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- PDB-4cy2: Crystal structure of the KANSL1-WDR5-KANSL2 complex. -

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Basic information

Entry
Database: PDB / ID: 4cy2
TitleCrystal structure of the KANSL1-WDR5-KANSL2 complex.
Components
  • KAT8 REGULATORY NSL COMPLEX SUBUNIT 1
  • KAT8 REGULATORY NSL COMPLEX SUBUNIT 2
  • WD REPEAT-CONTAINING PROTEIN 5
KeywordsTRANSCRIPTION / EPIGENETIC REGULATOR / HISTONE ACETYLATION / CHROMATIN
Function / homology
Function and homology information


: / : / : / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : ...: / : / : / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / Cardiogenesis / histone acetyltransferase binding / histone methyltransferase complex / regulation of tubulin deacetylation / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / kinetochore / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / actin cytoskeleton / Neddylation / chromatin organization / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Potential DNA-binding domain / KAT8 regulatory NSL complex subunit 2 / Potential DNA-binding domain / KAT8 regulatory NSL complex subunit 1 / PEHE domain / PEHE domain / PEHE / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Potential DNA-binding domain / KAT8 regulatory NSL complex subunit 2 / Potential DNA-binding domain / KAT8 regulatory NSL complex subunit 1 / PEHE domain / 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
WD repeat-containing protein 5 / KAT8 regulatory NSL complex subunit 1 / KAT8 regulatory NSL complex subunit 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD REPEAT-CONTAINING PROTEIN 5
C: KAT8 REGULATORY NSL COMPLEX SUBUNIT 2
D: KAT8 REGULATORY NSL COMPLEX SUBUNIT 1


Theoretical massNumber of molelcules
Total (without water)37,6623
Polymers37,6623
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-12.2 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.590, 86.600, 45.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein WD REPEAT-CONTAINING PROTEIN 5 / BMP2-INDUCED 3-KB GENE PROTEIN


Mass: 34620.289 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P61964
#2: Protein/peptide KAT8 REGULATORY NSL COMPLEX SUBUNIT 2 / KANSL2 / NSL COMPLEX PROTEIN NSL2 / NON-SPECIFIC LETHAL 2 HOMOLOG


Mass: 1430.429 Da / Num. of mol.: 1 / Fragment: RESIDUES 406-417 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9H9L4
#3: Protein/peptide KAT8 REGULATORY NSL COMPLEX SUBUNIT 1 / KANSL1 / MLL1/MLL COMPLEX SUBUNIT KANSL1 / MSL1 HOMOLOG 1 / HMSL1V1 / NSL COMPLEX PROTEIN NSL1 / ...KANSL1 / MLL1/MLL COMPLEX SUBUNIT KANSL1 / MSL1 HOMOLOG 1 / HMSL1V1 / NSL COMPLEX PROTEIN NSL1 / NON-SPECIFIC LETHAL 1 HOMOLOG


Mass: 1610.834 Da / Num. of mol.: 1 / Fragment: RESIDUES 585-598 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q7Z3B3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.14 Å3/Da / Density % sol: 0.43 % / Description: NONE
Crystal growpH: 6.9
Details: 20% (W/V) PEG 3350, 0.2 M POTASSIUM NITRATE, PH 6.9.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: May 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 22261 / % possible obs: 100 % / Observed criterion σ(I): 2.6 / Redundancy: 7.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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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: 2→43.3 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.415 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22183 1133 5.1 %RANDOM
Rwork0.19939 ---
obs0.20057 21128 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.616 Å2
Baniso -1Baniso -2Baniso -3
1--5.93 Å20 Å20 Å2
2--0.85 Å20 Å2
3---5.09 Å2
Refinement stepCycle: LAST / Resolution: 2→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 0 104 2610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192569
X-RAY DIFFRACTIONr_bond_other_d0.0010.022422
X-RAY DIFFRACTIONr_angle_refined_deg1.0411.9423488
X-RAY DIFFRACTIONr_angle_other_deg0.69635612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54425.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85315441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.815155
X-RAY DIFFRACTIONr_chiral_restr0.0630.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02561
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_it0.3231.4841301
X-RAY DIFFRACTIONr_mcbond_other0.3231.4831300
X-RAY DIFFRACTIONr_mcangle_it0.5582.2221622
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.2871.5161268
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 87 -
Rwork0.262 1545 -
obs--99.82 %
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)
12.18090.08840.06770.7747-0.02911.528-0.0361-0.00490.16550.08610.04450.0367-0.1563-0.0826-0.00840.02590.0141-0.00020.0099-0.00450.0315-13.022119.7386-14.1071
22.4238-0.3501-0.61616.3629-0.00563.64320.11670.4430.0227-0.4973-0.0822-0.14550.12730.061-0.03450.05350.02140.01740.1062-0.01250.0243-8.368713.1346-28.4131
35.4062-0.75062.941512.6425-3.06312.19140.0152-0.11280.19540.34330.03730.4837-0.1549-0.0656-0.05250.33970.02950.10220.2033-0.04050.217-21.587736.3389-2.4595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 334
2X-RAY DIFFRACTION2D585 - 596
3X-RAY DIFFRACTION3C408 - 416

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