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- PDB-3omc: Structure of human SND1 extended tudor domain in complex with the... -

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Basic information

Entry
Database: PDB / ID: 3omc
TitleStructure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R4me2s
Components
  • SYNTHETIC PEPTIDEPeptide synthesis
  • Staphylococcal nuclease domain-containing protein 1
KeywordsTRANSCRIPTION REGULATOR / staphylococcal nuclease domain-containing protein 1 / TDRD11 / SND1 / PIWIL1/Miwi / Structural Genomics Consortium / SGC / P100 extended Tudor domain / transcription regulation / symmetrically dimethylated arginine peptides derived from PIWIL1
Function / homology
Function and homology information


regulation of cell cycle process / miRNA catabolic process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / RISC complex / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / mRNA catabolic process ...regulation of cell cycle process / miRNA catabolic process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / RISC complex / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / mRNA catabolic process / RNA endonuclease activity / transcription coregulator activity / osteoblast differentiation / melanosome / Signaling by BRAF and RAF1 fusions / endonuclease activity / cadherin binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol
Similarity search - Function
: / RNA-induced silencing complex, nuclease component Tudor-SN / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / Thermonuclease active site / Thermonuclease family signature 2. ...: / RNA-induced silencing complex, nuclease component Tudor-SN / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Staphylococcal nuclease domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsLam, R. / Liu, K. / Guo, Y.H. / Bian, C.B. / Xu, C. / MacKenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. ...Lam, R. / Liu, K. / Guo, Y.H. / Bian, C.B. / Xu, C. / MacKenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain.
Authors: Liu, K. / Chen, C. / Guo, Y. / Lam, R. / Bian, C. / Xu, C. / Zhao, D.Y. / Jin, J. / MacKenzie, F. / Pawson, T. / Min, J.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 15, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _entity_name_com.name / _entity_src_gen.gene_src_common_name ..._entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Staphylococcal nuclease domain-containing protein 1
B: Staphylococcal nuclease domain-containing protein 1
C: SYNTHETIC PEPTIDE
D: SYNTHETIC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4065
Polymers61,3714
Non-polymers351
Water5,044280
1
A: Staphylococcal nuclease domain-containing protein 1
C: SYNTHETIC PEPTIDE


Theoretical massNumber of molelcules
Total (without water)30,6852
Polymers30,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-7 kcal/mol
Surface area12270 Å2
MethodPISA
2
B: Staphylococcal nuclease domain-containing protein 1
D: SYNTHETIC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7213
Polymers30,6852
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-13 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.622, 75.834, 80.177
Angle α, β, γ (deg.)90.000, 90.370, 90.000
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: 29797.428 Da / Num. of mol.: 2 / Fragment: Tudor domain (UNP residues 650-910)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SND1, TDRD11 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: Q7KZF4
#2: Protein/peptide SYNTHETIC PEPTIDE / Peptide synthesis


Mass: 888.031 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Symmetrically dimethylated arginine peptide R4me2s derived from PIWIL1
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 1.76 Å3/Da / Density % sol: 30.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG1500, 1:500 V8 PROTEASE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 11, 2010 / Details: VariMax HR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 41508 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Χ2: 1.002 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.77-1.833.50.28240350.9998
1.83-1.913.60.21541521.02799.5
1.91-1.993.60.15441411.0299.6
1.99-2.13.60.11241320.98499.8
2.1-2.233.60.08441630.942100
2.23-2.43.70.06741380.995100
2.4-2.643.70.05341250.973100
2.64-3.033.70.03741890.998100
3.03-3.813.80.02342001.109100
3.81-503.70.01842330.97899.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.94 Å25.96 Å
Translation1.94 Å25.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.6.0081refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O4X

2o4x


Resolution: 1.77→25.05 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.822 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 2088 5 %RANDOM
Rwork0.1786 ---
obs0.1803 41488 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80.11 Å2 / Biso mean: 29.3425 Å2 / Biso min: 14.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å2-0.85 Å2
2---0.43 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.77→25.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 1 280 3782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223583
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9584861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4525441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11824.045178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65715589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3241527
X-RAY DIFFRACTIONr_chiral_restr0.0830.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212769
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 148 -
Rwork0.216 2854 -
all-3002 -
obs--98.82 %
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)
10.1683-0.2350.32380.6176-0.46570.7607-0.02340.0099-0.00680.05410.0178-0.0102-0.04110.01790.00560.00920.0050.00760.0222-0.00470.02343.8630.7438.893
20.0925-0.18520.32030.6135-0.52211.3908-0.01210.0146-0.0039-0.0427-0.03560.0121-0.09460.07120.04770.0234-0.0057-0.0040.01290.00140.01793.8791.90147.771
31.7225-2.1884-1.9155.4071-0.93896.4581-0.1813-0.1040.07590.0179-0.2015-0.46270.46520.5380.38280.05350.07710.01080.13760.02340.068117.39-4.8878.305
472.0067-4.6180.203222.0773-27.712735.22710.82412.86340.45920.7336-1.1058-0.2584-0.99651.160.28170.0929-0.04350.07020.1927-0.05220.183711.094-6.44849.04
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A681 - 897
2X-RAY DIFFRACTION2B682 - 897
3X-RAY DIFFRACTION3C2 - 8
4X-RAY DIFFRACTION4D3

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