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- PDB-4cy3: Crystal structure of the NSL1-WDS complex. -

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Basic information

Entry
Database: PDB / ID: 4cy3
TitleCrystal structure of the NSL1-WDS complex.
Components
  • CG4699, ISOFORM D
  • PROTEIN WILL DIE SLOWLY
KeywordsTRANSCRIPTION / EPIGENETIC REGULATOR / HISTONE ACETYLATION / CHROMATIN
Function / homology
Function and homology information


Formation of WDR5-containing histone-modifying complexes / polytene chromosome interband / haltere development / germarium-derived female germ-line cyst formation / Neddylation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / larval somatic muscle development / germ-line stem cell population maintenance / eye development / MLL3/4 complex ...Formation of WDR5-containing histone-modifying complexes / polytene chromosome interband / haltere development / germarium-derived female germ-line cyst formation / Neddylation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / larval somatic muscle development / germ-line stem cell population maintenance / eye development / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone acetyltransferase binding / oogenesis / neuromuscular junction development / regulation of endocytosis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / heart development / histone binding / chromatin remodeling / nucleus / cytoplasm
Similarity search - Function
KAT8 regulatory NSL complex subunit 1 / PEHE domain / PEHE / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat ...KAT8 regulatory NSL complex subunit 1 / PEHE domain / PEHE / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Non-specific lethal 1, isoform D / Protein will die slowly
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDias, J. / Brettschneider, J. / Cusack, S. / Kadlec, J.
CitationJournal: Genes Dev. / Year: 2014
Title: Structural Analysis of the Kansl1/Wdr5/Kansl2 Complex Reveals that Wdr5 is Required for Efficient Assembly and Chromatin Targeting of the Nsl Complex.
Authors: Dias, J. / Van Nguyen, N. / Georgiev, P. / Gaub, A. / Brettschneider, J. / Cusack, S. / Kadlec, J. / Akhtar, A.
History
DepositionApr 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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

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Assembly

Deposited unit
A: PROTEIN WILL DIE SLOWLY
D: CG4699, ISOFORM D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5333
Polymers36,4412
Non-polymers921
Water3,603200
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-9 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.740, 98.850, 80.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2112-

HOH

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Components

#1: Protein PROTEIN WILL DIE SLOWLY / WDS


Mass: 34673.297 Da / Num. of mol.: 1 / Fragment: RESIDUES 50-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PFASTBACHTB / Cell line (production host): High Five / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9V3J8
#2: Protein/peptide CG4699, ISOFORM D


Mass: 1768.003 Da / Num. of mol.: 1 / Fragment: RESIDUES 714-729 / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly)
References: UniProt: A4V2Z1, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.16 Å3/Da / Density % sol: 0.43 % / Description: NONE
Crystal growpH: 7.2
Details: 20% (W/V) PEG 3350, 0.2 M POTASSIUM SODIUM TARTRATE, PH 7.2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93928
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93928 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 60987 / % possible obs: 98.9 % / Observed criterion σ(I): 2.4 / Redundancy: 7.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.9
Reflection shellResolution: 1.4→1.46 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.4 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G99

2g99


Resolution: 1.4→48.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.238 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18988 3098 5.1 %RANDOM
Rwork0.17942 ---
obs0.17995 57889 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.337 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å20 Å2
2--4.53 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 6 200 2631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0192529
X-RAY DIFFRACTIONr_bond_other_d0.0010.022397
X-RAY DIFFRACTIONr_angle_refined_deg1.0151.9453438
X-RAY DIFFRACTIONr_angle_other_deg0.71535558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5815326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.20424.54599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88615444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.045158
X-RAY DIFFRACTIONr_chiral_restr0.0610.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
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_it0.2830.9311262
X-RAY DIFFRACTIONr_mcbond_other0.28386.4811261
X-RAY DIFFRACTIONr_mcangle_it0.3591.3971578
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4161.0171267
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_restr2.47232529
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded1.74652466
LS refinement shellResolution: 1.404→1.441 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 204 -
Rwork0.234 4183 -
obs--98.74 %

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