refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→36.94 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.859 / SU B: 6.314 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28366 1275 5 %RANDOM
Rwork0.21949 ---
obs0.22262 24480 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.793 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.08 Å20.07 Å2
2--0.01 Å20.1 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 12 186 3405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023304
X-RAY DIFFRACTIONr_bond_other_d0.0010.022193
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9644492
X-RAY DIFFRACTIONr_angle_other_deg0.86135360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6845400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43624.803152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55715534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8331514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02672
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 73 -
Rwork0.284 1790 -
obs--94.52 %

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