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- PDB-5j39: Crystal Structure of the extended TUDOR domain from TDRD2 -

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Basic information

Entry
Database: PDB / ID: 5j39
TitleCrystal Structure of the extended TUDOR domain from TDRD2
ComponentsTudor and KH domain-containing protein
KeywordsTRANSCRIPTION / tudor domain / structural genomics consortium / SGC
Function / homology
Function and homology information


piP-body / pi-body / P granule organization / piRNA processing / male meiotic nuclear division / fertilization / P granule / PIWI-interacting RNA (piRNA) biogenesis / spermatogenesis / mitochondrion / RNA binding
Similarity search - Function
: / : / : / : / Tudor domain / Tudor domain profile. / KH domain / K Homology domain, type 1 / Tudor domain / Tudor domain ...: / : / : / : / Tudor domain / Tudor domain profile. / KH domain / K Homology domain, type 1 / Tudor domain / Tudor domain / Type-1 KH domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CACODYLATE ION / Tudor and KH domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhang, H. / Tempel, W. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2.
Authors: Zhang, H. / Liu, K. / Izumi, N. / Huang, H. / Ding, D. / Ni, Z. / Sidhu, S.S. / Chen, C. / Tomari, Y. / Min, J.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Derived calculations / Category: pdbx_related_exp_data_set / pdbx_struct_oper_list
Item: _pdbx_related_exp_data_set.data_reference / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Aug 15, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.6Dec 11, 2019Group: Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_struct_assembly ...diffrn_radiation_wavelength / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.7Sep 27, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tudor and KH domain-containing protein
B: Tudor and KH domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,53722
Polymers47,2632
Non-polymers27420
Water1,49583
1
A: Tudor and KH domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7689
Polymers23,6311
Non-polymers1378
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tudor and KH domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,76813
Polymers23,6311
Non-polymers13712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.692, 53.798, 108.063
Angle α, β, γ (deg.)90.000, 84.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tudor and KH domain-containing protein / Tudor domain-containing protein 2


Mass: 23631.334 Da / Num. of mol.: 2 / Fragment: unp residues 309-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDRKH, TDRD2 / Plasmid: pET28MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE3 / References: UniProt: Q9Y2W6
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 18 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15% PEG-8000, 0.2 M magnesium chloride, 0.1 sodium cacodylate. A putative peptide ligand was added to the protein but not found during crystal structure analysis.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97957 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.95→53.8 Å / Num. obs: 30647 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.052 / Rrim(I) all: 0.101 / Net I/σ(I): 12 / Num. measured all: 115581
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.95-23.81.1141.6806621240.6010.661.29699
8.94-53.83.40.0242.711733460.9990.0120.02398.9

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FDR

3fdr


Resolution: 1.95→34.11 Å / Cor.coef. Fo:Fc: 0.9452 / Cor.coef. Fo:Fc free: 0.9258 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.139
Details: the structure was solved by molecular replacement (PHASER software) and a model build automatically (ARP/WARP) using data from an isomorphous crystal. Further refinement was performed with ...Details: the structure was solved by molecular replacement (PHASER software) and a model build automatically (ARP/WARP) using data from an isomorphous crystal. Further refinement was performed with the programs REFMAC and AUTOBUSTER. TLS groups were defined by the TLSMD server. Model geometry was validated with phenix.molprobity. Not resolved in this version of the model: peaks in the anomalous difference fourier map near residues Y371/F391/D393 are currently modeled as cacodylate ions, but positive difference density coincides with high B-factors for the ion modeled near TDRD2 chain A. Orientation and identity of these ions remain in question.
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1872 6.11 %thin shells (sftools)
Rwork0.1902 ---
obs0.1922 30630 99.5 %-
Displacement parametersBiso max: 99.88 Å2 / Biso mean: 41.99 Å2 / Biso min: 15.47 Å2
Baniso -1Baniso -2Baniso -3
1--6.809 Å20 Å2-8.2215 Å2
2--4.2135 Å20 Å2
3---2.5955 Å2
Refinement stepCycle: final / Resolution: 1.95→34.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 28 85 3093
Biso mean--43.78 40.63 -
Num. residues----392
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1019SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes481HARMONIC5
X-RAY DIFFRACTIONt_it3154HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion407SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3413SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3154HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4327HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.62
X-RAY DIFFRACTIONt_other_torsion17.1
LS refinement shellResolution: 1.95→2.02 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2402 185 6.2 %
Rwork0.2023 2799 -
all0.2047 2984 -
obs--99.27 %
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)
10.83570.1125-0.0491.9012-1.57673.5842-0.0545-0.11490.24890.10510.09050.2024-0.1742-0.1883-0.0360.09820.02920.1101-0.08320.0211-0.044325.250211.0506110.8162
21.17230.1918-0.98485.38220.05241.4288-0.08130.2710.0166-0.52330.17480.43430.0171-0.1091-0.09350.0881-0.03350.0241-0.10250.0211-0.132726.65335.315192.8569
31.16760.06620.03663.8956-2.51514.61340.00680.0650.03950.37870.22190.3402-0.339-0.3764-0.22860.01950.01280.1082-0.1070.0272-0.140219.82752.4555120.271
40.1674-0.0677-0.90561.11380.65652.51330.0191-0.0708-0.10510.07930.0687-0.12450.13620.015-0.08790.1630.01960.0913-0.1556-0.0252-0.06318.13877.530356.8198
51.27260.2226-0.06464.8212-0.70162.1766-0.06010.26390.0028-0.14350.0408-0.49740.05610.16180.01940.07590.0040.0912-0.1035-0.0149-0.059817.407614.711744.8373
60.9807-0.2728-0.8432.73960.87521.9819-0.0283-0.14-0.01850.0417-0.03530.00070.12150.17370.06360.1147-0.00870.099-0.1249-0.0071-0.13113.808616.180170.2308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|301 - 339}A301 - 339
2X-RAY DIFFRACTION2{A|340 - 414}A340 - 414
3X-RAY DIFFRACTION3{A|415 - 497}A415 - 497
4X-RAY DIFFRACTION4{B|301 - 344}B301 - 344
5X-RAY DIFFRACTION5{B|345 - 414}B345 - 414
6X-RAY DIFFRACTION6{B|415 - 496}B415 - 496

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